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Sample records for papilloma virus genotyping

  1. Giant magnetoimpedance-based microchannel system for quick and parallel genotyping of human papilloma virus type 16/18

    NASA Astrophysics Data System (ADS)

    Yang, Hao; Chen, Lei; Lei, Chong; Zhang, Ju; Li, Ding; Zhou, Zhi-Min; Bao, Chen-Chen; Hu, Heng-Yao; Chen, Xiang; Cui, Feng; Zhang, Shuang-Xi; Zhou, Yong; Cui, Da-Xiang

    2010-07-01

    Quick and parallel genotyping of human papilloma virus (HPV) type 16/18 is carried out by a specially designed giant magnetoimpedance (GMI) based microchannel system. Micropatterned soft magnetic ribbon exhibiting large GMI ratio serves as the biosensor element. HPV genotyping can be determined by the changes in GMI ratio in corresponding detection region after hybridization. The result shows that this system has great potential in future clinical diagnostics and can be easily extended to other biomedical applications based on molecular recognition.

  2. Human Papilloma Virus Infections

    PubMed Central

    Wright, V. Cecil

    1989-01-01

    Genital warts are believed to be caused by human papilloma viruses and to be sexually transmitted. The viruses are classified by DNA types, which appear to cause different types of disease. The choice of treatment, and usually its success rate, vary according to the type of disease and its location. PMID:21248973

  3. High-risk human papilloma virus genotypes in cervical carcinoma of Serbian women: Distribution and association with pathohistological findings.

    PubMed

    Stamenković, Miodrag; Knežević, Aleksandra; Knežević, Ivana; Kuzmanović, Igor; Karalić, Danijela; Milenković, Sanja; Jovanović, Tanja

    2016-09-01

    A significant role of high-risk Human papilloma viruses (HR HPV) in the development of cervical carcinoma is well known. HR HPV 16 and 18 account for approximately 70% of all cases of cervical cancer worldwide. The incidence of cervical cancer in Serbia, is one of the highest in Europe. The aim of our study was to investigate the distribution of HR HPV types in cervical carcinoma of Serbian women, as well as association between the HPV types and pathohistological findings. The study included 80 archival cervical cancer tissues from the same number of patients. The presence of HPV DNA was determined using MY09/MY11 primers for L1 gene and GP1/GP2 primers for E1 gene. HPV was detected in 78.75% tissues. HR HPV genotypes found in the decreasing order of frequency were: HPV16 (80.39%), HPV33 (7.84%), HPV58 (5.88%), HPV18 (1.96%), HPV45 (1.96%) and HPV53 (1.96%). The examined tissues were 91.25% squamous cell carcinomas and 8.75% adenocarcinoma. The high frequency of HPV 16 was observed in both types of carcinoma (80.8% and 75%, respectively) while the prevalence of HPV18 was low. These results may contribute to the implementation of cervical carcinoma prevention program in Serbia, including the selection of the most appropriate vaccine and immunization program. PMID:27461126

  4. Human papilloma virus genotypes in women from Nayarit, Mexico, with squamous intraepithelial lesions and cervical cancer

    PubMed Central

    Ortega-Cervantes, Laura; Aguilar-Lemarroy, Adriana; Rojas-García, Aurora Elizabeth; Barrón-Vivanco, Briscia Socorro; Vallejo-Ruiz, Verónica; León, David Cantú-De; Hernández, Yael Yvette Bernal; Jáuregui-Martínez, Armando; Medina-Díaz, Irma Martha

    2016-01-01

    Objective In Mexico cervical cancer (CC) is the most common cause of death from neoplasia in women. Study aimed to analyze the current distribution of Human papillomavirus (HPV) types in women from Nayarit, Mexico, with Squamous intraepithelial lesions (SIL) and Cervical cancer (CC). Methodology Between January 2011 and July 2013, cervical samples were collected from female residents of the Mexican state of Nayarit and were analyzed by means of a LINEAR ARRAY® HPV genotyping test. Data analyses were performed using Stata ver. 8.0 statistical software. Results Of the samples analyzed, 91.2%, HPV DNA was detected. Of these positive samples, 82% were High-risk (HR) viral types. The most prevalent HPV genotypes identified were 16, 58, 31, 18, and 70. Forty two percent of participants had a single infection, while 23 and 26% of participants were infected with two or more HPV genotypes, respectively. HPV 16 was the most prevalent genotype identified and was frequently present as a co-infection with HPV types 18, 51, 52, 59, 66, or 70. Conclusion Women <20 years of age were most often infected with HPV, and the HPV Quadrivalent vaccine (types 16, 18, 6, and 11), currently available in Mexico, no confers protection against a subset of the HPV genotypes identified in the present study (58, 31, 70, and 35). Thus, it is important evaluate the geographical distribution of specific HPV genotypes in all health of center across Mexico in order to implement a successful vaccination program and to diagnose CC in its early stages. PMID:27610056

  5. Molecular cloning and characterization of human papilloma virus DNA derived from a laryngeal papilloma.

    PubMed Central

    Gissmann, L; Diehl, V; Schultz-Coulon, H J; zur Hausen, H

    1982-01-01

    Papilloma virus DNA from a laryngeal papilloma was cloned in phage lambda L 47 and characterized after cleavage with different restriction enzymes. Hybridization with the DNAs of human papilloma virus types 1, 2, 3, 4, 5, and 8 showed no homology under stringent hybridization conditions. Human papilloma virus type 6 DNA, however, was partially identical to laryngeal papilloma virus DNA; different restriction enzyme fragments hybridizing with the other DNA were identified on each genome. The degree of homology was determined by reassociation kinetics to be 25%. According to the present nomenclature, laryngeal papilloma virus therefore represents a different type of human papilloma virus and is tentatively designated as human papilloma virus type 11. Sequences homologous to laryngeal papilloma virus DNA were also found in four of nine additional laryngeal papillomas. Attempt to detect homologous DNA in 12 carcinomas of the larynx were negative. Images PMID:6292500

  6. The Association of High Risk Human Papillomaviruses in Patients With Cervical Cancer: An Evidence Based Study on Patients With Squamous Cell Dysplasia or Carcinoma for Evaluation of 23 Human Papilloma Virus Genotypes

    PubMed Central

    Piroozmand, Ahmad; Mostafavi Zadeh, Seyed Mostafa; Madani, Azita; Soleimani, Reza; Nedaeinia, Reza; Niakan, Mohammad; Avan, Amir; Manian, Mostafa; Moradi, Mohammad; Eftekhar, Zahra

    2016-01-01

    Background Cervical cancer is one of the leading causes of cancer-related death in females. Human papilloma virus (HPV) is the major risk factor of cervical cancer. Objectives The aim of the current study was to explore the frequency and role of 23 different HPVs in patients with cervical cancer. Materials and Methods Overall, 117 formalin-fix and paraffin-embedded (FFPE) tissues from cervical cancer patients with squamous cell carcinoma (SCC) or dysplasia were collected from Mirza-Kochakkhan-Jangali hospital, Tehran, Iran during year 2013, to investigate the presence of HPV- HPV- 67, 68, 6, 11, 13, 16, 17, 30, 69, 39, 40, 42, 64, 66 and 51 to 59 genotypes. Results The Pap smear report illustrated the presence of malignancy in 71 cases, while 11 cases had no evidence of malignancy. Among the patients, 26 cases had sexually transmitted disease with relative frequency of 0.58. Infection with papilloma virus was observed in 83.6% of SCC patients and 45% of the dysplasia group. The most prevalent HPV genotypes were 18 with 31.62% and 16 with 27.35% of cases. Moreover the relative frequencies of HPV-33, -6, -58, -52, -35 and -51, genotypes were 15.38, 7.69, 5.98, 5.12 and 3.41%, respectively. Among the different genotypes of HPV, 31 had the lowest and 16 had the highest relative frequency. Conclusions Our findings demonstrate that HPV-16 and -18 have a higher prevalence in our population than 31 and 51. Further investigations are required to evaluate the role of these genotypes in a larger multicenter setting for establishing their values for early detection of patients, which is useful for screening and vaccination programs of cancerous and precancerous lesions of cervical cancer. PMID:27279992

  7. Human papilloma virus infection and psoriasis: Did human papilloma virus infection trigger psoriasis?

    PubMed Central

    Jain, Sonia P.; Gulhane, Sachin; Pandey, Neha; Bisne, Esha

    2015-01-01

    Psoriasis is an autoimmune chronic inflammatory skin disease known to be triggered by streptococcal and HIV infections. However, human papilloma virus infection (HPV) as a triggering factor for the development of psoriasis has not been reported yet. We, hereby report a case of plaque type with inverse psoriasis which probably could have been triggered by genital warts (HPV infection) and discuss the possible pathomechanisms for their coexistence and its management. PMID:26692619

  8. Molecular identification of a papilloma virus from cutaneous lesions of captive and free-ranging Florida manatees

    USGS Publications Warehouse

    Woodruff, R.A.; Bonde, R.K.; Bonilla, J.A.; Romero, C.H.

    2005-01-01

    Cutaneous papillomatous lesions were biopsied from three captive Florida manatees (Trichechus manatus latirostris) at Homosassa Springs State Wildlife Park (HSSWP), Homosassa, Florida, USA, and from six free-ranging Florida manatees from Crystal and Homosassa rivers, Florida. Total DNA extracted from these lesions was assayed for the presence of papilloma virus genomes using the polymerase chain reaction (PCR) with primers that target the L1 capsid protein gene. The amplification generated DNA fragments 458 base pairs in length that encompassed a highly conserved domain within the L1 capsid protein and translated into identical polypeptides of 152 amino acids, suggesting the involvement of a single papilloma virus genotype. Multiple amino acid sequence and phylogenetic analyses of the L1 fragment indicated that the Florida manatee papilloma virus is a unique and quite distinct papillomavirus from other known papilloma viruses. The emergence of this new pathogen raises concerns about its potential impact on the already endangered Florida manatee.

  9. Molecular identification of a papilloma virus from cutaneous lesions of captive and free-ranging Florida manatees.

    PubMed

    Woodruff, Rebecca A; Bonde, Robert K; Bonilla, J Alfredo; Romero, Carlos H

    2005-04-01

    Cutaneous papillomatous lesions were biopsied from three captive Florida manatees (Trichechus manatus latirostris) at Homosassa Springs State Wildlife Park (HSSWP), Homosassa, Florida, USA, and from six free-ranging Florida manatees from Crystal and Homosassa rivers, Florida. Total DNA extracted from these lesions was assayed for the presence of papilloma virus genomes using the polymerase chain reaction (PCR) with primers that target the L1 capsid protein gene. The amplification generated DNA fragments 458 base pairs in length that encompassed a highly conserved domain within the L1 capsid protein and translated into identical polypeptides of 152 amino acids, suggesting the involvement of a single papilloma virus genotype. Multiple amino acid sequence and phylogenetic analyses of the L1 fragment indicated that the Florida manatee papilloma virus is a unique and quite distinct papillomavirus from other known papilloma viruses. The emergence of this new pathogen raises concerns about its potential impact on the already endangered Florida manatee. PMID:16107681

  10. Transitional cell papilloma of the penis associated with human papilloma virus infection. Report of two cases.

    PubMed

    Rodríguez-Pinilla, Socorro María; Rodríguez-Peralto, José Luis; Férnandez-Figueras, María Teresa

    2003-06-01

    Condylomas are one of the most common human papilloma virus (HPV)-related benign lesions of the male genitourinary tract. Although rarely, HPV has also been detected along the urinary tract, using molecular techniques, in transitional cell neoplasms without microscopic signs of koilocytic atypia. When affecting the urethra, condylomas are usually limited to its third distal portion. However, transitional cell neoplasms of the urethra are exceptional and in most of the cases remain limited to its proximal portion. To the best of our knowledge, 12 cases of transitional cell carcinomas and only one case of typical transitional cell papilloma have been described in the anterior urethra. We report two exceptional cases of typical transitional cell papilloma of the glans of the penis near the fossa navicularis which showed microscopic signs of HPV infection. PMID:12728314

  11. Chemical Studies on Polyoma and Shope Papilloma Viruses

    PubMed Central

    Kass, Sidney J.

    1970-01-01

    Polyoma and Shope papilloma viruses were purified and analyzed by chemical and physical methods. Disc electrophoresis of degraded virions indicated the presence, in both cases, of only one major species of polypeptide subunit. The weight of the peptide chain of polyoma virus was estimated in 8 m urea to be about 45,000 avograms, based on the sedimentation rate in a sucrose-urea gradient and the diffusion coefficient estimated from the differential migration in electrophoresis in gels of different pore size. The presence of a minor peptide of smaller size was suggested by carboxyl-terminal and sedimentation analyses. The amino acid composition of polyoma capsid protein was reported. Chemical analyses showed that polyoma virus and Shope papilloma virus contained 16 and 17.5% deoxyribonucleic acid, respectively. Light scattering by the polyoma virion showed it to have a molecular weight of 22 × 106 and a diameter of 54 nm. Images PMID:4314556

  12. Human papilloma virus vaccines: Current scenario.

    PubMed

    Pandhi, Deepika; Sonthalia, Sidharth

    2011-07-01

    Genital human papillomavirus (HPV) infection is the most common sexually transmitted infection with an estimated worldwide prevalence of 9-13% and approximately 6 million people being infected each year. Mostly acquired during adolescence or young adulthood, HPV presents clinically as anogenital warts and may progress to precancerous lesions and cancers of the cervix, vagina, vulva, penis and anus, and oropharynx. HPV infection is considered to contribute to almost 100% cervical cancers and at least 80% of anal and 40-60% of vulvar, vaginal, and penile cancers. At present, two prophylactic HPV vaccines are commercially available and both are prepared from purified L1 structural proteins. These proteins self-assemble to form virus-like particles that induce a protective immunity. Gardasil(®) is a quadrivalent vaccine against HPV types 6, 11, 16, and 18 and is recommended for use in females 9-26 years of age, for the prevention of cervical, vulvar, and vaginal cancers and intraepithelial neoplasia and condyloma acuminata and recently for vaccination in boys and men 9-26 years of age for the prevention of genital warts. Cervarix™ is a bivalent vaccine approved for the prevention of cervical cancer and precancerous lesions caused by HPV 16 and 18, in females 10-25 years. HPV vaccines are safe and efficacious against type-specific HPV-induced anogenital warts, precancerous lesions, and cervical cancer. The vaccines are most effective when given before the onset of sexual activity and provide long-term protection. Effective vaccination coverage in young adolescent females will substantially reduce the incidence of these anogenital malignancy-related morbidity and mortality. There is need to generate India-specific data on HPV epidemiology and HPV vaccination efficacy as well as continue worldwide surveillance and development of newer vaccines. PMID:22021967

  13. Human Papilloma Virus and Squamous Cell Carcinoma of the Anus

    PubMed Central

    Gami, Bhavna; Kubba, Faris; Ziprin, Paul

    2014-01-01

    The incidence of anal cancer is increasing. In the UK, the incidence is estimated at approximately 1.5 per 100,000. Most of this increase is attributed to certain at-risk populations. Persons who are human immunodeficiency virus (HIV)–positive and men who have sex with men (MSM), Organ transplant recipients, women with a history of cervical cancer, human papilloma virus (HPV), or cervical intraepithelial neoplasia (CIN) are known to have a greater risk for anal cancer. This paper will focus on HPV as a risk factor for anal intraepithelial neoplasia (AIN) and discusses the etiology, anatomy, pathogenesis, management of squamous cell carcinoma (SCC) of the anus. PMID:25288893

  14. Human papilloma virus (HPV) vaccination in childhood: challenges and perspectives

    PubMed Central

    Mammas, I; Maher, F; Theodoridou, M; Spandidos, D

    2011-01-01

    Vaccination against human papilloma virus (HPV) in childhood is a significant step forward in the reduction of HPV associated morbidity and mortality and a considerable scientific achievement. However, many challenges remain to be overcome if an effective HPV vaccine programme is to be successfully introduced worldwide. The aim of this review is to identify and summarize the new issues concerning HPV vaccination that have emerged since its introduction into clinical practice in school-aged girls. According to the literature, the overall impact of HPV vaccination on cervical cancer is unlikely to be apparent for the next decade. Cost-effectiveness is of particular importance, particularly in developing countries. Determining the age at which the vaccine should be administered, whether to include boys in addition to girls, the costs and the implications for cervical screening are issues that need to be addressed by conducting further research. PMID:24391408

  15. Ethical considerations of universal vaccination against human papilloma virus

    PubMed Central

    2014-01-01

    Background From an epidemiological perspective, the practice of universal vaccination of girls and young women in order to prevent human papilloma virus (HPV) infection and potential development of cervical cancer is widely accepted even though it may lead to the neglect of other preventive strategies against cervical cancer. Discussion It is argued that removing the deterrent effect – the fear of developing cancer – could encourage teenage sex. This paper reflects on the ethical legitimacy of the universal vaccination of girls and young women against HPV infection, especially regarding safety issues, the need to vaccinate people who have opted to abstain from sex, the presumption of early onset of sexual relations, the commercial interests of the companies that manufacture the vaccine, and the recommendation of universal vaccination in males. Summary Based on the aforementioned information, we believe that the universal vaccination against HPV in young women is acceptable from an ethical point of view, given the medical advantages it presents. PMID:24708813

  16. Immunohistochemistry and Polymerase Chain Reaction for Detection Human Papilloma Virus in Warts: A Comparative Study

    PubMed Central

    Lee, Hong Sun; Lee, Ji Hyun; Choo, Ji Yoon; Byun, Hee Jin; Jun, Jin Hyun

    2016-01-01

    Background Immunohistochemistry and polymerase chain reaction (PCR) are the most widely used methods for the detection of viruses. PCR is known to be a more sensitive and specific method than the immunohistochemical method at this time, but PCR has the disadvantages of high cost and skilled work to use widely. With the progress of technology, the immunohistochemical methods used in these days has come to be highly sensitive and actively used in the diagnostic fields. Objective To evaluate and compare the usefulness of immunohistochemistry and PCR for detection human papilloma virus (HPV) in wart lesions. Methods Nine biopsy samples of verruca vulgaris and 10 of condyloma accuminatum were examined. Immunohistochemical staining using monoclonal antibody to HPV L1 capsid protein and PCR were done for the samples. DNA sequencing of the PCR products and HPV genotyping were also done. Results HPV detection rate was 78.9% (88.9% in verruca vulgaris, 70.0% in condyloma accuminatum) on immunohistochemistry and 100.0% for PCR. HPV-6 genotype showed a lower positivity rate on immunohistochemistry (50.0%) as compared to that of the other HPV genotypes. Conclusion Immunohistochemistry for HPV L1 capsid protein showed comparable sensitivity for detection HPV. Considering the high cost and great effort needed for the PCR methods, we can use immunohistochemistry for HPV L1 capsid protein with the advantage of lower cost and simple methods for HPV detection. PMID:27489431

  17. Human Papilloma Virus and Oropharyngeal Carcinoma - Lessons from History.

    PubMed

    Vlantis, Alexander Chris

    2016-03-01

    The human papilloma virus (HPV) is a common virus that infects epithelium in 10% of the world's population. While most sexually active people become infected, the majority with a healthy natural immunity control their infection. When the infection becomes persistent in cervical mucosa for instance, it is associated with nearly all cervical cancers. Fortunately cervical cancer screening is both sensitive and specific and when accessed has led to significant reductions of this disease. Despite this, cervical cancer still remains one of the leading causes of death from cancer. Oropharyngeal mucosa is becoming persistently infected with HPV in an increasing number of people leading to a potential epidemic of oropharyngeal carcinoma. While only 10% of new oropharyngeal infections persist, those in elderly men who smoke are more likely to do so. Some centres report more than 70% of oropharyngeal cancers are associated with HPV infection, which is different to cancers caused by alcohol and tobacco. Other centres report only a 20% association. Education against high-risk sexual behaviour has been met with limited success. Screening for oropharyngeal HPV infection has been disappointing with a pickup rate of only 40%. Some hope lies in detecting viral DNA in both the saliva and plasma. A HPV vaccine has been available since 2006 but is not yet routinely given to both sexes in many countries. Its effect on the incidence of HPV-positive oropharyngeal carcinomas is currently unknown. Vigilance by dental and medical colleagues in the meantime is essential. PMID:26981602

  18. Prevalence of human papilloma virus among women with breast cancer since 2005-2009 in Isfahan

    PubMed Central

    Manzouri, Leila; Salehi, Rasoul; Shariatpanahi, Shervin; rezaie, Parisa

    2014-01-01

    Background: Human papilloma virus (HPV) DNA has been detected in breast carcinoma by different laboratorial techniques, suggesting that the virus could play a role in the pathogenesis of this tumor. Materials and Methods: It was a descriptive study. Systematic random sampling was used for selecting 55 cases of breast cancer and 51 controls of benign breast lesions from the file of Seyedshohada hospital of Isfahan since 2005-2009. A total of 106 paraffin-embedded specimens were selected and HPV DNA was analyzed by polymerase chain reaction and sequenced for different types of HPV in case of positivity for HPV DNA. Data analysis was performed by SPSS 16 software using descriptive statistic, Chi-square, and Fisher's exact tests. Results: Out of 55 malignant and 51 benign breast specimens, 18.2% (10) and 13.7% (7) were positive to HPV DNA, respectively (P = 0.53); 70% (7) malignant and 43% (3) benign breast specimens were positive to high-risk HPV genotypes. In malignant specimens, the most common high- and low-risk genotypes were HPV-16 (3.6%) and HPV-11 (3.6%), respectively. In benign specimens, the most common high- and low-risk genotypes were HPV-31 (3.9%) and HPV-43 (3.9%), respectively. Among malignant and benign specimens, ductal carcinoma and fibro adenoma were the most common lesions positive to different types of HPV, respectively. Conclusion: This study demonstrated the presence of HPV genome in both malignant and benign tumor tissues in women with breast lesions in Isfahan; therefore, further larger epidemiologic studies need to be analyzed to establish the exact role of this virus in the pathogenesis of breast cancer. PMID:24627883

  19. Predictors associated with the willingness to take human papilloma virus vaccination.

    PubMed

    Naing, Cho; Pereira, Joanne; Abe, Tatsuki; Eh Zhen Wei, Daniel; Rahman Bajera, Ibrizah Binti Abdul; Kavinda Perera, Undugodage Heshan

    2012-04-01

    Human papilloma virus vaccine is considered to be the primary form of cervical cancer prevention. The objectives were (1) to determine knowledge about, and perception of human papilloma virus infection in relation to cervical cancer, (2) to explore the intention of the community to be vaccinated with human papilloma virus vaccine, and (3) to identify variables that could predict the likelihood of uptake of the vaccine. A cross-sectional survey was carried out in a semi-urban Town of Malaysia, using a pre-tested structured questionnaire. Summary statistics, Pearson chi-square test and a binary logistic regression were used for data analysis. A total of 232 respondents were interviewed. Overall, only a few had good knowledge related to human papilloma virus (14%) or vaccination (8%). Many had misconceptions that it could be transmitted through blood transfusion (57%). Sixty percent had intention to take vaccination. In the binary logistic model, willingness to take vaccination was significant with 'trusts that vaccination would be effective for prevention of cervical cancer' (P = 0.001), 'worries for themselves' (P < 0.001) or 'their family members' (P = 0.003) and 'being Indian ethnicity' (P = 0.024). The model could fairly predict the likelihood of uptake of the vaccine (Cox & Snell R(2) = .415; Nagelkerke R(2) = 0.561). Results indicate that intensive health education dispelling misconception and risk perception towards human papilloma virus infection and cervical cancer would be helpful to increase the acceptability of vaccination program. PMID:21928103

  20. Human papilloma virus vaccines: need to be introduced in India.

    PubMed

    Verma, Ramesh; Khanna, Pardeep

    2013-01-01

    Human papilloma viruses (HPVs) infect the skin and mucosal epithelium of both men and women. There are about 100 types of HPVs, which are differentiated by the genetic sequence of the outer capsid protein L1. More than 30 types of HPVs are sexually transmitted. Most cases of carcinoma of the cervix are caused by HPV. Cervical cancer is one of the most common forms of cancer in women is the second biggest cause of female cancer mortality worldwide. The worldwide incidence of cervical carcinoma is 529,000 per year, and mortality is 275,000, of which an estimated 88% of deaths occur in developing countries. At least 20 million people worldwide are already chronically infected. Over 80% of cases of cervical carcinoma occurs in developing countries, with 25% estimated to occur in India. At least 50% of sexually active men and women encounter genital HPV at some time in their lives. Cervical cancer is ranked as the most frequent cancer in women in India. India has a population of approximately 366 million women above 15 y of age, who are at risk of developing cervical cancer. The current estimates indicate approximately 132,000 new cases diagnosed and 74,000 deaths annually in India, accounting for nearly one-third of the global cervical cancer deaths. HPV can be prevented by vaccination. Two types of HPV vaccines are available, as Gardasil and Cervarix, both of which are highly effective at preventing HPV infection. HPV vaccine is administered in a three-dose series administered by intramuscular injection, either in the deltoid muscle or in the antero-lateral thigh. The second and third doses should be administered 2 and 6 mo after the first dose respectively. The minimum interval between the first and second doses should be 4 weeks, between the second and third dose should be 12 weeks. PMID:23108360

  1. Multiple Human Papilloma Virus 16 Infection Presenting as Various Skin Lesions.

    PubMed

    Choi, Hwan Jun; Lee, Jun Ho

    2016-06-01

    The 53-year-old woman admitted with multiple persistent, progressive, slightly raised, red, and crusted plague form masses that suddenly occurred on left thumb, both upper and lower extremity about 10 years ago. There was no induration in the lesion or in its surrounding skin. There was no unusual opinion on a radiologic test and family history. And she had no history of working in the business related to any chemical product such as arsenic or tar which was carcinogen. The patient has had total hysterectomy to treat uterine myoma 10 years ago. The wide excision and split thickness skin graft of 2 × 1.5 cm was performed around mass in the size of 1.5 × 1.2 cm on the left thumb and wide excision and local advancement flap was done on the other sites. As a result of biopsy, masses were diagnosed as Bowen disease, actinic keratosis, and Seborrheic keratosis. These specimens were obtained during surgery: broom-type cell sampling devices were used to collect samples from the specimens, and they were placed into PreservCyt solution (Cytyc Corp, Boxborough, MA). Then, the collected samples underwent the Roche Linear Array HPV Genotyping Test (Roche Diagnostics, Branchburg, NJ) that allows for the simultaneous identification of human papilloma virus (HPV) types from liquid-based cell preparations. On histopathological examination of the surgical specimen, atypical squamous cells proliferate through the whole thickness of the epidermis. The entire tumor was confined to the epidermis and did not invade into the dermis. The cells were often highly atypical. That were the irregular shape which the resection margin of masses had a negative tumor component. And HPV 16 genotyping test was positive although vaginal examination of HPV 16 genotyping was negative. PMID:27192658

  2. Problem-Solving Test: The Mechanism of Action of a Human Papilloma Virus Oncoprotein

    ERIC Educational Resources Information Center

    Szeberenyi, Jozsef

    2009-01-01

    Terms to be familiar with before you start to solve the test: human papilloma virus; cervical cancer; oncoproteins; malignant transformation; retinoblastoma protein; cell cycle; quiescent and cycling cells; cyclin/cyclin-dependent kinase (Cdk) complexes; E2F; S-phase genes; enhancer element; proto-oncogenes; tumor suppressor genes; radioactive…

  3. Cloning of human papilloma virus genomic DNAs and analysis of homologous polynucleotide sequences.

    PubMed

    Heilman, C A; Law, M F; Israel, M A; Howley, P M

    1980-11-01

    The complete DNA genomes of four distinct human papilloma viruses (human papilloma virus subtype 1a [HPV-1a], HPV-1b, HPV-2a, and HPV-4) were molecularly cloned in Escherichia coli, using the certified plasmid vector pBR322. The restriction endonuclease patterns of the cloned HPV-1a and HPV-1b DNAs were similar to those already published for uncloned DNAs. Physical maps were constructed for HPV-2a DNA and HPV-4 DNA, since these viral DNAs had not been previously mapped. By using the cloned DNAs, the genomes of HPV-1a, HPV-2a, and HPV-4 were analyzed for nucleotide sequence homology. Under standard hybridization conditions (Tm = --28 degrees C), no homology was detectable among the genomes of these papilloma viruses, in agreement with previous reports. However, under less stringent conditions (i.e., Tm = --50 degrees C), stable DNA hybrids could be detected between these viral DNAs, indicating homologous segments in the genomes with approximately 30% base mismatch. By using specific DNA fragments immobilized on nitrocellulose filters, these regions of homology were mapped. Hybridization experiments between radiolabeled bovine papilloma virus type 1 (BPV-1) DNA and the unlabeled HPV-1a, HPV-2a, or HPV-4 DNA restriction fragments under low-stringency conditions indicated that the regions of homology among the HPV DNAs are also conserved in the BPV-1 genome with approximately the same degree of base mismatch. PMID:6253665

  4. [Cost effectiveness of human papilloma virus testing in cervical cancer screening: a literature review].

    PubMed

    Mejía, Aurelio; Salas, Walter

    2008-03-01

    Human papilloma virus DNA testing may improve the cost effectiveness of cervical cancer screening programs. However, the circumstances to get this improvement are not the same between countries. The objective of this paper is to evaluate the cost effectiveness of introducing human papilloma virus testing in the current screening practice both in developed and developing countries. We conducted a review of published articles since January 2000 until December 2006 related to the cost effectiveness of introducing human papilloma virus testing in cervical cancer screening programs. A total of 17 original researches and six reviews were analyzed. Human papilloma virus testing is cost effective in developed countries only if it is a complementary test to Pap test and used to determine the management of women with atypical squamus cells of undetermined significance, the interval among tests is increased more than two years and it is performed in women over 30 years. On the other hand, developing countries should establish first organized screening programs and guarantee full coverage and access to diagnosis and treatment. PMID:18645671

  5. Human papilloma virus, DNA methylation and microRNA expression in cervical cancer (Review)

    PubMed Central

    JIMÉNEZ-WENCES, HILDA; PERALTA-ZARAGOZA, OSCAR; FERNÁNDEZ-TILAPA, GLORIA

    2014-01-01

    Cancer is a complex disease caused by genetic and epigenetic abnormalities that affect gene expression. The progression from precursor lesions to invasive cervical cancer is influenced by persistent human papilloma virus (HPV) infection, which induces changes in the host genome and epigenome. Epigenetic alterations, such as aberrant miRNA expression and changes in DNA methylation status, favor the expression of oncogenes and the silencing of tumor-suppressor genes. Given that some miRNA genes can be regulated through epigenetic mechanisms, it has been proposed that alterations in the methylation status of miRNA promoters could be the driving mechanism behind their aberrant expression in cervical cancer. For these reasons, we assessed the relationship among HPV infection, cellular DNA methylation and miRNA expression. We conclude that alterations in the methylation status of protein-coding genes and various miRNA genes are influenced by HPV infection, the viral genotype, the physical state of the viral DNA, and viral oncogenic risk. Furthermore, HPV induces deregulation of miRNA expression, particularly at loci near fragile sites. This deregulation occurs through the E6 and E7 proteins, which target miRNA transcription factors such as p53. PMID:24737381

  6. Human papilloma virus, DNA methylation and microRNA expression in cervical cancer (Review).

    PubMed

    Jiménez-Wences, Hilda; Peralta-Zaragoza, Oscar; Fernández-Tilapa, Gloria

    2014-06-01

    Cancer is a complex disease caused by genetic and epigenetic abnormalities that affect gene expression. The progression from precursor lesions to invasive cervical cancer is influenced by persistent human papilloma virus (HPV) infection, which induces changes in the host genome and epigenome. Epigenetic alterations, such as aberrant miRNA expression and changes in DNA methylation status, favor the expression of oncogenes and the silencing of tumor-suppressor genes. Given that some miRNA genes can be regulated through epigenetic mechanisms, it has been proposed that alterations in the methylation status of miRNA promoters could be the driving mechanism behind their aberrant expression in cervical cancer. For these reasons, we assessed the relationship among HPV infection, cellular DNA methylation and miRNA expression. We conclude that alterations in the methylation status of protein-coding genes and various miRNA genes are influenced by HPV infection, the viral genotype, the physical state of the viral DNA, and viral oncogenic risk. Furthermore, HPV induces deregulation of miRNA expression, particularly at loci near fragile sites. This deregulation occurs through the E6 and E7 proteins, which target miRNA transcription factors such as p53. PMID:24737381

  7. Detection and Typing of Human Papilloma Viruses by Nested Multiplex Polymerase Chain Reaction Assay in Cervical Cancer

    PubMed Central

    Jalal Kiani, Seyed; Shatizadeh Malekshahi, Somayeh; Yousefi Ghalejoogh, Zohreh; Ghavvami, Nastaran; Shafiei Jandaghi, Nazanin Zahra; Shahsiah, Reza; Jahanzad, Isa; Yavarian, Jila

    2015-01-01

    Background: Cervical cancer is the leading cause of death from cancer in under-developed countries. Human papilloma virus (HPV) 16 and 18 are the most prevalent types associated with carcinogenesis in the cervix. Conventional Polymerase Chain Reaction (PCR), type-specific and consensus primer-based PCR followed by sequencing, Restriction Fragment Length Polymorphism (RFLP) or hybridization by specific probes are common methods for HPV detection and typing. In addition, some researchers have developed a multiplex PCR for simultaneous detection and typing of different HPVs. Objectives: The aim of the present study was to investigate the prevalence of HPV infection and its types in cervical Squamous Cell Carcinoma (SCC) using the Nested Multiplex PCR (NMPCR) assay. Patients and Methods: Sixty-six samples with histologically confirmed SCC were evaluated. Total DNA was isolated by phenol–chloroform extraction and ethanol precipitation. Nested multiplex PCR was performed with first-round PCR by GP-E6/E7 consensus primers for amplification of the genomic DNA of all known mucosal HPV genotypes and second-round PCR by type-specific multiplex PCR primer cocktails. Results: Human papilloma virus infection was detected in 78.8% of samples, with the highest prevalence of HPV 16 (60.6%) while concurrent infections with two types was detected in 10.6%. Conclusions: The NMPCR assay is more convenient and easy for analysis of results, which is important for fast diagnosis and patient management, in a type-specific manner. PMID:26865940

  8. Rome consensus conference - statement; human papilloma virus diseases in males

    PubMed Central

    2013-01-01

    Background Human Papillomavirus (HPV) is a very resistant, ubiquitous virus that can survive in the environment without a host. The decision to analyse HPV-related diseases in males was due to the broad dissemination of the virus, and, above all, by the need to stress the importance of primary and secondary prevention measures (currently available for women exclusively). The objective of the Consensus Conference was to make evidence-based recommendations that were designed to facilitate the adoption of a standard approach in clinical practice in Italy. Methods The Sponsoring Panel put a series of questions to the members of the Scientific Committee who prepared a summary of the currently available information, relevant for each question, after the review and grading of the existing scientific literature. The summaries were presented to a Jury, also called multidisciplinary Consensus Panel, who drafted a series of recommendations. Results The prevalence of HPV in males ranges between 1.3–72.9%;. The prevalence curve in males is much higher than that in females and does not tend to decline with age. Women appear to have a higher probability of acquiring HPV genotypes associated with a high oncogenic risk, whereas in males the probability of acquiring low- or high-risk genotypes is similar. The HPV-related diseases that affect males are anogenital warts and cancers of the penis, anus and oropharynx. The quadrivalent vaccine against HPV has proved to be effective in preventing external genital lesions in males aged 16–26 years in 90.4%; (95%; CI: 69.2–98.1) of cases. It has also proved to be effective in preventing precancerous anal lesions in 77.5%; (95%; CI: 39.6–93.3) of cases in a per-protocol analysis and in 91.7%; (95%; CI: 44.6–99.8) of cases in a post-hoc analysis. Early ecological studies demonstrate reduction of genital warts in vaccinated females and some herd immunity in males when vaccine coverage is high, although males who have sex with males

  9. Risk factors and distribution of oncogenic strains of human papilloma virus in women presenting for cervical cancer screening in Port Harcourt, Nigeria

    PubMed Central

    Kennedy, Nyengidiki Tamunomie; Ikechukwu, Durugbo; Goddy, Bassey

    2016-01-01

    Introduction Human papilloma virus(HPV) accounts for most cases of cervical cancer with high risk HPV(hrHPV) genotypes largely responsible. The objective is to ascertain the distribution of oncogenic strains of human papilloma virus genotypes and predisposing risk factors in women presenting for cervical cancer screening in Nigeria. Methods A cross-sectional study of 80 women who presented for cervical cancer screening. The biodata of the participants, the presence of risk factors to HPV were recorded and hrHPV were identified using PCR technique. The information obtained was processed using the SPSS version 20 software. Results were presented in tables, test of significance and association done using student's t-test and Odds ratio, with P value < 0.05 as significant. Results The age range of patients was 19-62 years with prevalence of hrHPV of 10%. HrHPV are more in patients with more than one life time sexual partner (OR 1.26,95%CI 0.13-29.99), multiple sexual partners (OR 1.55, 95% CI 0.28-8.70), early coitarche (OR 1.57, 95% CI 0.14-15.00) and previous STI (OR 150, 95%CI 9.53-1979. 62). Four hrHPV genotypes: 16, 18, 31 and 35 were detected. Conclusion HPV genotype 18 was predominant in Port Harcourt, Nigeria. High risk sexual behaviours are associated with acquisition of hrHPV. PMID:27222684

  10. “Saving lives”: Adapting and adopting Human Papilloma Virus (HPV) vaccination in Austria

    PubMed Central

    Paul, Katharina T.

    2016-01-01

    Vaccination against the sexually transmitted Human Papilloma Virus (HPV), a necessary agent for the development of cervical cancer, has triggered much debate. In Austria, HPV policy turned from “lagging behind” in 2008 into “Europe's frontrunner” by 2013. Drawing on qualitative research, the article shows how the vaccine was transformed and made “good enough” over the course of five years. By means of tinkering and shifting storylines, policy officials and experts disassociated the vaccine from gender, vaccine manufacturers, and youth sexuality. Ultimately, the HPV vaccine functioned to strengthen the national immunization program. To this end, preventing an effective problematization of the extant screening program was essential. PMID:26921834

  11. Development of procedures for the identification of human papilloma virus DNA fragments in laser plume

    NASA Astrophysics Data System (ADS)

    Woellmer, Wolfgang; Meder, Tom; Jappe, Uta; Gross, Gerd; Riethdorf, Sabine; Riethdorf, Lutz; Kuhler-Obbarius, Christina; Loening, Thomas

    1996-01-01

    For the investigation of laser plume for the existence of HPV DNA fragments, which possibly occur during laser treatment of virus infected tissue, human papillomas and condylomas were treated in vitro with the CO2-laser. For the sampling of the laser plume a new method for the trapping of the material was developed by use of water-soluble gelatine filters. These samples were analyzed with the polymerase chain reaction (PCR) technique, which was optimized in regard of the gelatine filters and the specific primers. Positive PCR results for HPV DNA fragments up to the size of a complete oncogene were obtained and are discussed regarding infectiousity.

  12. Persistent infection with high-risk human papilloma viruses: cohort study, Mérida, Venezuela

    PubMed Central

    Téllez, Luis; Michelli, Elvia; Mendoza, José Andrés; Vielma, Silvana; Noguera, María-Eugenia; Callejas, Diana; Cavazza, María; Correnti, María

    2015-01-01

    Cervical lesions have been associated with infection by high-risk human papilloma virus (high-risk HPV). In 409 women aged >15 years high-risk HPV lesions were identified. In a cohort of this population persistent infection was compared with cytological, colposcopic, and histological lesions. Cervical scrapes were taken and DNA was isolated. HPV was detected by PCR in the E6/E7 region. Genotyping was performed by PCR nested multiple E6/E7. HPV was detected in a 37.40% (153/409), high-risk HPV in 86% (153/178), HPV18 46.64% (83/178), HPV16 34.28% (61/178). Among these 53.93% (96/178) were multiple infections, and HPV18/16 (30/96) was the most frequent 31.25%. The cytology showed changes in 15% of positive patients. A 49.67% in women positive for HPV infection showed abnormalities in the colposcopic study, a relationship that turned out to be statistically significant ( p < 0.0019 test χ2). Among all 85% of the women were younger than 45 years of age. Fifty-seven patients were evaluated 15 months after the base study, with initial prevalence of morbidity 49.12% (28/57) and at the end 10.53% (6/57), showing in 89.29% (25/28) negative for HR-HPV infection, 10.34% (3/28) showed persistence of infection, 17.54% (10/57) presented cytological alterations, with 80% of positivity for HPV, and a regression of 100% (10/10) of the previously identified lesions. With colposcopy, 50% (14/28) presented alterations related to HPV, of these 85.71% (12/14) showed regression of such an alteration. The cumulative incidence for HPV was 10.34% (3/29). The incidence rate was 4.23% (3/71), which is equal to 4.23 new cases of HPV infection per 100 people, per year of follow-up. In conclusion, the present work shows a high frequency of infection by high-risk HPV, with predominance of HPV18 and 16 and in general for multiple infections. Colposcopy was better predictor than the Pap smear for infection. The follow-up study revealed a low percentage of persistent infection, and a high frequency

  13. A proposal to reduce the risk of transmission of human papilloma virus via transvaginal ultrasound.

    PubMed

    Combs, C Andrew; Fishman, Alan

    2016-07-01

    Three steps must be followed to prevent the transmission of infection via a contaminated transvaginal ultrasound probe: cleaning the probe after every use, high-level disinfection, and covering the probe with a single-use barrier during the examination. There may be critical flaws in at least 2 of these steps as they are currently practiced. First, 2 widely used disinfectants, glutaraldehyde and orthophthalaldehyde, have recently been found to be ineffective at neutralizing human papilloma virus type 16 and type 18. Second, commercial ultrasound probe covers have an unacceptable rate of leakage (8-81%) compared to condoms (0.9-2%). We recommend the use of a sonicated hydrogen peroxide disinfectant system rather than aldehyde-type disinfectants. We recommend that the probe be covered with a condom rather than a commercial probe cover during transvaginal ultrasound examination. Combined with probe cleaning, these 2 steps are estimated to result in an 800 million- to 250 billion-fold reduction in human papilloma virus viral load, which should translate to greatly enhanced patient safety. PMID:26994654

  14. 78 FR 18359 - Prospective Grant of Exclusive License: Papilloma Pseudovirus and Virus-Like Particles as a...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-26

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health Prospective Grant of Exclusive License: Papilloma Pseudovirus and Virus-Like Particles as a Delivery System for Human Cancer Therapeutics and Diagnostics...

  15. Respiratory papillomas

    PubMed Central

    Alagusundaramoorthy, Sayee Sundar; Agrawal, Abhinav

    2016-01-01

    Papillomas are known to occur in the lower respiratory tract. They are however, rare compared to their occurrence in the upper respiratory tract. These are generally exophytic tumors in the more proximal upper airways however cases with more distal location with an inverted growth pattern have also been described in the literature. These can be solitary or multiple and multifocality associated with multiple papillomas in the upper respiratory/aerodigestive tract. The four major types of respiratory papillomas are (1) Recurrent respiratory papillomas, (2) solitary squamous papillomas, (3) solitary glandular papillomas, (4) mixed papillomas. We review the incidence, etiopathology, diagnosis, and possible treatment modalities and algorithms for these respiratory papillomas. PMID:27625447

  16. Human papilloma virus strain detection utilising custom-designed oligonucleotide microarrays.

    PubMed

    Ayers, Duncan; Platt, Mark; Javad, Farzad; Day, Philip J R

    2011-01-01

    Within the past 15 years, the utilisation of microarray technology for the detection of specific pathogen strains has increased rapidly. Presently, it is possible to simply purchase a pre-manufactured "off the shelf " oligonucleotide microarray bearing a wide variety of known signature DNA sequences previously identified in the organism being studied. Consequently, a hybridisation analysis may be used to pinpoint which strain/s is present in any given clinical sample. However, there exists a problem if the study necessitates the identification of novel sequences which are not represented in commercially available microarray chips. Ideally, such investigations require an in situ oligonucleotide microarray platform with the capacity to synthesise microarrays bearing probe sequences designed solely by the researcher. This chapter will focus on the employment of the Combimatrix® B3 CustomArray™ for the synthesis of reusable, bespoke microarrays for the purpose of discerning multiple Human Papilloma Virus strains. PMID:20938834

  17. Human Papilloma Virus in Oral Squamous Cell Carcinoma - The Enigma Unravelled.

    PubMed

    Khot, Komal P; Deshmane, Swati; Choudhari, Sheetal

    2016-03-01

    Squamous cell carcinoma of the head and neck (HNSCC) has long been regarded as a disease entity having a remarkable incidence worldwide and a fairly onerous prognosis; thus encouraging further research on factors that might modify disease outcome. Squamous cell carcinomas encompass at least 90% of all oral malignancies. Several factors like tobacco and tobacco-related products, alcohol, genetic predisposition and hormonal factors are suspected as possible causative factors. Human papilloma virus (HPV), the causal agent of cervical cancer also appears to be involved in the aetiology of oral and oropharyngeal cancer. HPVpositive squamous cell carcinoma (SCC) seems to differ from HPV-negative SCC. Many questions about the natural history of oral HPV infection remain under investigation. The aim of this review is to highlight the current understanding of HPV-associated oral cancer with an emphasis on its prognosis, detection and management. PMID:26981603

  18. Oropharyngeal cancer and human papilloma virus: evolving diagnostic and management paradigms.

    PubMed

    Buckley, Lisa; Gupta, Ruta; Ashford, Bruce; Jabbour, Joe; Clark, Jonathan R

    2016-06-01

    The significant increase in human papilloma virus (HPV)-associated oropharyngeal carcinoma (OPC) over recent years has lead to a surge in research and an improved understanding of the disease. Most patients with HPV-associated OPC present with cystic nodal metastases with a small primary tumour, and respond well to all treatment modalities including primary surgery and primary chemoradiotherapy. Current research is evaluating treatment de-escalation to reduce long-term treatment-associated morbidities. Transoral robotic surgery (TORS) is particularly relevant as the transoral approach allows small primary tumours to be removed with lower morbidity than traditional surgical approaches. The current American Joint Committee on Cancer staging system for oropharyngeal cancer does not appropriately stratify HPV-associated OPC; hence, alternative risk stratification and staging classifications are being proposed. PMID:26687076

  19. Human Papilloma Virus Associated Squamous Cell Carcinoma of the Head and Neck

    PubMed Central

    Ajila, Vidya; Shetty, Harish; Babu, Subhas; Shetty, Veena; Hegde, Shruthi

    2015-01-01

    Oral cancer is one of the commonest causes for mortality and morbidity with squamous cell carcinoma being the sixth most frequent malignant tumour worldwide. In addition to tobacco and alcohol, human papilloma virus (HPV) is associated with a proportion of head and neck cancers. As in cervical cancers, HPV types 16 and 18 are the cause of malignant transformation. HPV-positive cancers of head and neck have unique characteristics such as occurrence in a younger age group, distinct clinical and molecular features, and better prognosis as compared to HPV-negative carcinomas. They also possess the potential for prevention by using vaccination. The present review describes in detail the salient features of HPV associated oral squamous cell carcinoma (OSCC), its differences from HPV-negative OSCC, diagnostic features, and recent strategies in prevention and management. PMID:26483987

  20. Determination of knowledge of Turkish midwifery students about human papilloma virus infection and its vaccines.

    PubMed

    Genc, Rabia Ekti; Sarican, Emine Serap; Turgay, Ayse San; Icke, Sibel; Sari, Dilek; Saydam, Birsen Karaca

    2013-01-01

    Human papilloma virus (HPV) is one of the most common sexually transmitted agents and its infection is the most established cause of cervical cancer. Midwives play a key position in the implementation of cervical cancer. This descriptive study aimed to determine the level of knowledge concerning HPV and HPV vaccination among 268 midwifery students. Data were collected between November 15 and 30, 2011, through a self-reported questionnaire. The mean age of participants was 20.75 ± 1.60. Among all students, 44.4% had heard of HPV, while 40.4% had heard of HPV vaccinatiob. The relationship between the midwifery student knowledge on HPV and HPV vaccine and their current educational year was significant (p=0.001). In conclusion midwifery students have moderate level of knowledge about HPV and its vaccine and relevant information should be included in their teaching curriculum. PMID:24377604

  1. Human papilloma virus vaccine: determinants of acceptability by mothers for adolescents in Nigeria.

    PubMed

    Ezeanochie, Michael C; Olagbuji, Biodun N

    2014-09-01

    Vaccination of adolescent females against Human Papilloma Virus (HPV), the causative agent for cervical cancer has recently become available. As minors, parental acceptance of the vaccines for adolescent daughters requires exploration. This was a cross-sectional survey of 201 mothers attending the gynaecology clinic in a University Teaching Hospital in Nigeria on acceptability of the HPV vaccines and its determinants. Although 70% accepted vaccination of their daughters, 30% were unwilling and the commonest reason for unwillingness was that it may encourage sexual promiscuity (62.3%). Mothers with poor knowledge of STI were significantly more unwilling to accept HPV vaccines compared to those with average or good knowledge (p = 0.002). Furthermore, perception of susceptibility to HPV infection by daughters was significantly associated with acceptance of the vaccines (p = 0.0001). Increased advocacy and public enlightenment on cervical cancer control and the role of HPV vaccines in its prevention is still necessary especially in developing countries. PMID:25508051

  2. Human papilloma virus vaccine: determinants of acceptability by mothers for adolescents in Nigeria.

    PubMed

    Ezeanochie, Michael C; Olagbuji, Biodun N

    2014-09-01

    Vaccination of adolescent females against Human Papilloma Virus (HPV), the causative agent for cervical cancer has recently become available. As minors, parental acceptance of the vaccines for adolescent daughters requires exploration. This was a cross-sectional survey of 201 mothers attending the gynaecology clinic in a University Teaching Hospital in Nigeria on acceptability of the HPV vaccines and its determinants. Although 70% accepted vaccination of their daughters, 30% were unwilling and the commonest reason for unwillingness was that it may encourage sexual promiscuity (62.3%). Mothers with poor knowledge of STI were significantly more unwilling to accept HPV vaccines compared to those with average or good knowledge (p = 0.002). Furthermore, perception of susceptibility to HPV infection by daughters was significantly associated with acceptance of the vaccines (p = 0.0001). Increased advocacy and public enlightenment on cervical cancer control and the role of HPV vaccines in its prevention is still necessary especially in developing countries. PMID:25438520

  3. [The care needs of women infected with the human papilloma virus: a comprehensive approach].

    PubMed

    Cestari, Maria Elisa Wotzasek; Merighi, Miriam Aparecida Barbosa; Garanhani, Mara Lúcia; Cardeli, Alexandrina Aparecida Maciel; de Jesus, Maria Cristina Pinto; Lopes, Dolores Ferreira de Melo

    2012-10-01

    This study is founded on the phenomenology of Martin Heidegger, with the objective to understand the care needs of women infected with the human papilloma virus. Participants were fourteen women who had been diagnosed with this infection. The guiding questions were: What is it like to have this diagnosis? Tell me your experience, from when you received your diagnosis until today. What has your health care been like? The questions revealed the theme - seeking care as solitude - which showed the importance of the support of family and friends. The presence of the infection as the cause of marital conflicts and separation was another highlighted aspect. The statements showed that there was a sense of resignation after an unsuccessful attempt to find accurate and clear information in order to make assertive decisions. Health interventions for infected women must overcome the traditional models of care, including interventions for health promotion and prevention, with trained professionals who are sensitive to the subjective dimension. PMID:23223722

  4. Effective nonvaccine interventions to be considered alongside human papilloma virus vaccine delivery.

    PubMed

    Hindin, Michelle J; Bloem, Paul; Ferguson, Jane

    2015-01-01

    World Health Organization recommends that girls, ages 9-13 years, get the human papilloma virus (HPV) vaccine. Global Alliance for Vaccines Initiative, which provides low-cost vaccine to eligible countries, requires that an additional intervention to be offered alongside the vaccine. We systematically searched and assessed the published literature in lower- and middle-income countries to identify effective interventions. We conducted systematic searches of four databases: PubMed, EMBASE, Global Index Medicus Regional Databases, and Cochrane Reviews for effective adolescent health interventions that could be delivered with the HPV vaccine in the following areas: (1) iron and folic acid supplementation (iron alone or with folic acid); (2) voucher delivery and cash transfer programs; (3) hand washing and soap provision; (4) vision screening; (5) promotion of physical activity/exercise; (6) menstrual hygiene education; (7) sexual and reproductive health education; (8) human immunodeficiency virus prevention activities; and (9) condom promotion, condom use skill building, and demonstration. We found limited evidence of consistent positive impact. Iron supplementation reduced iron-deficiency anemia and raised serum ferritin levels. Promotion of physical activity lowered blood pressure and reduced weight gain. Sexual and reproductive health and human immunodeficiency virus interventions improved adolescent communication with adults but did not influence behavioral outcomes. Countries should consider locally relevant and proven interventions to be offered alongside the HPV vaccine. PMID:25287988

  5. Human papilloma virus in neoplastic and non-neoplastic conditions of the external eye

    PubMed Central

    Karcioglu, Z.; Issa, T.

    1997-01-01

    AIM—Human papilloma virus (HPV) types 16 and 18 have been associated with neoplastic conditions of the conjunctiva. However, the presence of this virus has not been reported in non-neoplastic disorders of the external eye nor has it been studied in normal conjunctival tissues.
METHODS—Ninety six paraffin embedded tissue specimens with neoplastic and non-neoplastic lesions and 19 conjunctiva samples free from overt disease were studied for HPV types 16 and 18 positivity with the polymerase chain reaction.
RESULTS—HPV types 16 and 18 DNA were identified in 57% of in situ squamous cell carcinoma, in 55% of invasive squamous cell carcinoma, in 20% of climatic droplet keratopathy, in 35% of scarred corneas, and in 32% of normal conjunctival tissue obtained during routine cataract extractions.
CONCLUSION—These findings indicate that HPV types 16 and 18 are detectable with the polymerase chain reaction not only in epithelial neoplasms of the ocular mucous membrane but also in non-neoplastic lesions as well as in apparently healthy conjunctiva.

 PMID:9290377

  6. [Human papilloma viruses: other risk factor of head and neck carcinoma].

    PubMed

    Woto-Gaye, G; M'Farrej, M K; Doh, K; Thiam, I; Touré, S; Diop, R; Dial, C

    2016-08-01

    Head and neck carcinoma (HNC) occupy the sixth place as the most frequent type of cancer worldwide. Next to alcohol and tobacco intoxication, other risk factors (RF) are suspected, including the human papilloma viruses (HPVs). The aim of this study was to highlight the prevalence of HPVs and histo-epidemiological characteristics of HNC HPV+ in Senegal. This is a prospective, multicenter preliminary study of 18 months (January 1, 2012-June 30, 2014). The cases of HNC histologically confirmed in Senegal were then sent to the bio-pathology department of the Curie Institute in Paris to search HPVs. In the 90 included cases, the PCR technique was successful in 54 cases (60%). HPVs were found in seven cases, that is, a prevalence of 13%. HPVs were associated with 5 cases of hypopharyngeal carcinoma and 2 cases of carcinoma of the oral cavity. Patients with HNC HPV+ had a median age of 42 years against 49 years for HPV-patients. Three patients (42.8%) with HPV+ carcinomas were smokers. Of the 47 HPV-patients, 40 patients (87.1%) had alcohol intoxication and/or smoking. The concept of oral sex was refuted by all our patients. Squamous cell carcinoma was the only histological type found. HPV+ cell carcinoma showed no specific histological appearance. HPVs are another certain RF of HNC in Senegal. The major therapeutic and prognostic impact of HPVinduced cancers requires the systematic search of the viruses by the PCR technique. PMID:27325173

  7. Periodontal pocket as a potential reservoir of high risk human papilloma virus: A pilot study

    PubMed Central

    Dayakar, Manjunath Mundoor; Shipilova, Anna; Gupta, Dinesh

    2016-01-01

    Aim: Human papilloma viruses (HPVs) are small DNA viruses that have been identified in periodontal pocket as well as gingival sulcus. High risk HPVs are also associated with a subset of head and neck carcinomas. HPV detection in periodontium has previously involved DNA detection. This study attempts to: (a) Detect the presence or absence of high risk HPV in marginal periodontiun by identifying E6/E7 messenger RNA (mRNA) in cells from samples obtained by periodontal pocket scraping. (b) Detect the percentage of HPV E6/E7 mRNA in cells of pocket scrapings, which is responsible for producing oncoproteins E6 and E7. Materials and Methods: Pocket scrapings from the periodontal pockets of eight subjects with generalized chronic periodontitis were taken the detection of presence or absence of E6, E7 mRNA was performed using in situ hybridization and flow cytometry. Results: HPV E6/E7 mRNA was detected in four of the eight samples. Conclusion: Presence of high risk human papillomaviruses in periodontal pockets patients of diagnosed with chronic periodontitis, not suffering from head and neck squamous cell carcinoma in the present day could link periodontitis to HPV related squamous cell carcinoma. Prevalence studies are needed detecting the presence of HPV in marginal periodontium as well as prospective studies of HPV positive periodontitis patients are required to explore this possible link. PMID:27143823

  8. Association of human papilloma virus with pterygia and ocular-surface squamous neoplasia.

    PubMed

    Di Girolamo, N

    2012-02-01

    There are more microorganisms that colonize the human body than resident cells; some are commensal whereas others are pathogenic. Pathogenic microorganisms are sensed by the innate or adaptive immune system, an immune response is initiated, and the infection is often cleared. Some microorganisms have developed strategies to evade immune defenses, ensuring their long-term survival with potentially devastating consequences for the host. Approximately 18% of all cancers can be attributed to infective agents; the most common being Helicobacter pylori, Human papilloma virus (HPV) and Hepatitis B and C virus in causing stomach, cervical and liver carcinoma, respectively. This review focuses on whether HPV infection is necessary for initiating pterygia, a common benign condition and ocular-surface squamous neoplasia (OSSN), a rare disease with metastatic potential. The search engine PubMed was used to identify articles from the literature related to HPV and pterygium or conjunctival neoplasia. From 34 investigations that studied HPV in pterygia and OSSN, a prevalence rate of 18.6% (136/731) and 33.8% (144/426), respectively, was recorded. The variation in HPV prevalence (0-100%) for both disease groups may have arisen from study-design faults and the techniques used to identify the virus. Overall, the data suggest that HPV is not necessary for initiating either condition but may be a co-factor in susceptible hosts. Currently, over 60 million people worldwide have been immunized with HPV vaccines, but any effect on pterygium and OSSN development may not be known for some time as these lesions can evolve over decades or occur in older individuals. PMID:22134594

  9. Intraductal papilloma

    MedlinePlus

    ... page: //medlineplus.gov/ency/article/001238.htm Intraductal papilloma To use the sharing features on this page, please enable JavaScript. Intraductal papilloma is a small, noncancerous (benign) tumor that grows ...

  10. Expectation prior to human papilloma virus vaccination: 11 to 12-Year-old girls' written narratives.

    PubMed

    Forsner, M; Nilsson, S; Finnström, B; Mörelius, E

    2016-09-01

    Expectations prior to needle-related procedures can influence individuals' decision making and compliance with immunization programmes. To protect from human papilloma virus (HPV) and cervical cancer, the immunization needs to be given before sexual debut raising interest for this study's aim to investigate how 11 to 12-year-old girls narrate about their expectations prior to HPV vaccination. A total of 27 girls aged 11 to 12 years participated in this qualitative narrative study by writing short narratives describing their expectations. The requirement for inclusion was to have accepted HPV vaccination. Data were subjected to qualitative content analysis. Findings showed the following expectations: going to hurt, going to be scared and going to turn out fine. The expectations were based on the girls' previous experiences, knowledge and self-image. The latent content revealed that the girls tried to transform uneasiness to confidence. The conclusion drawn from this study is that most girls of this age seem confident about their ability to cope with possible unpleasantness related to vaccinations. However, nurses need to find strategies to help those children who feel uneasy about needle-related procedures. PMID:26311482

  11. Human Papilloma Virus Infection in Patients with Male Accessory Gland Infection: Usefulness of the Ultrasound Evaluation

    PubMed Central

    Condorelli, Rosita A.; Vicari, Enzo; Mongioi, Laura M.

    2016-01-01

    This study evaluated the ultrasound (US) features of 20 patients with MAGI and concomitant papilloma virus (HPV) infection compared to 20 patients with microbial (presence of Chlamydia trachomatis alone) MAGI and 20 patients with amicrobial (inflammatory) MAGI. Patients with HPV infection showed significantly (p < 0.05) higher total prostate, seminal vesicles, and epididymal US signs (18.0 ± 2.0) compared to the other 2 groups (12.0 ± 4.0 versus 10.0 ± 3.0, resp.). In addition, patients with MAGI and HPV had a higher prevalence of complicated forms of MAGI [prostatovesiculitis (PV) and prostate-vesiculo-epididymitis (PVE)] and a higher frequency of the fibrosclerotic variant compared to the other groups (70.0 ± 10.0% versus 48.0 ± 5.0% versus 15.0 ± 10.0%). Moreover, HPV infected patients had a higher number of US criteria suggestive for MAGI in the periurethral region of the prostate compared to the other groups. In particular, the patients showed a higher ratio between periurethral and lobar US criteria distribution (5.0 versus 0.5). Finally, the seminal fluid concentration of CD45pos leukocytes (2.0 ± 0.2 versus 1.3 ± 0.3 versus 1.0 ± 0.3 mil/mL) was significantly higher and sperm progressive motility was significantly lower in these patients compared to other groups. PMID:27242899

  12. [Withdrawal of an advertising campaign to promote the quadrivalent human papilloma virus vaccine in Spain].

    PubMed

    Martín-Llaguno, Marta; Alvarez-Dardet, Carlos

    2010-01-01

    The inclusion of the quadrivalent human papilloma virus (HPV) vaccine in the schedule of the Spanish National Health System sparked the debate over Gardasil, which was presented to the public as a "vaccine against cervical cancer". In this context, Sanofi Pasteur MSD was sued for misleading advertising in the campaign "cuentaselo.org". Although the complaint was not admitted, the lawsuit triggered five changes in the ownership of the web domain which, although backed by scientific societies, was not supported by law. Because of the violation of the Law of the Society of Information Services, and prompted by the suspicion that the pharmaceutical company was behind these changes (as it could not advertise the product), the platform for the moratorium on the HPV vaccine filed a complaint against the Spanish Society of Gynecology and Obstetrics (whose logo appeared on the webpage) for breaching the code of advertising self-regulation. Sanofi Pasteur MSD, the advertiser which was not mentioned, "accepted the complaint and removed the webpage", thus corroborating its involvement. PMID:19523720

  13. Perceptions of Nigerian Women about Human Papilloma Virus, Cervical Cancer, and HPV Vaccine

    PubMed Central

    Akanbi, Olusola Anuoluwapo; Iyanda, Abiodun; Osundare, Folakemi; Opaleye, Oluyinka Oladele

    2015-01-01

    Background. Cervical cancer caused by human papilloma virus (HPV) though preventable has claimed the lives of many women worldwide. This study was embarked upon to evaluate the general knowledge and perceptions of Nigerian women on HPV, cervical cancer, and HPV vaccine. Methods. Structured questionnaires were administered to a cross section of 737 women randomly selected from the general population in two southwestern States of Nigeria. Statistical analysis was done using SPSS computer software version 16. A P value >0.05 was considered statistically significant. Results. One hundred and seventy-six (23.9%) of the respondents had knowledge of HPV; 474 (64.3%) are aware of cervical cancer but only 136 (18.5%) know that HPV causes cervical cancer. 200 (27.1%) are aware that there is an HPV vaccine while 300 (40.7%) had knowledge of Pap smear test. Two hundred and sixty (35.3%) of the respondents know that early detection of HPV can prevent cervical cancer and in spite of this, only 110 (14.9%) have taken the Pap smear test before while 151 (20.5%) are not willing to go for the test at all. Conclusions. There is therefore the need to create proper awareness on the HPV and its possible consequence of cervical carcinoma. PMID:26550522

  14. Origin of replication in episomal bovine papilloma virus type 1 DNA isolated from transformed cells.

    PubMed Central

    Waldeck, W; Rösl, F; Zentgraf, H

    1984-01-01

    The origin of replication of bovine papilloma virus type 1 (BPV-1) has been determined by isolating replicative intermediates (RI) of BPV-transformed hamster embryo fibroblasts (HEF-BPV). These RI were treated with single cut restriction enzymes to determine the start-position (origin) of the extending replication eyes using electron microscopic techniques. 'Cairns'-type RI molecules were shown to contain one replication eye in monomeric as well as in dimeric molecules. The position of this eye was localized at 6940 +/- 5% bp in the physical map. In a second set of experiments BPV-1 DNA fragments cloned in pBR322 were tested for transient episomal replication. Transfected cells were harvested after increasing periods of time and screened for replication with isoschizomeric restriction enzymes to differentiate between input and replicated DNA. The part of the BPV genome harboring the replication origin spans the BPV ClaI-C restriction fragment corresponding to the non-coding region of the BPV genome and coincides with the DNase I-hypersensitive control region in the chromatin, isolated from transformed cells. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 7. PMID:6092063

  15. Repression of bovine papilloma virus replication is mediated by a virally encoded trans-acting factor.

    PubMed

    Berg, L; Lusky, M; Stenlund, A; Botchan, M R

    1986-08-29

    Cells transformed with bovine papilloma virus type 1 mutants in the E6 or E6/7 genes are resistant to high-copy-number amplification of wild-type DNA after supertransfection. Transient and stable replication assays demonstrate this effect. If the supertransfected DNA has a mutation in a newly defined gene (M), this cellular immunity to high-copy-number replication is overcome, resulting in transient replication of the input DNA. In contrast, the resident plasmid does not participate in amplification and is maintained at a constant low copy number. Cotransformation of M- mutants and wild-type DNA into these cells leads to shutoff of replication of both genomes. Thus, M- mutants define a trans-acting negative modulator that regulates viral replication. This function is distinct from the positive factors required for replication. We propose a model that explains why the loss of E6 and E6/7 function leads to immunity of the infected cell. PMID:3017567

  16. [Clinical usefulness of diagnostic methods for human papilloma virus dependent lesions].

    PubMed

    Suwalska, Anna; Owczarek, Witold; Fiedor, Piotr

    2014-02-01

    Persistent infection of Human Papilloma Virus (HPV) is confirmed necessary factor for development of cervical cancer and anogenital neoplasia. DNA HPV is detected in 96% of cervical cancer, 40% of vulvar and vaginal cancer, 90% of anal cancer and 26% of oral cavity cancer cases in general population. The most common high-risk HPV types observed in anogenital intraepithelial neoplasia or anogenital cancer are HPV 16, 18 and 45. Numerous diagnostic methods of detection of HPV infection and lesions causes by persistent HPV infection are widely used. Epidemiological data reveals correlation of incidence and mortality reduction due to cervical cancer and consequent prosecution and improvement of screening programmes based on morphological assessment of exfoliative smears. In last decade some limitations of conventional smear method were pointed out and a new diagnostic techniques were introduced: liquid-based cytology and HPV DNA testing. Combination of cytological examination and HPV DNA testing seems to be optimal solution to be introduced in large population because of combining high sensitivity of molecular test with high specificity of cytological smear. PMID:24720112

  17. Human papilloma virus DNAs immortalize normal human mammary epithelial cells and reduce their growth factor requirements

    SciTech Connect

    Band, V.; Zajchowski, D.; Kulesa, V.; Sager, R. )

    1990-01-01

    Human papilloma virus (HPV) types 16 and 18 are most commonly associated with cervical carcinoma in patients and induce immortalization of human keratinocytes in culture. HPV has not been associated with breast cancer. This report describes the immortalization of normal human mammary epithelial cells (76N) by plasmid pHPV18 or pHPV16, each containing the linearized viral genome. Transfectants were grown continuously for more than 60 passages, whereas 76N cells senesce after 18-20 passages. The transfectants also differ from 76N cells in cloning in a completely defined medium called D2 and growing a minimally supplemented defined medium (D3) containing epidermal growth factor. All transfectant tested contain integrated HPV DNA, express HPV RNA, and produce HPV E7 protein. HPV transfectants do not form tumors in a nude mouse assay. It is concluded that products of the HPV genome induce immortalization of human breast epithelial cells and reduce their growth factor requirements. This result raises the possibility that HPV might be involved in breast cancer. Furthermore, other tissue-specific primary epithelial cells that are presently difficult to grown and investigate may also be immortalized by HPV.

  18. [QUANTITATIVE DNA EVALUATION OF THE HIGH CARCINOGENIC RISK OF HUMAN PAPILLOMA VIRUSES AND HUMAN HERPES VIRUSES IN MALES WITH FERTILITY DISORDERS].

    PubMed

    Evdokimov, V V; Naumenko, V A; Tulenev, Yu A; Kurilo, L F; Kovalyk, V P; Sorokina, T M; Lebedeva, A L; Gomberg, M A; Kushch, A A

    2016-01-01

    Infertility is an actual medical and social problem. In 50% of couples it is associated with the male factor and in more than 50% of cases the etiology of the infertility remains insufficiently understood. The goal of this work was to study the prevalence and to perform quantitative analysis of the human herpes viruses (HHV) and high carcinogenic risk papilloma viruses (HR HPV) in males with infertility, as well as to assess the impact of these infections on sperm parameters. Ejaculate samples obtained from 196 males fall into 3 groups. Group 1 included men with the infertility of unknown etiology (n = 112); group 2, patients who had female partners with the history of spontaneous abortion (n = 63); group 3 (control), healthy men (n = 21). HHV and HR HPV DNA in the ejaculates were detected in a total of 42/196 (21.4%) males: in 31 and 11 patients in groups 1 and 2, respectively (p > 0.05) and in none of healthy males. HHV were detected in 24/42; HR HPV, in 18/42 males (p > 0.05) without significant difference between the groups. Among HR HPV genotypes of the clade A9 in ejaculate were more frequent (14/18, p = 0.04). Comparative analysis of the sperm parameters showed that in the ejaculates of the infected patients sperm motility as well as the number of morphologically normal cells were significantly reduced compared with the healthy men. The quantification of the viral DNA revealed that in 31% of the male ejaculates the viral load was high: > 3 Ig10/100000 cells. Conclusion. The detection of HHV and HR HPV in the ejaculate is associated with male infertility. Quantification of the viral DNA in the ejaculate is a useful indicator for monitoring viral infections in infertility and for decision to start therapy. PMID:27451497

  19. Hepatitis C virus genotypes in Myanmar.

    PubMed

    Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

    2016-07-21

    Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined. PMID:27468202

  20. Hepatitis B virus: the genotype E puzzle.

    PubMed

    Andernach, Iris E; Hübschen, Judith M; Muller, Claude P

    2009-07-01

    Hepatitis B virus (HBV) is highly endemic throughout sub-Saharan Africa. One of the two genotypes A and E dominates in most countries. With several subgenotypes and variants, genotype A is more diverse in Africa (4.00%) than in the rest of the world (2.96%), suggesting an African origin and a long history on the continent. Despite the African slave trade, genotype E has only sporadically been found within the Americas, indicating that this genotype was introduced only during the past 200 years into the general African population. A short history for this genotype in Africa is also supported by its conspicuously low genetic diversity (1.75%), which contrasts, however, with its excessively high HBsAg prevalence and its extensive spread throughout the vast West-African genotype E crescent. We discuss the spread and routes of transmission of genotype E and suggest that the distribution and current high prevalence levels of HBV (genotype E) in Africa are the result of the extensive use of unsafe needles, potentially solving the current African genotype E puzzle and shedding new light on the high HBV prevalence in Africa. PMID:19475565

  1. Hepatitis C virus genotypes in Myanmar

    PubMed Central

    Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

    2016-01-01

    Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined. PMID:27468202

  2. A human papilloma virus type 11 transcript encoding an E1--E4 protein.

    PubMed

    Nasseri, M; Hirochika, R; Broker, T R; Chow, L T

    1987-08-01

    The human papilloma virus (HPV) associated with a genital wart (condyloma acuminatum) was determined to be type 11. The majority of the viral DNA molecules were monomeric circles present in the cells at high copy number, as demonstrated by one- and two-dimensional agarose gell electrophoretic separation followed by Southern blot analysis. A cDNA library in phage lambda gt11 was constructed from poly(A)-selected mRNA recovered from the tissue. Recombinant clones corresponding to the most abundant 1.2-kb viral mRNA species detected by Northern blot hybridization and by electron microscopic analysis of R loops were isolated and their nucleotide sequence was determined. Comparison to the prototype HPV-11 DNA sequence revealed that this message consisted of two exons. The promotor-proximal exon spanned nucleotides 716 through 847 and the distal exon included nucleotides 3325 through 4390 or 4392. The mRNAs were alternatively polyadenylated after either of these latter two sites, in both cases following a G and preceding a U residue. Fourteen or sixteen bases upstream from the poly(A) was the hexanucleotide AGUAAA, which apparently serves as the signal for cleavage and polyadenylation of the nascent message. The splice donor and acceptor sites conformed to the usual /GU. . .AG/pattern. The exons joined open reading frame (ORF) E1, which contributed the initiation codon and four additional triplets, to ORF E4, which specified 85 amino acids to encode a protein of 10,022 Da. The cDNA also contained the ORFs E5a and E5b toward the 3' end. The complete sequence of the cDNA revealed three single-base changes from the prototype HPV-11, two resulting in altered amino acids in E4. Neither affects the coding potential of the overlapping E2 ORF. The function of the E1--E4 protein is unknown. PMID:2887066

  3. A Small Molecule Inhibitor Selectively Induces Apoptosis in Cells Transformed by High Risk Human Papilloma Viruses.

    PubMed

    Sheaffer, Amy K; Lee, Min S; Qi, Huilin; Chaniewski, Susan; Zheng, Xiaofan; Farr, Glen A; Esposito, Kim; Harden, David; Lei, Ming; Schweizer, Liang; Friborg, Jacques; Agler, Michele; McPhee, Fiona; Gentles, Robert; Beno, Brett R; Chupak, Lou; Mason, Stephen

    2016-01-01

    A phenotypic high-throughput cell culture screen was performed to identify compounds that prevented proliferation of the human Papilloma virus type 16 (HPV-16) transformed cell line Ca Ski. A series of quinoxaline compounds exemplified by Compound 1 was identified. Testing against a panel of cell lines demonstrated that Compound 1 selectively inhibited replication of all HPV-16, HPV-18, and HPV-31 transformed cell lines tested with 50% Inhibitory Concentration (IC50) values of 2 to 8 μM relative to IC50 values of 28 to 73 μM in HPV-negative cell lines. Treatment with Compound 1 resulted in a cascade of multiple apoptotic events, including selective activation of effector caspases 3 and 7, fragmentation of cellular DNA, and PARP (poly(ADP-ribose) polymerase) cleavage in HPV-positive cells relative to HPV-negative cells. Unregulated proliferation of HPV transformed cells is dependent on the viral oncogenes, E6 and E7. Treatment with Compound 1 resulted in a decrease in HPV E7 protein in Ca Ski cells. However, the timing of this reduction relative to other effects of compound treatment suggests that this was a consequence, rather than a cause, of the apoptotic cascade. Likewise, compound treatment resulted in no obvious effects on the E6- and E7- mediated down regulation of p53 and Rb, or their downstream effectors, p21 or PCNA. Further investigation of apoptotic signals induced by Compound 1 revealed cleavage of Caspase-8 in HPV-positive cells as early as 2 hours post-treatment, suggesting the compound initiates apoptosis through the extrinsic, death receptor-mediated, pathway of cell death. These studies provide proof of concept that cells transformed by oncogenic Papillomaviruses can be selectively induced to undergo apoptosis by compound treatment. PMID:27280728

  4. Basics of tumor development and importance of human papilloma virus (HPV) for head and neck cancer

    PubMed Central

    Wittekindt, Claus; Wagner, Steffen; Mayer, Christina Sabine; Klussmann, Jens Peter

    2012-01-01

    Head and Neck Squamous Cell Carcinomas (HNSCC) are the 6th most common cancers worldwide. While incidence rates for cancer of the hypopharynx and larynx are decreasing, a significant increase in cancer of the oropharynx (OSCC) is observed. Classical risk factors for HNSCC are smoking and alcohol. It has been shown for 25 to 60% of OSCC to be associated with an infection by oncogenic human papilloma viruses (HPV). The development of “common” cancer of the head and neck is substantially enhanced by an accumulation of genetic changes, which lead to an inactivation of tumor suppressor genes or activation of proto-oncogenes. A more or less uniform sequence of different DNA-damages leads to genetic instability. In this context, an early and frequent event is deletion on the short arm of chromosome 9, which results in inactivation of the p16-gene. In contrast, for HPV-induced carcinogenesis, expression of the viral proteins E6 and E7 is most important, since they lead to inactivation of the cellular tumor-suppressor-proteins p53 and Rb. The natural route of transoral infection is a matter of debate; peroral HPV-infections might be frequent and disappear uneventfully in most cases. Smoking seems to increase the probability for developing an HPV-associated OSCC. The association of HNSCC with HPV can be proven with established methods in clinical diagnostics. In addition to classical prognostic factors, diagnosis of HPV-association may become important for selection of future therapies. Prognostic relevance of HPV probably surmounts many known risk-factors, for example regional metastasis. Until now, no other molecular markers are established in clinical routine. Future therapy concepts may vary for the two subgroups of patients, particularly patients with HPV-associated OSCC may take advantage of less aggressive treatments. Finally, an outlook will be given on possible targeted therapies. PMID:23320061

  5. Vaccination Against Human Papilloma Viruses Leads to a Favorable Cytokine Profile of Specific T Cells.

    PubMed

    Luckau, Stefanie; Wehrs, Tim P; Brandau, Sven; Horn, Peter A; Lindemann, Monika

    2016-10-01

    Several human papilloma viruses (HPV) are known to cause malignant transformation. The high-risk type HPV 16 is associated with cervical carcinoma and head and neck squamous cell carcinoma. HPV 16-positive tumor cells exclusively carry the HPV 16 oncogenes E6 and E7. These oncogenes appear as excellent targets for an adoptive immunotherapy. We here addressed the question whether specific T cells from HPV-vaccinated healthy volunteers could be especially suitable for an HPV-specific cellular immunotherapy. Of note, vaccines contain HPV 16. To quantify HPV 16 E6-specific and E7-specific cells, enzyme-linked immunospot assays to measure interferon-γ (IFN-γ) and interleukin-10 (Th1-Th2 balance) and the secretion of the cytotoxic molecules granzyme B and perforin have been optimized. The frequency of peripheral blood mononuclear cells secreting IFN-γ and perforin was significantly (P<0.05) increased in HPV-vaccinated versus nonvaccinated volunteers. Overall, however, the median frequency of HPV 16-specific cells with a favorable secretion profile (Th1 balanced and cytotoxic) was low even in vaccinated volunteers (IFN-γ: 0.0018% and 0.0023%, perforin: 0.01% and 0.0087% for E6-specific and E7-specific cells, respectively). But some vaccinated volunteers showed up to 0.1% HPV-specific, IFN-γ or perforin-secreting cells. In conclusion, our data suggest that vaccinated volunteers are superior to nonvaccinated donors for HPV-specific cellular cancer immunotherapy. PMID:27548034

  6. A Small Molecule Inhibitor Selectively Induces Apoptosis in Cells Transformed by High Risk Human Papilloma Viruses

    PubMed Central

    Lee, Min S.; Qi, Huilin; Chaniewski, Susan; Zheng, Xiaofan; Farr, Glen A.; Esposito, Kim; Harden, David; Lei, Ming; Schweizer, Liang; Friborg, Jacques; Agler, Michele; McPhee, Fiona; Gentles, Robert; Beno, Brett R.; Chupak, Lou; Mason, Stephen

    2016-01-01

    A phenotypic high-throughput cell culture screen was performed to identify compounds that prevented proliferation of the human Papilloma virus type 16 (HPV-16) transformed cell line Ca Ski. A series of quinoxaline compounds exemplified by Compound 1 was identified. Testing against a panel of cell lines demonstrated that Compound 1 selectively inhibited replication of all HPV-16, HPV-18, and HPV-31 transformed cell lines tested with 50% Inhibitory Concentration (IC50) values of 2 to 8 μM relative to IC50 values of 28 to 73 μM in HPV-negative cell lines. Treatment with Compound 1 resulted in a cascade of multiple apoptotic events, including selective activation of effector caspases 3 and 7, fragmentation of cellular DNA, and PARP (poly(ADP-ribose) polymerase) cleavage in HPV-positive cells relative to HPV-negative cells. Unregulated proliferation of HPV transformed cells is dependent on the viral oncogenes, E6 and E7. Treatment with Compound 1 resulted in a decrease in HPV E7 protein in Ca Ski cells. However, the timing of this reduction relative to other effects of compound treatment suggests that this was a consequence, rather than a cause, of the apoptotic cascade. Likewise, compound treatment resulted in no obvious effects on the E6- and E7- mediated down regulation of p53 and Rb, or their downstream effectors, p21 or PCNA. Further investigation of apoptotic signals induced by Compound 1 revealed cleavage of Caspase-8 in HPV-positive cells as early as 2 hours post-treatment, suggesting the compound initiates apoptosis through the extrinsic, death receptor-mediated, pathway of cell death. These studies provide proof of concept that cells transformed by oncogenic Papillomaviruses can be selectively induced to undergo apoptosis by compound treatment. PMID:27280728

  7. Human Papilloma Virus Awareness Among Hispanic Females with Inflammatory Bowel Disease.

    PubMed

    Rivera-Acosta, José E; Aponte, Maysabel; Villamil, Irene; Romaguera, Josefina; Ortiz, Ana P; Torres, Esther A

    2016-03-01

    Women with inflammatory bowel disease (IBD) may be at increased risk of human papilloma virus (HPV) infection and HPV-related malignancies, as many are immunocompromised secondary to the use of immunosuppressant agents. Several studies have addressed the knowledge about cervical cancer risk factors in different populations, particularly HPV infection and its association with cervical malignancies; most of these studies show poor patient knowledge. The purpose of this study is to describe the knowledge of females with IBD about HPV infection and the HPV vaccine. We performed a cross-sectional study in 147 consecutive patients attending the clinics of the University of Puerto Rico Center for IBD from 2009 to 2010. An interviewer-administered questionnaire was used to collect information on demographics, lifestyles, and HPV-related knowledge of participants. Bivariate analysis using the chi-square statistics and Fisher's exact test was used to examine factors associated with HPV awareness. The mean age of participants was 36.6 years (SD = 13.91 years). Three fourth (77 %) of women had awareness of the existence of HPV, and 58 % did know about the existence of HPV vaccines. Among those who had heard about HPV, 79.6 % knew that HPV can cause cervical cancer, and 57.5 % knew that the virus is sexually transmitted. Among those who knew of the vaccine, 75.3 % learned about its existence through the media, while only 15.3 %, through their health-care provider. Only three women within recommended ages (2 %) had been vaccinated against HPV, although 50 % of participants indicated that they would definitely/probably vaccinate against HPV in the future. A significant trend was observed, where more educated women were more likely to have heard of HPV (p for trend = 0.0017). Women who were high school graduates/some college (OR = 6.63, 95 % CI = 1.71-25.66) and those with at least an associate degree (OR = 11.69, 95 % CI = 3.05-45.89) were more

  8. Schneiderian papilloma of the temporal bone

    PubMed Central

    van der Putten, Lisa; Bloemena, Elisabeth; Merkus, Paul; Hensen, Erik F

    2013-01-01

    Temporal bone Schneiderian papilloma may present as a primary tumour originating from the middle ear and mastoid process, or an extension from sinonasal disease. Both forms are rare, this being only the 18th case of primary temporal bone Schneiderian papilloma described to date. Although the current patient has remained disease free after excision of the papilloma, the reported recurrence rate is high, comparable to sinonasal Schneiderian papilloma with extrasinus extension. Malignant progression of primary Schneiderian papillomas is significantly reduced as compared to Schneiderian papillomas that extend from the sinonasal tract into the temporal bone. A positive human papilloma virus status, as found in this case, is a common feature and prognostic factor of sinonasal Schneiderian papilloma but an infrequent finding in temporal bone disease. Owing to the high recurrence rate, the risk of malignant progression and the absence of reliable prognostic markers, stringent follow-up consisting of otoscopy, nasendoscopy and imaging is essential. PMID:24311418

  9. Cost-Effectiveness Evaluation of Quadrivalent Human Papilloma Virus Vaccine for HPV-Related Disease in Iran

    PubMed Central

    Khatibi, Mohsen; Rasekh, Hamid Reza; Shahverdi, Zohreh; jamshidi, Hamid Reza

    2014-01-01

    Human Papilloma Virus (HPV) vaccine has been added recently to the Iran Drug List. So, decision makers need information beyond that available from RCTs to recommend funding for this vaccination program to add it to the National Immunization program in Iran. Modeling and economic studies have addressed some of those information needs in foreign countries. In order to determine the long term benefit of this vaccine and impact of vaccine program on the future rate of cervical cancer in Iran, we described a model, based on the available economic and health effects of human papilloma virus (HPV), to estimate the cost-effectiveness of HPV vaccination of 15-year-old girls in Iran. Our objective is to estimate the cost-effectiveness of HPV vaccination in Iran against cervical cancer based on available data; incremental cost-effectiveness ratio (ICER) calculations were based on a model comparing a cohort of 15-year-old girls with and without vaccination. We developed a static model based on available data in Iran on the epidemiology of HPV related health outcome. The model compared the cohort of all 15-year old girls alive in the year 2013 with and without vaccination. The cost per QALY, which was found based on our assumption for the vaccination of 15-years old girl to current situation was 439,000,000 Iranian Rial rate (IRR). By considering the key parameters in our sensitivity analysis, value varied from 251,000,000 IRR to 842,000,000 IRR. In conclusion, quadrivalent HPV vaccine (Gardasil) is not cost-effective in Iran based on the base-case parameters value. PMID:24711850

  10. Evidence for and Localization of Vegetative Viral DNA Replication by Autoradiographic Detection of RNA·DNA Hybrids in Sections of Tumors Induced by Shope Papilloma Virus

    PubMed Central

    Orth, Gérard; Jeanteur, Philippe; Croissant, Odile

    1971-01-01

    The occurrence and localization of vegetative viral DNA replication was studied in sections of tumors induced by the rabbit Shope papilloma virus, in cottontail and domestic rabbit papillomas, in primary domestic rabbit carcinoma, and in transplantable VX2 carcinoma, by in situ hybridization of radioactive RNA complementary to viral DNA. Vegetative viral DNA replication and viral protein synthesis were compared by means of cytological hybridization and immunofluorescence techniques on adjacent frozen sections. Vegetative viral DNA replication is completely repressed in the proliferating cellular layers of these tumors, which suggests a provirus state of the viral genome, as in other cells transformed by oncogenic DNA viruses. Vegetative viral DNA replication is induced, after initiation of the keratinization, in cells of cottonail rabbit papillomas, where it is usually followed by viral protein synthesis; this illustrates the influence of the physiological state of the host cell on the control of viral functions. Vegetative viral DNA replication is deteced only in a few cells of domestic rabbit papillomas, at the end of the keratinization process; this observation provides indirect evidence that the DNA synthesis specifically induced in these tumors after the onset of keratinization reflects mostly the induction of cellular DNA synthesis. Images PMID:4331563

  11. Enhancing the Sensitivity of DNA Microarray Using Dye-Doped Silica Nanoparticles: Detection of Human Papilloma Virus

    NASA Astrophysics Data System (ADS)

    Enrichi, F.; Riccò, R.; Meneghello, A.; Pierobon, R.; Canton, G.; Cretaio, E.

    2010-10-01

    DNA microarray is a high-throughput technology used for detection and quantification of nucleic acid molecules and others of biological interest. The analysis is based on the specific hybridization between probe sequences deposited in array and a target ss-DNA amplified by PCR and functionalized by a fluorescent dye. Organic labels have well known disadvantages like photobleaching and low signal intensities, which put a limitation to the lower amount of DNA material that can be detected. Therefore for trace analysis the development of more efficient biomarkers is required. With this aim we present in this paper the synthesis and application of alternative hybrid nanosystems obtained by incorporating standard fluorescent molecules into monodisperse silica nanoparticles. Efficient application to the detection of Human Papilloma Virus is demonstrated. This virus is associated to the formation of cervical cancer, a leading cause of death by cancer for women worldwide. It is shown that the use of the novel biomarkers increases the optical signal of about one order of magnitude with respect to the free dyes or quantum dots in conventional instruments. This is due to the high number of molecules that can be accommodated into each nanoparticle, to the reduced photobleaching and to the improved environmental protection of the dyes when encapsulated in the silica matrix. The cheap and easy synthesis of these luminescent particles, the stability in water, the surface functionalizability and bio-compatibility make them very promising for present and future bio-labeling and bio-imaging applications.

  12. Merkel cell polyomavirus and human papilloma virus in proliferative skin lesions arising in patients treated with BRAF inhibitors.

    PubMed

    Falchook, G S; Rady, P; Konopinski, J C; Busaidy, N; Hess, K; Hymes, S; Nguyen, H P; Prieto, V G; Bustinza-Linares, E; Lin, Q; Parkhurst, K L; Hong, D S; Sherman, S; Tyring, S K; Kurzrock, R

    2016-07-01

    The potential role of oncogenic viruses mediating development of proliferative skin lesions in patients treated with RAF inhibitors is poorly understood. The objective of this study was to investigate human papilloma virus (HPV) and Merkel cell polyomavirus (MCPyV) in skin lesions among patients treated with RAF inhibitors with the help of a case series describing prevalence of HPV, MCPyV, and RAS mutations in skin biopsies obtained from patients receiving RAF inhibitors and developing cutaneous lesions. HPV-DNA was amplified by PCR utilizing multiple nested primer systems designed for detection of a broad range of HPV types. MCPyV copy number determination with real time PCR technology was performed by a "Quantification of MCPyV, small t region" kit. Thirty-six patients were tested (squamous cell carcinoma (SCC) = 14; verruca vulgaris = 15; other = 11). Nine of 12 SCCs (75 %) and eight of 13 verruca vulgaris lesions (62 %) tested positive for MCPyV whereas none of the normal skin biopsies obtained from nine of these patients tested positive for MCPyV (p = 0.0007). HPV incidence in cutaneous SCCs was not different compared to normal skin (50 vs. 56 %, p = 0.86). The association between MCPyV and proliferative skin lesions after RAF inhibitor therapy merits further investigation. PMID:27098388

  13. Human papilloma virus, herpes simplex virus and epstein barr virus in oral squamous cell carcinoma from eight different countries.

    PubMed

    Jalouli, Jamshid; Jalouli, Miranda M; Sapkota, Dipak; Ibrahim, Salah O; Larsson, Per-Anders; Sand, Lars

    2012-02-01

    Oral squamous cell carcinoma (OSCC) is a major health problem in many parts of the world, and the major causative agents are thought to be the use of alcohol and tobacco. Oncogenic viruses have also been suggested to be involved in OSCC development. This study investigated the prevalence of human papillomaviruses (HPV), herpes simplex virus (HSV) and Epstein-Barr virus (EBV) in 155 OSCC from eight different countries from different ethnic groups, continents and with different socioeconomic backgrounds. 41 A total of OSCCs were diagnosed in the tongue (26%) and 23 in the floor of the mouth (15%); the other 91 OSCCs were diagnosed in other locations (59%). The patients were also investigated regarding the use of alcohol and smoking and smokeless tobacco habits. Tissue samples were obtained from formalin-fixed, paraffin-embedded samples of the OSCC. DNA was extracted and the viral genome was examined by single, nested and semi-nested PCR assays. Sequencing of double-stranded DNA from the PCR product was carried out. Following sequencing of the HPV-, HSV- and EBV-positive PCR products, 100% homology between the sampels was found. Of all the 155 OSCCs examined, 85 (55%) were positive for EBV, 54 (35%) for HPV and 24 (15%) for HSV. The highest prevalence of HPV was seen in Sudan (65%), while HSV (55%) and EBV (80%) were most prevalent in the UK. In 34% (52/155) of all the samples examined, co-infection by two (46/155=30%) or three (6/155=4%) virus specimens was detected. The most frequent double infection was HPV with EBV in 21% (32/155) of all OSCCs. There was a statistically significant higher proportion of samples with HSV (p=0.026) and EBV (p=0.015) in industrialized countries (Sweden, Norway, UK and USA) as compared to developing countries (Sudan, India, Sri Lanka and Yemen). Furthermore, there was a statistically significant higher co-infection of HSV and EBV in samples from industrialized countries (p=0.00031). No firm conclusions could be drawn regarding the

  14. Squamous papilloma of the hard palate

    PubMed Central

    Babaji, Prashant; Singh, Vikram; Chaurasia, Vishwajit Rampratap; Masamatti, Vinaykumar S; Sharma, Akanksha Manmohan

    2014-01-01

    Oral squamous papillomas are benign proliferating lesions induced by human papilloma virus. These lesions are painless and slowly growing masses. As an oral lesion, it raises concern because of its clinical appearance. These lesions commonly occur between age 30 and 50 years, and sometimes can occur before the age of 10 years. Oral squamous papilloma accounts for 8% of all oral tumors in children. Common site predilection for the lesion is the tongue and soft palate, and may occur on any other surface of the oral cavity such as the uvula and vermilion of the lip. Here, we are presenting a case of squamous papilloma on the palate. PMID:25565755

  15. Factors associated with future commitment and past history of human papilloma virus vaccination among female college students in northern Taiwan

    PubMed Central

    Kuo, Ping-Fen; Yeh, Ying-Tse; Sheu, Shuh-Jen

    2014-01-01

    Objective To investigate factors influencing commitment to human papilloma virus (HPV) vaccination and prior vaccination among female college students in northern Taiwan. Methods A quota sample of 400 female college students was recruited from nine colleges in northern Taiwan during March 2013. Of these, 398 completed the self administered questionnaire which was designed based on the health promotion model. Results The results showed that factors associated with prior vaccination behavior were family history of gynecologic malignancy, ever being advised to get HPV vaccination, perceived barriers of action and perceived self-efficacy. Predictors for commitment to HPV vaccination in the next 6 months were the cost of vaccination, ever being advised to get HPV vaccination, perceived self-efficacy and situational influences. Perceived self-efficacy was significantly influenced by relationship status, past receipt of a recommendation for HPV vaccination and level of knowledge about HPV. Conclusion When formulating vaccination policies, governmental or medical institutions should include these factors to promote vaccination. PMID:25045431

  16. The role of human papilloma virus (HPV) infection in non-anogenital cancer and the promise of immunotherapy: a review.

    PubMed

    Cobos, Chris; Figueroa, José A; Mirandola, Leonardo; Colombo, Michela; Summers, Gabby; Figueroa, Alejandro; Aulakh, Amardeep; Konala, Venu; Verma, Rashmi; Riaz, Jehanzeb; Wade, Raymond; Saadeh, Charles; Rahman, Rakhshanda L; Pandey, Apurva; Radhi, Saba; Nguyen, Diane D; Jenkins, Marjorie; Chiriva-Internati, Maurizio; Cobos, Everardo

    2014-10-01

    Over the past 30 years, human papilloma virus (HPV) has been shown to play a role in the development of various cancers. Most notably, HPV has been linked to malignant progression in neoplasms of the anogenital region. However, high-risk HPV has also been suggested to play a significant role in the development of cancers in other anatomic locations, such as the head and neck, lung, breast and bladder. In 2006, the first vaccine for HPV, Gardasil, was approved for the prevention of subtypes 6, 11, 16 and 18. A few years later, Cevarix was approved for the prevention of subtypes 16 and 18, the HPV subtypes most frequently implicated in malignant progression. Although increased awareness and vaccination could drastically decrease the incidence of HPV-positive cancers, these approaches do not benefit patients who have already contracted HPV and developed cancer as a result. For this reason, researchers need to continue developing treatment modalities, such as targeted immunotherapies, for HPV-positive lesions. Here, we review the potential evidence linking HPV infection with the development of non-anogenital cancers and the potential role of immunotherapy in the prevention and eradication of HPV infection and its oncogenic sequela. PMID:24811210

  17. Papillary urothelial carcinoma with squamous differentiation in association with human papilloma virus: case report and literature review

    PubMed Central

    Guma, Sergei; Maglantay, Remegio; Lau, Ryan; Wieczorek, Rosemary; Melamed, Jonathan; Deng, Fang-Ming; Zhou, Ming; Makarov, Danil; Lee, Peng; Pincus, Matthew R; Pei, Zhi-Heng

    2016-01-01

    Background: The human papilloma virus (HPV) is a carcinogen known for its strong association with cervical cancers and cervical lesions. It is also known to be associated with a variety of squamous cell carcinomas in other areas, such as the penis, vulva, anus and head and neck. However, the association with urothelial carcinoma remains controversial. Here, we report a case of urothelial carcinoma with squamous differentiation associated with HPV-6/HPV-11. Case presentation: This is a case of a 70 year old man who presented with nocturia and pressure during urination. During the TURP procedure for what was clinically thought to be benign prostate hyperplasia with pathologic diagnosis as prostate carcinoma, a 2 cm papillary mass was found in the distal penile urethra. The papillary mass was found to be a high grade urothelial carcinoma positive for GATA 3 expression, with focal areas of squamous differentiation. The areas with squamous differentiation demonstrated koilocytic differentiation, which were positive for strong p16 expression. The tumor was found to harbor low risk HPV 6/11 by in situ hybridization. Conclusions: This study case demonstrates HPV infection with a low risk subtype (HPV 6/11) associated with an urothelial carcinoma with squamous differentiation and condylomatous features. PMID:27069958

  18. Circulating interleukin-10 levels and human papilloma virus and Epstein–Barr virus-associated cancers: evidence from a Mendelian randomization meta-analysis based on 11,170 subjects

    PubMed Central

    Qu, Kai; Pang, Qing; Lin, Ting; Zhang, Li; Gu, Mingliang; Niu, Wenquan; Liu, Chang; Zhang, Ming

    2016-01-01

    Recent studies have showed interleukin 10 (IL-10) is a critical cytokine that determines antiviral immune response and is related to virus-associated cancers. However, whether genetically elevated circulating IL-10 levels are associated with the risk of human papilloma virus and Epstein–Barr virus-associated cancers (HEACs) is still unclear. Mendelian randomization method was implemented to meta-analyze available observational studies by employing IL-10 three variants (−592C>A, −819C>T, and −1082A>G) as instruments. A total of 24 articles encompassing 11,170 subjects were ultimately eligible for the meta-analysis. Overall, there was a significant association between IL-10 promoter variant −1082A>G and HEACs under allelic and dominant models (both P<0.01). Subgroup analysis by cancer type indicated that the risk estimate of −1082A>G was significant for nasopharyngeal cancer under allelic, homozygous genotypic and dominant models (all P<0.001). Moreover by ethnicity, carriers of −1082G allele had a 74% increased risk for nasopharyngeal cancer in Asians under dominant model (odds ratio [OR] =1.737; 95% confidence interval [CI]: 1.280–2.358; P<0.001). In further Mendelian randomization analysis, the predicted OR for 10 pg/mL increment in IL-10 levels was 1.14 (95% CI: 1.01–16.99) in HEACs. Our findings provided strong evidence for a critical role of genetically elevated circulating IL-10 levels in the development of HEACs, especially in Asian population and for nasopharyngeal cancer. PMID:27022283

  19. Hepatitis B virus genotypes in Mongols and Australian Aborigines.

    PubMed

    Alestig, E; Hannoun, C; Horal, P; Lindh, M

    2001-12-01

    Hepatitis B virus (HBV) is spread worldwide. Seven genotypes, A-G, have been described, differing by more than 8% of the genome. In eastern Asia and Oceania genotypes B and C are predominant. However, little is known about genotypes in Mongolia and Australian aborigines. We analysed the preS and S regions of HBV from 9 Mongols and 5 Australian Aborigines. All Mongolian strains were of genotype D and were most similar to Central Asian sequences. All the Australian strains were genetically of serotype ayw3, and could not be reliably classified by the S region analysis, but placed on a separate branch. By preS analysis, they were however clearly of genotype C. The 6-7% nucleotide difference from published Asian genotype C sequences suggests that they diverged from Asian genotype C branch more than 1000 years ago. PMID:11811682

  20. Viral DNA load of high-risk human papilloma virus is closely associated with the grade of cervical lesions

    PubMed Central

    Shen, Guqun; Cheng, Jingxin; Wang, Yan; Zhou, Ping; Zhang, Guoqing

    2014-01-01

    This study is to explore the correlation between the viral load of high-risk human papilloma virus (HPV) and the degree of cervical lesions, as well as the follow-up monitoring role of high-risk HPV measurements in the treatment of patients with cervical lesions. Hybrid capture-2 method was used to measure the amount of high-risk HPV load of 361 patients who were enrolled from January 2009 to December 2010 at the Affiliated Tumor Hospital of Xinjiang Medical University, including 76 cases of cervical squamous carcinoma, 119 cases of cervical intraepithelial neoplasia and 166 cases of cervicitis. The correlation between the viral load of high-risk HPV and the degree of cervical lesions was analyzed using correlation analysis. Patients with cervical intraepithelial neoplasia (CIN) and cervical squamous carcinoma were followed up until December 2013, with the follow-up time being 37-60 months. Statistically significant differences in the high-risk HPV load existed between cervicitis group, CIN group and cervical squamous carcinoma group (P = 0.000). In addition, the viral load was increased with the increase of the severity of cervical lesions, showing a positive correlation (r = 0.436, P = 0.000). During the follow-up, 6 cases of vaginal intraepithelial neoplasia, 3 cases of recurrence CIN and 1 case of vaginal squamous cell carcinoma of the vulva were found, which were shown to relate with the continuing high-risk HPV infection in vagina. Viral load of high-risk HPV were positively correlated with the severity of cervical lesions, playing an important role in the monitoring of patients with cervical lesions after treatment. PMID:25664114

  1. Investigating the Prevalence of Human Papilloma Virus in Squamous Cell Carcinoma of the Larynx and Its Correlation with Disease Prognosis

    PubMed Central

    Atighechi, Saeid; Meybodian, Mojtaba; Dadgarnia, Mohammad Hossein; Baradaranfar, Mohammad Hossein; Behniafard, Nasim

    2016-01-01

    Introduction: The human papilloma virus (HPV) can play a role in the development of head and neck squamous cell carcinoma (SCC). Our aim was to assess the prevalence of HPV DNA in SCC of the larynx. The impact of HPV infection on patient survival was also evaluated. Materials and Methods: This case-control study was performed in 44 patients with SCC of the larynx (case group), while the control group comprised samples obtained from cadavers with no previous history of malignancy. A preliminary pathologic evaluation was performed on all samples in the control group (36 samples) to ensure the absence of dysplasia or malignancy. Polymerase chain reaction (PCR) was used to detect HPV DNA. After completing the treatment protocol, patients were followed to assess the impact of HPV infection on overall survival (OS). Results: PCR evaluation in the case group showed that HPV DNA was successfully isolated from 11 (25%) samples, while only two (5.6%) HPV DNA-positive were obtained from cadavers. According to these results, a significant difference was obtained in the prevalence of HPV DNA and laryngeal SCC between cases and controls (P=0.031). No statistically significant difference was observed in the OS of patients with or without HPV infection in the case group (P=0.235). Conclusion: Based on these results, we suggest that the prevalence of HPV infection is higher in laryngeal SCC subjects compared with healthy individuals. Although a longer OS was seen in HPV-positive patients, survival analysis did not show a significant difference in the comparison of HPV-positive and negative findings in SCC patients. PMID:27429948

  2. Knowledge of Saudi female university students regarding cervical cancer and acceptance of the human papilloma virus vaccine

    PubMed Central

    Al-Shaikh, Ghadeer K.; Almussaed, Eman M.; Fayed, Amel A.; Khan, Farida H.; Syed, Sadiqa B.; Al-Tamimi, Tahani N.; Elmorshedy, Hala N.

    2014-01-01

    Objectives: To assess the level of knowledge regarding cervical cancer and the acceptance of the human papilloma virus (HPV) vaccine among Saudi female students in health colleges. Methods: This cross-sectional study of a convenient sample encompassed 1400 students in Health Colleges at Princess Nora Bint Abdul Rahman University, Riyadh, Saudi Arabia was conducted between December 2013 and February 2014. A self-administrated questionnaire was distributed to all participants. Data collected included socio-demographic data, knowledge of cervical cancer risk factors and clinical presentation, Pap smear, and HPV vaccine acceptance. The questionnaire reliability as tested by Cronbach’s alpha was 0.82. Results: The response rate was 89.9%, and data analysis revealed that 95.7% of students had poor knowledge level. The Pap smear was poorly recognized as a screening tool, with 46.7% of students having heard of the test. Senior and medical students had a significantly higher knowledge score. Father’s health profession, high monthly income, and presence of cervical cancer among family members or friends increased the level of knowledge. Vaccine acceptance is influenced by its price, approximately 80% of students thought that an affordable vaccine price should not exceed 300 Saudi Riyals. Perceived barriers to the vaccine were fear of injections and vaccine side effects. Conclusion: There is a lack of knowledge and misinformation regarding cervical cancer, Pap smear, and HPV as a major risk factor for cancer of the cervix. These data can be used as a benchmark to formulate effective awareness programs. PMID:25316467

  3. Distribution of Hepatitis C Virus Genotypes in Bahrain

    PubMed Central

    Janahi, Essam M.; Al-Mannai, Mariam; Singh, Hemlata; Jahromi, Mohamed M.

    2015-01-01

    Background: Approximately 170 million people are infected with Hepatitis C virus (HCV) worldwide, making it one of the world’s major infectious diseases. There are no published population based studies about the prevalence of HCV genotypes in Bahrain. Objectives: Therefore, the aim of the present study was to investigate the prevalence and distribution of HCV genotypes and subtypes among a large sample of patients with chronic HCV infection in Bahrain. Patients and Methods: Serum samples were collected from 202 HCV positive patients; of them 128 had a viral load (> 500 IU/mL) suitable for the type-specific genotyping assay. Gender-wise and age-wise differences in the distribution of HCV genotypes were determined by Chi Square and Fisher’s Exact tests. Results: The predominant genotype among Bahraini patients was type 1 (36.71%), followed by genotypes 3 and 4 (15.6% each) and the lowest frequency was found for genotype 2 (3.9%). Among genotype 1, subtype 1b had the highest frequency (21.09%), followed by subtype 1a (14.06%). Among genotype 3, subtype 3a had the highest frequency (11.72%), while among genotype 4, most of subtypes were undetermined. The frequency of all different HCV genotypes was higher in male patients compared to female patients. Genotype 1 was most common in the age group of 51 - 60 years (38.3%), genotype 2 in 21 - 30 years (60%) and genotype 3 in 51 - 60 years (30%), while genotype 4 was most frequent among the age group > 61 (40%). Conclusions: The most common HCV genotype in Bahrain was subtype 1b followed by 1a and 3a. Further studies involving sources of transmission in Bahrain are required to enhance control measures for HCV infection. PMID:26977163

  4. Global Distribution and Prevalence of Hepatitis C Virus Genotypes

    PubMed Central

    Messina, Jane P; Humphreys, Isla; Flaxman, Abraham; Brown, Anthony; Cooke, Graham S; Pybus, Oliver G; Barnes, Eleanor

    2015-01-01

    Hepatitis C virus (HCV) exhibits high genetic diversity, characterized by regional variations in genotype prevalence. This poses a challenge to the improved development of vaccines and pan-genotypic treatments, which require the consideration of global trends in HCV genotype prevalence. Here we provide the first comprehensive survey of these trends. To approximate national HCV genotype prevalence, studies published between 1989 and 2013 reporting HCV genotypes are reviewed and combined with overall HCV prevalence estimates from the Global Burden of Disease (GBD) project. We also generate regional and global genotype prevalence estimates, inferring data for countries lacking genotype information. We include 1,217 studies in our analysis, representing 117 countries and 90% of the global population. We calculate that HCV genotype 1 is the most prevalent worldwide, comprising 83.4 million cases (46.2% of all HCV cases), approximately one-third of which are in East Asia. Genotype 3 is the next most prevalent globally (54.3 million, 30.1%); genotypes 2, 4, and 6 are responsible for a total 22.8% of all cases; genotype 5 comprises the remaining <1%. While genotypes 1 and 3 dominate in most countries irrespective of economic status, the largest proportions of genotypes 4 and 5 are in lower-income countries. Conclusion: Although genotype 1 is most common worldwide, nongenotype 1 HCV cases—which are less well served by advances in vaccine and drug development—still comprise over half of all HCV cases. Relative genotype proportions are needed to inform healthcare models, which must be geographically tailored to specific countries or regions in order to improve access to new treatments. Genotype surveillance data are needed from many countries to improve estimates of unmet need. (Hepatology 2015;61:77–87) PMID:25069599

  5. Hepatitis B virus genotype A: design of reference sequences for sub-genotypes.

    PubMed

    Cai, Qun; Zhu, Huilan; Zhang, Yafei; Li, Xu; Zhang, Zhenhua

    2016-06-01

    Genotype A of hepatitis B virus (HBV/A) is widespread and is currently divided into six sub-genotypes. Suitable reference sequences for different sub-genotypes can facilitate research on HBV/A. However, the current reference sequences for this virus are insufficient. In the present work, we retrieved 442 full-length HBV/A genomic sequences from the GenBank database and classified them into sub-genotypes by phylogenetic analysis. By the maximum likelihood method using the MEGA6.0 software, we established the reference sequences for different HBV/A sub-genotypes. Our analyses demonstrated that these reference sequences clustered phylogenetically with known strains, indicating that the reference sequences we established indeed belonged to the right sub-genotypes. HBV/A subtype sequences were selected by geographic origins and grouped as sub-genotypes including A1-South Africa, A2-Europe, A3-Cameroon, and A5-Haiti. Reference sequences of sub-genotypes A1, A2, A3, and A5 were constructed and deposited into GenBank (KP234050-KP234053). By applying phylogenetic analyses, we further determined the time to most recent common ancestor of HBV/A lineages. In conclusion, these newly established reference sequences can provide suitable reference standards for studies on the molecular biology and virology of HBV genotype A. PMID:27002608

  6. Citrus tristeza virus: Evolution of Complex and Varied Genotypic Groups

    PubMed Central

    Harper, S. J.

    2013-01-01

    Amongst the Closteroviridae, Citrus tristeza virus (CTV) is almost unique in possessing a number of distinct and characterized strains, isolates of which produce a wide range of phenotype combinations among its different hosts. There is little understanding to connect genotypes to phenotypes, and to complicate matters more, these genotypes are found throughout the world as members of mixed populations within a single host plant. There is essentially no understanding of how combinations of genotypes affect symptom expression and disease severity. We know little about the evolution of the genotypes that have been characterized to date, little about the biological role of their diversity and particularly, about the effects of recombination. Additionally, genotype grouping has not been standardized. In this study we utilized an extensive array of CTV genomic information to classify the major genotypes, and to determine the major evolutionary processes that led to their formation and subsequent retention. Our analyses suggest that three major processes act on these genotypes: (1) ancestral diversification of the major CTV lineages, followed by (2) conservation and co-evolution of the major functional domains within, though not between CTV genotypes, and (3) extensive recombination between lineages that have given rise to new genotypes that have subsequently been retained within the global population. The effects of genotype diversity and host-interaction are discussed, as is a proposal for standardizing the classification of existing and novel CTV genotypes. PMID:23630519

  7. Joint action of a chemical carcinogen and a neoplastic virus to induce cancer in rabbits; results of exposing epidermal cells to a carcinogenic hydrocarbon at time of infection with the Shope papilloma virus.

    PubMed

    ROGERS, S; ROUS, P

    1951-05-01

    Areas of rabbit skin previously rendered hyperplastic with turpentine were scarified, inoculated with the Shope papilloma virus, and covered with a dressing that contained 20-methylcholanthrene (MC) or 9:10-dimethyl-1:2-benzanthracene (9:10). The dressing was left on until healing had been well completed, a matter of 5 to 7 days. The papillomas which subsequently arose often appeared later, were fewer, and remained less vigorous than those due to the action of virus alone, but throughout several months they appeared to differ from these in no other ways. Then, more or less abruptly, the large majority became carcinomatous, frequently at several situations, whereas with few exceptions the control growths underwent no such alteration. The cancers were of the sorts ordinarily deriving, by secondary change, from epidermal cells infected with the virus. Collateral data have made plain that the hydrocarbons acted in their carcinogenic capacity to bring on the cancers. Indeed in control tests 9: 10 sometimes conferred latent neoplastic potentialities on uninoculated epidermis exposed to it while healing after scarification, a fact disclosed months later by painting these expanses with chloroform until hyperplasia occurred. Under the promoting influence of this agent papillomas formed which had the distinctive morphology of those induced by the chemical carcinogens. So strong and enduring were the effects of MC and 9:10 as to cause cancers to arise from many virus papillomas which were retrogressing after months of proliferation, that is to say under circumstances ordinarily unfavorable to malignant change. The facts justify the conclusion that the virus and the hydrocarbons acted jointly and in their carcinogenic capacities. PMID:14832395

  8. Prevalence of cervical neoplastic lesions and Human Papilloma Virus infection in Egypt: National Cervical Cancer Screening Project

    PubMed Central

    Abd El All, Howayda S; Refaat, Amany; Dandash, Khadiga

    2007-01-01

    Background Data from Egyptian studies provide widely varying estimates on the prevalence of pre-malignant and malignant cervical abnormalities and human papilloma virus (HPVs) infection. To define the prevalence and risk factors of pre-invasive and invasive cervical cancer (cacx), a community based full-scale cross sectional, household survey including 5453 women aged between 35 and 60 years was conducted. Methods The study period was between February 2000 and December 2002. Initially, conventional Papanicolaou (Pap) smears were evaluated using the Bethesda system (TBS), followed by colposcopic guided biopsy (CGB) for all epithelial abnormalities (EA). In a third step, HPV was tested on all EA by in-situ hybridization (ISH) using first the broad spectrum HPV probe recognizing HPVs 6, 11, 16, 18, 30, 31, 35, 45, 51 and 52 followed by subtyping with probes 6/11, 16/18 and 31/33. Lastly, unequivocal cases were immunostained for herpes simplex type-2 (HSV-2), cytomegalovirus (CMV), and human immunodeficiency virus (HIV). Results EA representing 7.8% (424/5453), were categorized into atypical squamous cell of undetermined significance (ASCUS) (34.4%), atypical glandular cell of undetermined significance (AGCUS) (15.3%), combined ASCUS and AGCUS (3.1%), low grade squamous intraepithelial lesions (SIL) (41.0%), high grade SIL (5.2%) and invasive lesions (1%). CGB of EA (n = 281) showed non neoplastic lesions (12.8%), atypical squamous metaplasia (ASM) (19.2%), cervical intraepithelial neoplasia I (CIN) (44.4%), CIN II (4.4%), CINIII (2.8%), endocervical lesions (5.2%), combined squamous and endocervical lesions (10.0%), invasive squamous cell carcinoma (SCC) (0.02%) and extranodal marginal zone B cell lymphoma (MZBCL) (0.02%). The overall predictive value of cytology was 87% while the predictive value for high grade lesions was 80%. On histological basis, HPVs were present in 94.3% of squamous lesions while it was difficult to be identified in endocervical ones. ISH

  9. ASSOCIATION AMONG HISTOLOGICAL FINDINGS SUGGESTIVE OF PAPILLOMA VIRUS ON HEMORRHOIDECTOMY SPECIMENS

    PubMed Central

    da SILVA, Soraya Souto; NAKAJIMA, Gerson Suguiyama; GUIMARÃES, Ricardo Alexandre; MOURÃO, Flávia da Costa

    2015-01-01

    Background: Many researchers studied human Papillomavirus infection in the anal area supposing it represents a risk factor for precursor lesions of anal cancer. Aim: To study the association between histological findings suggestive of injury by the virus in hemorrhoidectomy specimens. Method: Prevalence study was carried out based on histopathological analysis of hemorrhoidectomy specimens to find viral cytopathic effects. These findings were compared with anal condyloma acuminata that had no relationship with hemorrhoidectomy for microscopic comparison. Results: Of the 91 hemorroidectomies analyzed, eight had findings suggestive of viral cytopathic effects, with the presence of irregular acanthosis in 63%, koilocytes in 50% and other indirect viral cytopathic effects, such as hyperkeratosis (38%), parakeratosis (25% ) and papillomatosis (13%). Conclusion: This study was unable to conclude that there is an association between these two pathologic entities. PMID:26734795

  10. Using Behavioral Risk Factor Data as a surveillance tool to monitor the prevalence of initiation, continuation and completion of Human Papilloma Virus vaccination in children

    PubMed Central

    Barboza, Gia Elise; Dominguez, Silvia

    2016-01-01

    The Human Papilloma Virus (“HPV”) is a common sexually transmitted disease that has infected approximately 79 million men and women in the United States alone. A vaccination is available but in order to be effective it must be received prior to becoming sexually active and recipients must complete a three-dose sequence. In this article we explore the predisposing, enabling and need-based factors associated with parents’ or guardians’ decision to have their child initiate, continue and complete the Human Papilloma Virus (HPV) vaccine. The data file includes 5531 parents and guardians with presumptive knowledge regarding the number of HPV vaccination their child received. Data includes information on the child (e.g. child׳s age) as well as the adult respondent (e.g. health insurance status). A smaller subset of the dataset along with the code to run the model are supplied with this article. The interpretation of these data can be found in the research article published by the authors in the Journal of Preventive Medicine in 2015 http://dx.doi.org/10.1016/j.ypmed.2016.01.010[1]. PMID:27222864

  11. Using Behavioral Risk Factor Data as a surveillance tool to monitor the prevalence of initiation, continuation and completion of Human Papilloma Virus vaccination in children.

    PubMed

    Barboza, Gia Elise; Dominguez, Silvia

    2016-06-01

    The Human Papilloma Virus ("HPV") is a common sexually transmitted disease that has infected approximately 79 million men and women in the United States alone. A vaccination is available but in order to be effective it must be received prior to becoming sexually active and recipients must complete a three-dose sequence. In this article we explore the predisposing, enabling and need-based factors associated with parents' or guardians' decision to have their child initiate, continue and complete the Human Papilloma Virus (HPV) vaccine. The data file includes 5531 parents and guardians with presumptive knowledge regarding the number of HPV vaccination their child received. Data includes information on the child (e.g. child׳s age) as well as the adult respondent (e.g. health insurance status). A smaller subset of the dataset along with the code to run the model are supplied with this article. The interpretation of these data can be found in the research article published by the authors in the Journal of Preventive Medicine in 2015 http://dx.doi.org/10.1016/j.ypmed.2016.01.010[1]. PMID:27222864

  12. Geographic distribution of hepatitis C virus genotypes in Brazil.

    PubMed

    Campiotto, S; Pinho, J R R; Carrilho, F J; Da Silva, L C; Souto, F J D; Spinelli, V; Pereira, L M M B; Coelho, H S M; Silva, A O; Fonseca, J C; Rosa, H; Lacet, C M C; Bernardini, A P

    2005-01-01

    Brazil is a country of continental dimension with a population of different ethnic backgrounds. Thus, a wide variation in the frequencies of hepatitis C virus (HCV) genotypes is expected to occur. To address this point, 1,688 sequential samples from chronic HCV patients were analyzed. HCV-RNA was amplified by the RT-PCR from blood samples collected from 1995 to 2000 at different laboratories located in different cities from all Brazilian States. Samples were collected in tubes containing a gel separator, centrifuged in the site of collection and sent by express mail in a refrigerated container to Laboratório Bioquímico Jardim Paulista, São Paulo, SP, Brazil. HCV-RNA was extracted from serum and submitted to RT and nested PCR using standard procedures. Nested PCR products were submitted to cycle sequencing reactions without prior purification. Sequences were analyzed for genotype determination and the following frequencies were found: 64.9% (1,095) for genotype 1, 4.6% (78) for genotype 2, 30.2% (510) for genotype 3, 0.2% (3) for genotype 4, and 0.1% (2) for genotype 5. The frequencies of HCV genotypes were statistically different among Brazilian regions (P = 0.00017). In all regions, genotype 1 was the most frequent (51.7 to 74.1%), reaching the highest value in the North; genotype 2 was more prevalent in the Center-West region (11.4%), especially in Mato Grosso State (25.8%), while genotype 3 was more common in the South (43.2%). Genotypes 4 and 5 were rarely found and only in the Southeast, in São Paulo State. The present data indicate the need for careful epidemiological surveys throughout Brazil since knowing the frequency and distribution of the genotypes would provide key information for understanding the spread of HCV. PMID:15665987

  13. The human papilloma virus 16E6 gene sensitizes human mammary epithelial cells to apoptosis induced by DNA damage.

    PubMed Central

    Xu, C; Meikrantz, W; Schlegel, R; Sager, R

    1995-01-01

    Programmed cell death (apoptosis) is a normal physiological process, which could in principle be manipulated to play an important role in cancer therapy. The key importance of p53 expression in the apoptotic response to DNA-damaging agents has been stressed because mutant or deleted p53 is so common in most kinds of cancer. An important strategy, therefore, is to find ways to induce apoptosis in the absence of wild-type p53. In this paper, we compare apoptosis in normal human mammary epithelial cells, in cells immortalized with human papilloma virus (HPV), and in mammary carcinoma cell lines expressing wild-type p53, mutant p53, or no p53 protein. Apoptosis was induced with mitomycin C (MMC), a DNA cross-linking and damaging agent, or with staurosporine (SSP), a protein kinase inhibitor. The normal and HPV-transfected cells responded more strongly to SSP than did the tumor cells. After exposure to MMC, cells expressing wild-type p53 underwent extensive apoptosis, whereas cells carrying mutated p53 responded weakly. Primary breast cancer cell lines null for p53 protein were resistant to MMC. In contrast, two HPV immortalized cell lines in which p53 protein was destroyed by E6-modulated ubiquitinylation were highly sensitive to apoptosis induced by MMC. Neither p53 mRNA nor protein was induced in the HPV immortalized cells after MMC treatment, although p53 protein was elevated by MMC in cells with wild-type p53. Importantly, MMC induced p21 mRNA but not p21 protein expression in the HPV immortalized cells. Thus, HPV 16E6 can sensitize mammary epithelial cells to MMC-induced apoptosis via a p53- and p21-independent pathway. We propose that the HPV 16E6 protein modulates ubiquitin-mediated degradation not only of p53 but also of p21 and perhaps other proteins involved in apoptosis. Images Fig. 1 Fig. 2 Fig. 4 PMID:7644500

  14. Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

    PubMed Central

    Mello, Francisco CA; Souto, Francisco JD; Nabuco, Leticia C; Villela-Nogueira, Cristiane A; Coelho, Henrique Sergio M; Franz, Helena Cristina F; Saraiva, Joao Carlos P; Virgolino, Helaine A; Motta-Castro, Ana Rita C; Melo, Mabel MM; Martins, Regina MB; Gomes, Selma A

    2007-01-01

    Background Hepatitis B virus (HBV) isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil. Results Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%), and most of these isolates were classified as subgenotype A1 (138/153; 90.2%). Genotype D was the most common genotype in the South (84.2%) and Central (47.6%) regions. The prevalence of genotype F was low (13%) countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5%) belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was adw4. The remaining isolate showed a leucine-to-isoleucine substitution at position 127. Conclusion The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin) indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F isolates belonged to

  15. Genotypic and Pathotypic Characterization of Newcastle Disease Viruses from India

    PubMed Central

    Tirumurugaan, Krishnaswamy G.; Vijayarani, Kumanan; Kumanan, Kathaperumal; Elankumaran, Subbiah

    2011-01-01

    Newcastle disease virus (NDV) is an avian paramyxovirus that causes significant economic losses to the poultry industry in most parts of the world. The susceptibility of a wide variety of avian species coupled with synanthropic bird reservoirs has contributed to the vast genomic diversity of this virus as well as diagnostic failures. Since the first panzootic in 1926, Newcastle disease (ND) became enzootic in India with recurrent outbreaks in multiple avian species. The genetic characteristics of circulating strains in India, however, are largely unknown. To understand the nature of NDV genotypes in India, we characterized two representative strains isolated 13 years apart from a chicken and a pigeon by complete genome sequence analysis and pathotyping. The viruses were characterized as velogenic by pathogenicity indices devised to distinguish these strains. The genome length was 15,186 nucleotides (nt) and consisted of six non-overlapping genes, with conserved and complementary 3′ leader and 5′ trailer regions, conserved gene starts, gene stops, and intergenic sequences similar to those in avian paramyxovirus 1 (APMV-1) strains. Matrix gene sequence analysis grouped the pigeon isolate with APMV-1 strains. Phylogeny based on the fusion (F), and hemagglutinin (HN) genes and complete genome sequence grouped these viruses into genotype IV. Genotype IV strains are considered to have “died out” after the first panzootic (1926–1960) of ND. But, our results suggest that there is persistence of genotype IV strains in India. PMID:22174801

  16. New Hepatitis E Virus Genotype in Camels, the Middle East

    PubMed Central

    Lau, Susanna K.P.; Teng, Jade L.L.; Tsang, Alan K. L.; Joseph, Marina; Wong, Emily Y.M.; Tang, Ying; Sivakumar, Saritha; Xie, Jun; Bai, Ru; Wernery, Renate; Wernery, Ulrich; Yuen, Kwok-Yung

    2014-01-01

    In a molecular epidemiology study of hepatitis E virus (HEV) in dromedaries in Dubai, United Arab Emirates, HEV was detected in fecal samples from 3 camels. Complete genome sequencing of 2 strains showed >20% overall nucleotide difference to known HEVs. Comparative genomic and phylogenetic analyses revealed a previously unrecognized HEV genotype. PMID:24856611

  17. Hepatitis E Virus Genotype 4 Outbreak, Italy, 2011

    PubMed Central

    Garbuglia, Anna R.; Scognamiglio, Paola; Petrosillo, Nicola; Mastroianni, Claudio Maria; Sordillo, Pasquale; Gentile, Daniele; La Scala, Patrizia; Girardi, Enrico

    2013-01-01

    During 2011, 5 persons in the area of Lazio, Italy were infected with a monophyletic strain of hepatitis E virus that showed high sequence homology with isolates from swine in China. Detection of this genotype in Italy parallels findings in other countries in Europe, signaling the possible spread of strains new to Western countries. PMID:23260079

  18. Hepatitis E Virus Genotype 3 in Humans and Swine, Bolivia

    PubMed Central

    Cavallo, Annalisa; Gonzales, José Luis; Bonelli, Sara Irene; Valda, Ybar; Pieri, Angela; Segundo, Higinio; Ibañez, Ramón; Mantella, Antonia; Bartalesi, Filippo; Tolari, Francesco; Bartoloni, Alessandro

    2011-01-01

    We determined the seroprevalence of hepatitis E virus (HEV) in persons in 2 rural communities in southeastern Bolivia and the presence of HEV in human and swine fecal samples. HEV seroprevalence was 6.3%, and HEV genotype 3 strains with high sequence homology were detected. PMID:21801630

  19. Hepatitis E virus genotype 3 in wild rats, United States.

    PubMed

    Lack, Justin B; Volk, Kylie; Van Den Bussche, Ronald A

    2012-08-01

    The role of rodents in the epidemiology of zoonotic hepatitis E virus (HEV) infection has been a subject of considerable debate. Seroprevalence studies suggest widespread HEV infection in commensal Rattus spp. rats, but experimental transmission has been largely unsuccessful and recovery of zoonotic genotype 3 HEV RNA from wild Rattus spp. rats has never been confirmed. We surveyed R. rattus and R. norvegicus rats from across the United States and several international populations by using a hemi-nested reverse transcription PCR approach. We isolated HEV RNA in liver tissues from 35 of 446 rats examined. All but 1 of these isolates was relegated to the zoonotic HEV genotype 3, and the remaining sequence represented the recently discovered rat genotype from the United States and Germany. HEV-positive rats were detected in urban and remote localities. Genetic analyses suggest all HEV genotype 3 isolates obtained from wild Rattus spp. rats were closely related. PMID:22840202

  20. Hepatitis E Virus Genotype 3 in Wild Rats, United States

    PubMed Central

    Volk, Kylie; Van Den Bussche, Ronald A.

    2012-01-01

    The role of rodents in the epidemiology of zoonotic hepatitis E virus (HEV) infection has been a subject of considerable debate. Seroprevalence studies suggest widespread HEV infection in commensal Rattus spp. rats, but experimental transmission has been largely unsuccessful and recovery of zoonotic genotype 3 HEV RNA from wild Rattus spp. rats has never been confirmed. We surveyed R. rattus and R. norvegicus rats from across the United States and several international populations by using a hemi-nested reverse transcription PCR approach. We isolated HEV RNA in liver tissues from 35 of 446 rats examined. All but 1 of these isolates was relegated to the zoonotic HEV genotype 3, and the remaining sequence represented the recently discovered rat genotype from the United States and Germany. HEV-positive rats were detected in urban and remote localities. Genetic analyses suggest all HEV genotype 3 isolates obtained from wild Rattus spp. rats were closely related. PMID:22840202

  1. Herpes and papilloma viruses

    SciTech Connect

    De Palo, G.; Rilke, F.; Zur Hausen, H.

    1986-01-01

    This book contains over 25 selections. Some of the titles are: Seroepidemiologic Asociation of HSV-2 with Cervical Cancers: Transforming Viral Genes; Organization and Expression of Human Papillomavirus DNA in Cervical Cancer Cell Lines; An Investigation of Cervical Scrapes by DNA Hybridization: and Human Papillomaviruses in Genital Tissue: Examination by Immunohistochemistry and in situ DNA Hybridization.

  2. Phylogeography of Japanese Encephalitis Virus: Genotype Is Associated with Climate

    PubMed Central

    Schuh, Amy J.; Ward, Melissa J.; Leigh Brown, Andrew J.; Barrett, Alan D. T.

    2013-01-01

    The circulation of vector-borne zoonotic viruses is largely determined by the overlap in the geographical distributions of virus-competent vectors and reservoir hosts. What is less clear are the factors influencing the distribution of virus-specific lineages. Japanese encephalitis virus (JEV) is the most important etiologic agent of epidemic encephalitis worldwide, and is primarily maintained between vertebrate reservoir hosts (avian and swine) and culicine mosquitoes. There are five genotypes of JEV: GI-V. In recent years, GI has displaced GIII as the dominant JEV genotype and GV has re-emerged after almost 60 years of undetected virus circulation. JEV is found throughout most of Asia, extending from maritime Siberia in the north to Australia in the south, and as far as Pakistan to the west and Saipan to the east. Transmission of JEV in temperate zones is epidemic with the majority of cases occurring in summer months, while transmission in tropical zones is endemic and occurs year-round at lower rates. To test the hypothesis that viruses circulating in these two geographical zones are genetically distinct, we applied Bayesian phylogeographic, categorical data analysis and phylogeny-trait association test techniques to the largest JEV dataset compiled to date, representing the envelope (E) gene of 487 isolates collected from 12 countries over 75 years. We demonstrated that GIII and the recently emerged GI-b are temperate genotypes likely maintained year-round in northern latitudes, while GI-a and GII are tropical genotypes likely maintained primarily through mosquito-avian and mosquito-swine transmission cycles. This study represents a new paradigm directly linking viral molecular evolution and climate. PMID:24009790

  3. Determination of hepatitis C virus genotype by Pyrosequencing.

    PubMed

    Elahi, Elahe; Pourmand, Nader; Chaung, Ramsey; Rofoogaran, Ara; Boisver, Judie; Samimi-Rad, Katayon; Davis, Ronald W; Ronaghi, Mostafa

    2003-05-01

    A simple sequencing-based assay is described for genotyping of hepatitis C virus (HCV). RT-PCR was employed to amplify a 237-nucleotide-long fragment from the 5' untranslated region (UTR) of the genome using one biotinylated and one normal primer. Subsequent to capture of the PCR products on streptavidin-coated beads, single-stranded DNA separation, and hybridization of sequencing primer, Pyrosequencing was performed. The genotype of 98 samples out of which 77 samples were from American veterans and 21 samples were from Iran was determined. The samples from the American veterans contained six different subtypes, while five subtypes were found in Iranian samples. For rapid population-specific HCV subtyping, a multiplex assay was developed. This study demonstrates the suitability of this technology for low-cost, high throughput and accurate microbial genotyping. PMID:12711060

  4. Identification of a new genotype of bovine leukemia virus.

    PubMed

    Balić, Davor; Lojkić, Ivana; Periškić, Marin; Bedeković, Tomislav; Jungić, Andreja; Lemo, Nina; Roić, Besi; Cač, Zeljko; Barbić, Ljubo; Madić, Josip

    2012-07-01

    To investigate the degree of genetic variability of bovine leukemia virus (BLV) strains circulating in Croatia, 29 isolates from the six largest dairy farms were examined by PCR for a segment of the gp51 env gene, followed by DNA sequencing and phylogenetic analysis. The nucleotide sequences were compared with other previously characterized BLV strains from different geographical areas, comprising all seven known BLV genotypes. The Croatian sequences showed six to eight nucleotide substitutions: six silent substitutions and two amino acid changes. Four of those substitutions were within epitopes. In comparison to the sequences of other BLV genotypes, our isolates showed the closest relationship to genotype 1 isolates PL-3252 (FJ808585) and AL-148 (FJ808573) from Argentina. The degree of variation between our sequences and those of genotype 1 was 0.2- 4.6 %. In phylogenetic trees based on 400-nt and 519-nt sequences, all of the Croatian sequences clustered separately from the other sequences, revealing a new genotype. PMID:22488472

  5. The Role of Polymerase Chain Reaction of High-Risk Human Papilloma Virus in the Screening of High-Grade Squamous Intraepithelial Lesions in the Anal Mucosa of Human Immunodeficiency Virus-Positive Males Having Sex with Males

    PubMed Central

    Hidalgo-Tenorio, Carmen; Rivero-Rodriguez, Mar; Gil-Anguita, Concepción; Esquivias, Javier; López-Castro, Rodrigo; Ramírez-Taboada, Jessica; de Hierro, Mercedes López; López-Ruiz, Miguel A.; Martínez, R. Javier; Llaño, Juan P.

    2015-01-01

    Objectives To evaluate the advantages of cytology and PCR of high-risk human papilloma virus (PCR HR-HPV) infection in biopsy-derived diagnosis of high-grade squamous intraepithelial lesions (HSIL = AIN2/AIN3) in HIV-positive men having sex with men (MSM). Methods This is a single-centered study conducted between May 2010 and May 2014 in patients (n = 201, mean age 37 years) recruited from our outpatient clinic. Samples of anal canal mucosa were taken into liquid medium for PCR HPV analysis and for cytology. Anoscopy was performed for histology evaluation. Results Anoscopy showed 33.8% were normal, 47.8% low-grade squamous intraepithelial lesions (LSIL), and 18.4% HSIL; 80.2% had HR-HPV. PCR of HR-HPV had greater sensitivity than did cytology (88.8% vs. 75.7%) in HSIL screening, with similar positive (PPV) and negative predictive value (NPV) of 20.3 vs. 22.9 and 89.7 vs. 88.1, respectively. Combining both tests increased the sensitivity and NPV of HSIL diagnosis to 100%. Correlation of cytology vs. histology was, generally, very low and PCR of HR-HPV vs. histology was non-existent (<0.2) or low (<0.4). Area under the receiver operating characteristics (AUROC) curve analysis of cytology and PCR HR-HPV for the diagnosis of HSIL was poor (<0.6). Multivariate regression analysis showed protective factors against HSIL were: viral suppression (OR: 0.312; 95%CI: 0.099-0.984), and/or syphilis infection (OR: 0.193; 95%CI: 0.045-0.827). HSIL risk was associated with HPV-68 genotype (OR: 20.1; 95%CI: 2.04-197.82). Conclusions When cytology and PCR HR-HPV findings are normal, the diagnosis of pre-malignant HSIL can be reliably ruled-out in HIV-positive patients. HPV suppression with treatment protects against the appearance of HSIL. PMID:25849412

  6. Epidemiology and genetic characterization of hepatitis A virus genotype IIA.

    PubMed

    Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

    2010-09-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5' untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored. PMID:20592136

  7. Epidemiology and Genetic Characterization of Hepatitis A Virus Genotype IIA▿

    PubMed Central

    Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

    2010-01-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5′ untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored. PMID:20592136

  8. Antibodies Targeting Novel Neutralizing Epitopes of Hepatitis C Virus Glycoprotein Preclude Genotype 2 Virus Infection.

    PubMed

    Deng, Kai; Liu, Ruyu; Rao, Huiying; Jiang, Dong; Wang, Jianghua; Xie, Xingwang; Wei, Lai

    2015-01-01

    Currently, there is no effective vaccine to prevent hepatitis C virus (HCV) infection, partly due to our insufficient understanding of the virus glycoprotein immunology. Most neutralizing antibodies (nAbs) were identified using glycoprotein immunogens, such as recombinant E1E2, HCV pseudoparticles or cell culture derived HCV. However, the fact that in the HCV acute infection phase, only a small proportion of patients are self-resolved accompanied with the emergence of nAbs, indicates the limited immunogenicity of glycoprotein itself to induce effective antibodies against a highly evolved virus. Secondly, in previous reports, the immunogen sequence was mostly the genotype of the 1a H77 strain. Rarely, other genotypes/subtypes have been studied, although theoretically one genotype/subtype immunogen is able to induce cross-genotype neutralizing antibodies. To overcome these drawbacks and find potential novel neutralizing epitopes, 57 overlapping peptides encompassing the full-length glycoprotein E1E2 of subtype 1b were synthesized to immunize BALB/c mice, and the neutralizing reactive of the induced antisera against HCVpp genotypes 1-6 was determined. We defined a domain comprising amino acids (aa) 192-221, 232-251, 262-281 and 292-331 of E1, and 421-543, 564-583, 594-618 and 634-673 of E2, as the neutralizing regions of HCV glycoprotein. Peptides PUHI26 (aa 444-463) and PUHI45 (aa 604-618)-induced antisera displayed the most potent broad neutralizing reactive. Two monoclonal antibodies recognizing the PUHI26 and PUHI45 epitopes efficiently precluded genotype 2 viral (HCVcc JFH and J6 strains) infection, but they did not neutralize other genotypes. Our study mapped a neutralizing epitope region of HCV glycoprotein using a novel immunization strategy, and identified two monoclonal antibodies effective in preventing genotype 2 virus infection. PMID:26406225

  9. Antibodies Targeting Novel Neutralizing Epitopes of Hepatitis C Virus Glycoprotein Preclude Genotype 2 Virus Infection

    PubMed Central

    Rao, Huiying; Jiang, Dong; Wang, Jianghua; Xie, Xingwang; Wei, Lai

    2015-01-01

    Currently, there is no effective vaccine to prevent hepatitis C virus (HCV) infection, partly due to our insufficient understanding of the virus glycoprotein immunology. Most neutralizing antibodies (nAbs) were identified using glycoprotein immunogens, such as recombinant E1E2, HCV pseudoparticles or cell culture derived HCV. However, the fact that in the HCV acute infection phase, only a small proportion of patients are self-resolved accompanied with the emergence of nAbs, indicates the limited immunogenicity of glycoprotein itself to induce effective antibodies against a highly evolved virus. Secondly, in previous reports, the immunogen sequence was mostly the genotype of the 1a H77 strain. Rarely, other genotypes/subtypes have been studied, although theoretically one genotype/subtype immunogen is able to induce cross-genotype neutralizing antibodies. To overcome these drawbacks and find potential novel neutralizing epitopes, 57 overlapping peptides encompassing the full-length glycoprotein E1E2 of subtype 1b were synthesized to immunize BALB/c mice, and the neutralizing reactive of the induced antisera against HCVpp genotypes 1–6 was determined. We defined a domain comprising amino acids (aa) 192–221, 232–251, 262–281 and 292–331 of E1, and 421–543, 564–583, 594–618 and 634–673 of E2, as the neutralizing regions of HCV glycoprotein. Peptides PUHI26 (aa 444–463) and PUHI45 (aa 604–618)-induced antisera displayed the most potent broad neutralizing reactive. Two monoclonal antibodies recognizing the PUHI26 and PUHI45 epitopes efficiently precluded genotype 2 viral (HCVcc JFH and J6 strains) infection, but they did not neutralize other genotypes. Our study mapped a neutralizing epitope region of HCV glycoprotein using a novel immunization strategy, and identified two monoclonal antibodies effective in preventing genotype 2 virus infection. PMID:26406225

  10. Dengue virus 3 genotype I in Aedes aegypti mosquitoes and eggs, Brazil, 2005-2006.

    PubMed

    Vilela, Ana P P; Figueiredo, Leandra B; dos Santos, João R; Eiras, Alvaro E; Bonjardim, Cláudio A; Ferreira, Paulo C P; Kroon, Erna G

    2010-06-01

    Dengue virus type 3 genotype I was detected in Brazil during epidemics in 2002-2004. To confirm this finding, we identified this virus genotype in naturally infected field-caught Aedes aegypti mosquitoes and eggs. Results showed usefulness of virus investigations in vectors as a component of active epidemiologic surveillance. PMID:20507754

  11. Dengue Virus 3 Genotype I in Aedes aegypti Mosquitoes and Eggs, Brazil, 2005–2006

    PubMed Central

    Vilela, Ana P.P.; Figueiredo, Leandra B.; dos Santos, João R.; Eiras, Álvaro E.; Bonjardim, Cláudio A.; Ferreira, Paulo C.P.

    2010-01-01

    Dengue virus type 3 genotype I was detected in Brazil during epidemics in 2002–2004. To confirm this finding, we identified this virus genotype in naturally infected field-caught Aedes aegypti mosquitoes and eggs. Results showed usefulness of virus investigations in vectors as a component of active epidemiologic surveillance. PMID:20507754

  12. Simultaneous Genotyping and Quantification of Hepatitis B Virus for Genotypes B and C by Real-Time PCR Assay▿

    PubMed Central

    Zhao, Yao; Zhang, Xiu-Yu; Guo, Jin-Jun; Zeng, Ai-Zhong; Hu, Jie-Li; Huang, Wen-Xiang; Shan, You-Lan; Huang, Ai-Long

    2010-01-01

    Hepatitis B virus (HBV) is an important cause of human chronic liver diseases and is a major public health problem. Viral load and HBV genotype play critical roles in determining clinical outcomes and response to antiviral treatment in hepatitis B patients. Viral genotype detection and quantification assays are currently in use with different levels of effectiveness. In this study, the performance of a real-time genotyping and quantitative PCR (GQ-PCR)-based assay was evaluated. Through the use of genotype-specific primers and probes, this assay provides simultaneous identification and quantification of genotypes B and C in a single reaction. Our GQ-PCR correctly identified all predefined genotypes B and C, and no cross-reaction between genotypes B and C were observed. The GQ-PCR identified more cases of HBV infections with mixed genotypes B and C than direct sequencing did. Samples from 127 HBV-infected Chinese patients were genotyped with GQ-PCR, revealing 56.7% HBV as genotype B, 13.4% as genotype C, and 29.8% as mixed genotypes B and C. This assay provides a reliable, efficient, and cost-effective means for quantification of the B and C genotypes of HBV in single or mixed infections. This assay is suitable for sequential monitoring of viral load levels and for determining the relationship between the genotype viral load and stage of disease in Asians. PMID:20720032

  13. Biological and phylogenetic characterization of a genotype VII Newcastle disease virus from Venezuela: Efficacy of vaccination

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Here we describe the characterization a virulent genotype VII Newcastle disease virus (NDV) from Venezuela and evaluate the efficacy of heterologous genotype commercial vaccination under field and controlled rearing conditions. Biological pathotyping and molecular analysis were applied. Results sh...

  14. Pepino mosaic virus genotype shift in North America and rapid genotype identification using loop-mediated isothermal amplification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pepino mosaic, once an emerging disease a decade ago, has become endemic on greenhouse tomatoes worldwide in recent years. Three distinct genotypes of Pepino mosaic virus (PepMV), including EU, US1 and CH2 have been recognized. Our earlier study in 2006-2007 demonstrated a predominant EU genotype ...

  15. Cloacal papillomas in psittacines.

    PubMed

    Sundberg, J P; Junge, R E; O'Banion, M K; Basgall, E J; Harrison, G; Herron, A J; Shivaprasad, H L

    1986-04-01

    Papilloma-like masses affecting the cloaca of 19 Amazons, 16 macaws, 3 parrots, 1 conure, and 1 parakeet were examined. Papillomatous lesions were characterized by proliferation of the lining epithelium on thin fibrovascular stalks. Carcinoma in situ was diagnosed in the cloaca of a macaw in addition to the other 16 macaws with papillomas. Papillomavirus group-specific antigens were not detected in any of the 41 lesions, using the peroxidase-antiperoxidase technique. The DNA extracts from 6 different frozen papillomas did not contain papillomavirus genomes detectable by Southern blot hybridization, using an African gray parrot cutaneous papillomavirus as a probe. Evidence of an infective agent was not found by electron microscopic examination of 8 of the papillomas. Inoculations of partially purified homogenates of a cloacal papilloma from a yellow-crowned Amazon did not induce lesion formation on cloacal mucosa of an adult yellow-crowned Amazon, green and yellow macaw, sulphur-crested cockatoo, or mollucan cockatoo. PMID:2421621

  16. Identification of new sub-genotypes of virulent Newcastle disease virus with potential panzootic features.

    PubMed

    Miller, Patti J; Haddas, Ruth; Simanov, Luba; Lublin, Avishay; Rehmani, Shafqat Fatima; Wajid, Abdul; Bibi, Tasra; Khan, Taseer Ahmad; Yaqub, Tahir; Setiyaningsih, Surachmi; Afonso, Claudio L

    2015-01-01

    Virulent Newcastle disease virus (NDV) isolates from new sub-genotypes within genotype VII are rapidly spreading through Asia and the Middle East causing outbreaks of Newcastle disease (ND) characterized by significant illness and mortality in poultry, suggesting the existence of a fifth panzootic. These viruses, which belong to the new sub-genotypes VIIh and VIIi, have epizootic characteristics and do not appear to have originated directly from other genotype VII NDV isolates that are currently circulating elsewhere, but are related to the present and past Indonesian NDV viruses isolated from wild birds since the 80s. Viruses from sub-genotype VIIh were isolated in Indonesia (2009-2010), Malaysia (2011), China (2011), and Cambodia (2011-2012) and are closely related to the Indonesian NDV isolated in 2007, APMV1/Chicken/Karangasem, Indonesia (Bali-01)/2007. Since 2011 and during 2012 highly related NDV isolates from sub-genotype VIIi have been isolated from poultry production facilities and occasionally from pet birds, throughout Indonesia, Pakistan and Israel. In Pakistan, the viruses of sub-genotype VIIi have replaced NDV isolates of genotype XIII, which were commonly isolated in 2009-2011, and they have become the predominant sub-genotype causing ND outbreaks since 2012. In a similar fashion, the numbers of viruses of sub-genotype VIIi isolated in Israel increased in 2012, and isolates from this sub-genotype are now found more frequently than viruses from the previously predominant sub-genotypes VIId and VIIb, from 2009 to 2012. All NDV isolates of sub-genotype VIIi are approximately 99% identical to each other and are more closely related to Indonesian viruses isolated from 1983 through 1990 than to those of genotype VII, still circulating in the region. Similarly, in addition to the Pakistani NDV isolates of the original genotype XIII (now called sub-genotype XIIIa), there is an additional sub-genotype (XIIIb) that was initially detected in India and Iran

  17. Genotyping of feline leukemia virus in Mexican housecats.

    PubMed

    Ramírez, Hugo; Autran, Marcela; García, M Martha; Carmona, M Ángel; Rodríguez, Cecilia; Martínez, H Alejandro

    2016-04-01

    Feline leukemia virus (FeLV) is a retrovirus with variable rates of infection globally. DNA was obtained from cats' peripheral blood mononuclear cells, and proviral DNA of pol and env genes was detected using PCR. Seventy-six percent of cats scored positive for FeLV using env-PCR; and 54 %, by pol-PCR. Phylogenetic analysis of both regions identified sequences that correspond to a group that includes endogenous retroviruses. They form an independent branch and, therefore, a new group of endogenous viruses. Cat gender, age, outdoor access, and cohabitation with other cats were found to be significant risk factors associated with the disease. This strongly suggests that these FeLV genotypes are widely distributed in the studied feline population in Mexico. PMID:26747244

  18. Hepatitis C virus genotyping in Greece: unexpected high prevalence of genotype 5a in a Greek island.

    PubMed

    Karatapanis, Stylianos; Tsoplou, Panagiota; Papastergiou, Vasilios; Vasiageorgi, Aggeliki; Stampori, Maria; Saitis, Ioannis; Tsitsopoulos, Eustathios; Lisgos, Phillipos; Skorda, Lamprini; Ketikoglou, Ioannis; Goulis, Ioannis

    2012-02-01

    Hepatitis C virus (HCV) genotype 5 (G5) is a rare genotype reported mainly in South Africa. However, increasing data suggest the sporadic presence of this genotype in different European countries. To assess the epidemiology of HCV-G5 in Greece, genotyping was performed in 973 consecutive patients infected with HCV, referred to 7 hepatology centers throughout Greece, from January 2005 to December 2009. Genotype 5a (19 patients, 1.9%) was the fifth most prevalent genotype after genotype 1 (408 patients, 41.9%), genotype 3 (318 patients, 32.7%), genotype 4 (158 patients, 16.2%), and genotype 2 (70 patients, 7.2%). The majority of patients infected with G5 (16/19,84.2%) were referred to the General Hospital of Rhodes, an island in south-east Greece. The HCV genotype distribution in that particular island, indicates a particularly high G5 prevalence of 12.8%, after genotype 1 (40%), genotype 3 (28%), and genotype 4 (15%). Among the patients from Rhodes infected with G5 (n = 16), 13 (81.2%) were females. The mean age was 62.3 ± 6.5 years, significantly older than the patients infected with other HCV genotypes (mean age 40.6 ± 7.2, P < 0.0001). Nine out of the 16 cases (56.2%) presented features of high pre-treatment viral loads. Advanced liver fibrosis (Metavir F3-F4) was found in four out of five performed liver biopsies. Ten patients received treatment with pegylated interferon plus ribavirin and a sustained viral response were achieved in six cases. The source of infection is unknown but parenteral iatrogenic routes of transmission seem to have contributed significantly to the spread of genotype 5a in this region. PMID:22170541

  19. Detection of low copy human papilloma virus DNA and mRNA in routine paraffin sections of cervix by non-isotopic in situ hybridisation.

    PubMed Central

    Burns, J; Graham, A K; Frank, C; Fleming, K A; Evans, M F; McGee, J O

    1987-01-01

    In analysing human papilloma virus (HPV) infection of the cervix in formalin fixed paraffin sections by non-isotopic in situ hybridisation two main problems were found: detachment of sections from the glass during hybridisation and probe detection; inadequate sensitivity and inability to assess sensitivity of the in situ procedure. The first problem was investigated by assessing the efficiency of various tissue adhesives individually and in combination. The second problem was addressed by optimising conditions for DNA unmasking, hybridisation, and biotinylated probe detection. Sensitivity of the final in situ procedure developed was assessed by using the detection of pHY2.1 repeats as a built-in control. Extrapolation of data showed that less than 10 copies of HPV DNA can be visualised by these procedures. HPV nucleic acid, mainly in the form of DNA, was detected not only in koilocytic nuclei but also in suprabasal cells in condylomas and CIN lesions. HPV mRNA was also visualised in the cytoplasm (and probably also nuclei) of the same cell types. These non-isotopic in situ procedures give results comparable to those obtained with radiolabelled probes, but they are less time consuming and provide better morphological resolution. Images Fig 1 Fig 2 Fig 3 Fig 4 Fig 5 Fig 6 Fig 7 Fig 8 PMID:2821078

  20. Sensitivity of in situ detection with biotinylated probes of human papilloma virus type 16 DNA in frozen tissue sections of squamous cell carcinomas of the cervix.

    PubMed

    Walboomers, J M; Melchers, W J; Mullink, H; Meijer, C J; Struyk, A; Quint, W G; van der Noordaa, J; ter Schegget, J

    1988-06-01

    The sensitivity of human papilloma virus type 16 (HPV-16) DNA detection by DNA in situ hybridization using biotinylated probes (bio-DISH) was estimated by performing this technique on snap-frozen tissue sections of 10 cervical squamous cell carcinomas containing increasing amounts of HPV-16 as determined by Southern blot hybridization. A protocol using serial sections for bio-DISH and DNA extraction was used. The number of positively stained cells and the detection limit were strongly dependent on the treatment of the sections with proteinase K prior to hybridization. At low proteinase K concentration (0.1 micrograms/ml), the detection limit appeared to be 30-40 HPV-16 DNA copies per carcinoma cell, whereas morphology was preserved. A high proteinase K concentration (1-5 micrograms/ml) often resulted in an increase in the number of positively stained cells but also in a poor morphology. The detection limit was improved to at least 20 HPV-16 DNA copies per carcinoma cell. PMID:2837906

  1. The prevalence of human papilloma virus (HPV) infections in oral squamous cell carcinomas: a retrospective analysis of 88 patients and literature overview.

    PubMed

    Krüger, M; Pabst, A M; Walter, C; Sagheb, K; Günther, C; Blatt, S; Weise, K; Al-Nawas, B; Ziebart, T

    2014-10-01

    In addition to tobacco and alcohol consumption, the two main risk factors for oral squamous cell carcinoma (OSCC), recent studies have revealed infections with human papilloma virus (HPV) as an additional risk factor for OSCC development. In the field of head and neck malignancies, the prevalence of HPV infections in oropharyngeal cancer (OC) ranges in different studies up to 84%. While HPV infection is discussed as an independent risk factor in this region, its distinguished role in carcinogenesis of tumours localized to the oral cavity remains still uncertain. In this study, we analysed the HPV status in 88 consecutive patients with OSCCs localized anterior of the palatoglossal arch who were treated in the Department of Oral and Maxillofacial Surgery at the University Medical Center Mainz. The HPV status analysis was performed using DNA-PCR and immunostaining of p16 protein. The prevalence of HPV-positive OSCCs was about 6% (5 patients). In 3 patients the HPV subtypes 16/18 were found. No significant differences between the HPV positive and negative patients regarding age, gender, smoking and alcohol consumption, localization and TNM level could be detected. Contrary to other studies focussing on cancers of the lingual and palatine tonsil, the prevalence of HPV infections was much lower in the oral cavity. Therefore HPV infection might play a less important role in oral carcinogenesis. PMID:24947612

  2. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. 866.3950 Section 866.3950 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay....

  3. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. 866.3950 Section 866.3950 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay....

  4. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. 866.3950 Section 866.3950 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay....

  5. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. 866.3950 Section 866.3950 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay....

  6. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. 866.3950 Section 866.3950 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay....

  7. Pathogenesis of new sub-genotypes of Newcastle disease virus strains from Israel and Pakistan

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Newcastle disease (ND) is a devastating disease of poultry worldwide caused by virulent strains of Newcastle disease virus (NDV). New genotypes and sub-genotypes of NDV frequently emerge. In the past few years, NDV strains belonging to sub-genotype VIIi and XIIIb emerged in the Middle East and Asi...

  8. Viral fitness does not correlate with three genotype displacement events involving infectious hematopoietic necrosis virus.

    PubMed

    Kell, Alison M; Wargo, Andrew R; Kurath, Gael

    2014-09-01

    Viral genotype displacement events are characterized by the replacement of a previously dominant virus genotype by a novel genotype of the same virus species in a given geographic region. We examine here the fitness of three pairs of infectious hematopoietic necrosis virus (IHNV) genotypes involved in three major genotype displacement events in Washington state over the last 30 years to determine whether increased virus fitness correlates with displacement. Fitness was assessed using in vivo assays to measure viral replication in single infection, simultaneous co-infection, and sequential superinfection in the natural host, steelhead trout. In addition, virion stability of each genotype was measured in freshwater and seawater environments at various temperatures. By these methods, we found no correlation between increased viral fitness and displacement in the field. These results suggest that other pressures likely exist in the field with important consequences for IHNV evolution. PMID:25068402

  9. Viral fitness does not correlate with three genotype displacement events involving infectious hematopoietic necrosis virus

    PubMed Central

    Kell, Alison M; Wargo, Andrew R; Kurath, Gael

    2014-01-01

    Viral genotype displacement events are characterized by the replacement of a previously dominant virus genotype by a novel genotype of the same virus species in a given geographic region. We examine here the fitness of three pairs of infectious hematopoietic necrosis virus (IHNV) genotypes involved in three major genotype displacement events in Washington state over the last 30 years to determine whether increased virus fitness correlates with displacement. Fitness was assessed using in vivo assays to measure viral replication in single infection, simultaneous co-infection, and sequential superinfection in the natural host, steelhead trout. In addition, virion stability of each genotype was measured in freshwater and seawater environments at various temperatures. By these methods, we found no correlation between increased viral fitness and displacement in the field. These results suggest that other pressures likely exist in the field with important consequences for IHNV evolution. PMID:25068402

  10. Viral fitness does not correlate with three genotype displacement events involving infectious hematopoietic necrosis virus

    USGS Publications Warehouse

    Kell, Alison M.; Wargo, Andrew R.; Kurath, Gael

    2014-01-01

    Viral genotype displacement events are characterized by the replacement of a previously dominant virus genotype by a novel genotype of the same virus species in a given geographic region. We examine here the fitness of three pairs of infectious hematopoietic necrosis virus (IHNV) genotypes involved in three major genotype displacement events in Washington state over the last 30 years to determine whether increased virus fitness correlates with displacement. Fitness was assessed using in vivo assays to measure viral replication in single infection, simultaneous co-infection, and sequential superinfection in the natural host, steelhead trout. In addition, virion stability of each genotype was measured in freshwater and seawater environments at various temperatures. By these methods, we found no correlation between increased viral fitness and displacement in the field. These results suggest that other pressures likely exist in the field with important consequences for IHNV evolution.

  11. Distribution of Hepatitis C Virus Genotypes Among Patients With Hepatitis C Virus Infection in Hormozgan, Iran

    PubMed Central

    Mousavi, Seyedeh Farzaneh; Moosavy, Seyed Hamid; Alavian, Seyed Moayed; Eghbali, Hajar; Mahboobi, Hamidreza

    2013-01-01

    Background More than 170 million people in the world are infected with Hepatitis C virus (HCV). Determination of HCV genotype before starting the treatment is required, because HCV genotype affects the course of treatment and drug dosage Objectives We aimed to evaluate HCV genotypes among patients with positive results for anti-HCV in Bandar Abbas from 2011 to 2012. Patients and Methods Five hundred and nine consecutive patients with established chronic HCV infection referred to Behavioral Diseases Consultation Center, Blood Transfusion and Center for Special Diseases from March 2011 to March 2012 were enrolled in this cross sectional study. Five mL of peripheral blood was taken from precipitants and viral RNA extracted after plasma separation. Hepatitis C virus RNA was detected by reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) assay and then HCV genotypes analyzed using restriction fragment length polymorphism (RFLP) method. Results In overall, 509 patients enrolled to this study. The mean age of these patients was 38.87 ± 9.55 years ranging from 1 to 90 years. Routs of transmission were: 238 (46.7%) inject of substance, 149 (29.3%) unknown rout, 62 (12.2%) blood transfusion, 50 (9.8%) sexual contact, and 10 (2%) mother to child. Frequency of HCV genotypes were: 316 (62.1%) 1a, 117 (23%) 1b, and 76 (14.9%) 3a. there was no significant association between HCV genotypes and gender, educational degree, risk factor of Hepatitis C, job, monthly income, HIV infection, Hepatitis B virus (HBV) infection, Intravenous drug injection, and underlying disease (P > 0.05). Conclusions This results the same as many similar studies demonstrated that common HCV genotypes in Iranian patients were 1a, 3a and 1b, respectively. Patients with 1a and 1b genotypes have lower responses to interferon treatment, and it is reasonable to perform early screening to diagnose and determine HCV genotype for effective treatment and diagnose high-risk cases. PMID:24403914

  12. Nucleotide sequence variation of the envelope protein gene identifies two distinct genotypes of yellow fever virus.

    PubMed Central

    Chang, G J; Cropp, B C; Kinney, R M; Trent, D W; Gubler, D J

    1995-01-01

    The evolution of yellow fever virus over 67 years was investigated by comparing the nucleotide sequences of the envelope (E) protein genes of 20 viruses isolated in Africa, the Caribbean, and South America. Uniformly weighted parsimony algorithm analysis defined two major evolutionary yellow fever virus lineages designated E genotypes I and II. E genotype I contained viruses isolated from East and Central Africa. E genotype II viruses were divided into two sublineages: IIA viruses from West Africa and IIB viruses from America, except for a 1979 virus isolated from Trinidad (TRINID79A). Unique signature patterns were identified at 111 nucleotide and 12 amino acid positions within the yellow fever virus E gene by signature pattern analysis. Yellow fever viruses from East and Central Africa contained unique signatures at 60 nucleotide and five amino acid positions, those from West Africa contained unique signatures at 25 nucleotide and two amino acid positions, and viruses from America contained such signatures at 30 nucleotide and five amino acid positions in the E gene. The dissemination of yellow fever viruses from Africa to the Americas is supported by the close genetic relatedness of genotype IIA and IIB viruses and genetic evidence of a possible second introduction of yellow fever virus from West Africa, as illustrated by the TRINID79A virus isolate. The E protein genes of American IIB yellow fever viruses had higher frequencies of amino acid substitutions than did genes of yellow fever viruses of genotypes I and IIA on the basis of comparisons with a consensus amino acid sequence for the yellow fever E gene. The great variation in the E proteins of American yellow fever virus probably results from positive selection imposed by virus interaction with different species of mosquitoes or nonhuman primates in the Americas. PMID:7637022

  13. Virus-Like Particle Secretion and Genotype-Dependent Immunogenicity of Dengue Virus Serotype 2 DNA Vaccine

    PubMed Central

    Galula, Jedhan U.; Shen, Wen-Fan; Chuang, Shih-Te

    2014-01-01

    ABSTRACT Dengue virus (DENV), composed of four distinct serotypes, is the most important and rapidly emerging arthropod-borne pathogen and imposes substantial economic and public health burdens. We constructed candidate vaccines containing the DNA of five of the genotypes of dengue virus serotype 2 (DENV-2) and evaluated the immunogenicity, the neutralizing (Nt) activity of the elicited antibodies, and the protective efficacy elicited in mice immunized with the vaccine candidates. We observed a significant correlation between the level of in vitro virus-like particle secretion, the elicited antibody response, and the protective efficacy of the vaccines containing the DNA of the different DENV genotypes in immunized mice. However, higher total IgG antibody levels did not always translate into higher Nt antibodies against homologous and heterologous viruses. We also found that, in contrast to previous reports, more than 50% of total IgG targeted ectodomain III (EDIII) of the E protein, and a substantial fraction of this population was interdomain highly neutralizing flavivirus subgroup-cross-reactive antibodies, such as monoclonal antibody 1B7-5. In addition, the lack of a critical epitope(s) in the Sylvatic genotype virus recognized by interdomain antibodies could be the major cause of the poor protection of mice vaccinated with the Asian 1 genotype vaccine (pVD2-Asian 1) from lethal challenge with virus of the Sylvatic genotype. In conclusion, although the pVD2-Asian 1 vaccine was immunogenic, elicited sufficient titers of Nt antibodies against all DENV-2 genotypes, and provided 100% protection against challenge with virus of the homologous Asian 1 genotype and virus of the heterologous Cosmopolitan genotype, it is critical to monitor the potential emergence of Sylvatic genotype viruses, since vaccine candidates under development may not protect vaccinated humans from these viruses. IMPORTANCE Five genotype-specific dengue virus serotype 2 (DENV-2) DNA vaccine

  14. Determination of genotypes of hepatitis C virus in Venezuela by restriction fragment length polymorphism.

    PubMed Central

    Pujol, F H; Loureiro, C L; Devesa, M; Blitz, L; Parra, K; Beker, S; Liprandi, F

    1997-01-01

    Hepatitis C virus genotypes in Venezuela were analyzed by restriction fragment length polymorphism in the 5' noncoding region. The absence of BstUI digestion was found to be a useful marker for genotype 2 specimens. From 122 serum samples, 66, 20, and 2.5% were classified as genotypes 1, 2, and 3, respectively; 0.8% were classified as genotype 4; and 10% appeared to be mixed infections. PMID:9196212

  15. Hepatitis E Virus Genotype 3 in Sewage and Genotype 1 in Acute Hepatitis Cases, Israel.

    PubMed

    Ram, Daniela; Manor, Yossi; Gozlan, Yael; Schwartz, Eli; Ben-Ari, Ziv; Mendelson, Ella; Mor, Orna

    2016-07-01

    Hepatitis E virus (HEV) is an emerging infectious agent in developed countries. HEV genotypes 1 (G1) and 3 (G3) have been identified in environmental and clinical samples in Europe. In Israel, the overall prevalence of anti-HEV IgG antibodies was found to be 10.6%; however, reports of HEV infection are scarce. In this study, the presence of HEV in Israel was investigated using 169 sewage samples from 32 treatment facilities and 49 samples from acute hepatitis patients, all collected between 2013 and 2015. Fourteen sewage samples, from Haifa (11/18 samples), Tel Aviv (2/29 samples), and Beer Sheva (1/17 samples), regions with good sanitary conditions and middle-high socioeconomic populations, were HEV positive. Among the patient samples, 6.1% (3/49) were HEV positive, all returning travelers from India. Genotype analysis revealed G1 HEV in patients and G3 HEV sequences in sewage. Evidence that HEV could be establishing itself in our region may justify more active surveillance to monitor its spread. PMID:27246446

  16. Newcastle Disease Virus in Madagascar: Identification of an Original Genotype Possibly Deriving from a Died Out Ancestor of Genotype IV

    PubMed Central

    Maminiaina, Olivier F.; Gil, Patricia; Briand, François-Xavier; Albina, Emmanuel; Keita, Djénéba; Andriamanivo, Harentsoaniaina Rasamoelina; Chevalier, Véronique; Lancelot, Renaud; Martinez, Dominique; Rakotondravao, R.; Rajaonarison, Jean-Joseph; Koko, M.; Andriantsimahavandy, Abel A.; Jestin, Véronique; Servan de Almeida, Renata

    2010-01-01

    In Madagascar, Newcastle disease (ND) has become enzootic after the first documented epizootics in 1946, with recurrent annual outbreaks causing mortality up to 40%. Four ND viruses recently isolated in Madagascar were genotypically and pathotypically characterised. By phylogenetic inference based on the F and HN genes, and also full-genome sequence analyses, the NDV Malagasy isolates form a cluster distant enough to constitute a new genotype hereby proposed as genotype XI. This new genotype is presumably deriving from an ancestor close to genotype IV introduced in the island probably more than 50 years ago. Our data show also that all the previously described neutralising epitopes are conserved between Malagasy and vaccine strains. However, the potential implication in vaccination failures of specific amino acid substitutions predominantly found on surface-exposed epitopes of F and HN proteins is discussed. PMID:21085573

  17. Variability and pathogenicity of hepatitis E virus genotype 3 variants

    PubMed Central

    Ijaz, Samreen; Tedder, Richard S.; Hogema, Boris; Zaaijer, Hans L.; Izopet, Jacques; Bradley-Stewart, Amanda; Gunson, Rory; Harvala, Heli; Kokki, Inka; Simmonds, Peter

    2015-01-01

    Infection with hepatitis E virus (HEV) can be clinically inapparent or produce symptoms and signs of hepatitis of varying severity and occasional fatality. This variability in clinical outcomes may reflect differences in host susceptibility or the presence of virally encoded determinants of pathogenicity. Analysis of complete genome sequences supports the division of HEV genotype 3 (HEV-3) variants into three major clades: 3ra comprising HEV isolates from rabbits, and 3efg and 3abchij comprising the corresponding named subtypes derived from humans and pigs. Using this framework, we investigated associations between viral genetic variability of HEV-3 in symptomatic and asymptomatic infections by comparing HEV-3 subgenomic sequences previously obtained from blood donors with those from patients presenting with hepatitis in the UK (54 blood donors, 148 hepatitis patients), the Netherlands (38 blood donors, 119 hepatitis patients), France (24 blood donors, 55 hepatitis patients) and Germany (14 blood donors, 36 hepatitis patients). In none of these countries was evidence found for a significant association between virus variants and patient group (P>0.05 Fisher's exact test). Furthermore, within a group of 123 patients in Scotland with clinically apparent HEV infections, we found no evidence for an association between variants of HEV-3 and disease severity or alanine aminotransferase level. The lack of detectable virally encoded determinants of disease outcomes in HEV-3 infection implies a more important role for host factors in its clinical phenotype. PMID:26282123

  18. Hepatitis E virus genotype 3 in mussels (Mytilus galloprovinciallis), Spain.

    PubMed

    Mesquita, João R; Oliveira, Danielle; Rivadulla, Enrique; Abreu-Silva, Joana; Varela, Miguel F; Romalde, Jesús L; Nascimento, Maria S J

    2016-09-01

    Coastal waters can become contaminated with both human waste from sewage treatment plants and runoff following manure application. Thus, shellfish produced close to land can bioaccumulate enteric viruses of human and animal origin, including zoonotic hepatitis E virus that infect both human and swine. The goal of this study was to evaluate the presence of HEV in shellfish from Galicia (NW Spain), a densely populated region with a strong tradition of swine farming, and one of the most important regions in the world for mussel production. We tested 81 mussel batches by RT-qPCR followed by conventional broad-spectrum nested RT-PCR and phylogenetic analysis. We have obtained 12 positive samples by RT-qPCR (14.81%) with HEV contamination levels ranging from 6.7 × 10(1) to 8.6 × 10(4) RNA copies/g digestive tissue. Phylogenetic analysis based on a 330 nt region of the ORF 1 showed that all sequenced isolates belonged to the zoonotic genotype 3 subgenotype e, being closely related to strains of human and swine origin. Results show that shellfish may be a potential route for HEV transmission to humans. PMID:27217353

  19. Genotypic Testing for Human Immunodeficiency Virus Type 1 Drug Resistance

    PubMed Central

    Shafer, Robert W.

    2002-01-01

    There are 16 approved human immunodeficiency virus type 1 (HIV-1) drugs belonging to three mechanistic classes: protease inhibitors, nucleoside and nucleotide reverse transcriptase (RT) inhibitors, and nonnucleoside RT inhibitors. HIV-1 resistance to these drugs is caused by mutations in the protease and RT enzymes, the molecular targets of these drugs. Drug resistance mutations arise most often in treated individuals, resulting from selective drug pressure in the presence of incompletely suppressed virus replication. HIV-1 isolates with drug resistance mutations, however, may also be transmitted to newly infected individuals. Three expert panels have recommended that HIV-1 protease and RT susceptibility testing should be used to help select HIV drug therapy. Although genotypic testing is more complex than typical antimicrobial susceptibility tests, there is a rich literature supporting the prognostic value of HIV-1 protease and RT mutations. This review describes the genetic mechanisms of HIV-1 drug resistance and summarizes published data linking individual RT and protease mutations to in vitro and in vivo resistance to the currently available HIV drugs. PMID:11932232

  20. Sociodemographic and Behavioral Correlates of Anogenital Warts and Human Papilloma Virus-Related Knowledge Among Men who have Sex with Men and Trans Women in Lima, Peru

    PubMed Central

    Brown, Brandon; Monsour, Emmi; Klausner, Jeffrey D.; Galea, Jerome T.

    2015-01-01

    Background Human papilloma virus (HPV) is the most common sexually transmitted infection (STI) globally, with a high burden of anogenital warts (AGW) among men who have sex with men (MSM) and transwomen (TW). Methods Six-hundred HIV negative MSM and TW (300 with AGW, 300 without) were recruited for a prospective cohort study to examine HPV outcomes and HPV vaccine knowledge. Participants completed a self-administered online questionnaire. Logistic regression was used to assess the association between sociodemographic and behavioral characteristics with HPV vaccine knowledge. Results The average participant age was 25.5 years. Most (67%) were single and 41.2% self-reported STI symptoms. The average age of first anal intercourse was 17 years, with self-reported sexual role as active (36%), passive (36%), and both (27%). Three quarters (77%) of participants reported engaging in condomless anal or oral sex up to six months prior to the study. Less than half (48%) of participants had heard of HPV. Participants with AGW were more likely to report that condoms helped prevent HPV (p=0.01) and that the absence of genital warts does not mean the absence of HPV (p<0.01). Conclusion Study participants had low levels of HPV knowledge but likely high HPV exposure due to condomless anal sex. The HPV knowledge gap may be explained in part by the stigma of sex work, underreporting of STIs, the high cost of the HPV vaccine in Peru, and misinformation about HPV vaccine. More work is needed to educate MSM and TW on HPV and the HPV vaccine. PMID:25763672

  1. Human papilloma virus 16 E6 RNA interference enhances cisplatin and death receptor-mediated apoptosis in human cervical carcinoma cells.

    PubMed

    Tan, Shinta; Hougardy, Brigitte M T; Meersma, Gert J; Schaap, Bessel; de Vries, Elisabeth G E; van der Zee, Ate G J; de Jong, Steven

    2012-05-01

    In cervical cancer, the p53 and retinoblastoma (pRb) tumor suppressor pathways are disrupted by the human papilloma virus (HPV) E6 and E7 oncoproteins, because E6 targets p53 and E7 targets pRb for rapid proteasome-mediated degradation. We have investigated whether E6 suppression with small interfering RNA (siRNA) restores p53 functionality and sensitizes the HPV16-positive cervical cancer cell line SiHa to apoptosis by cisplatin, irradiation, recombinant human tumor necrosis factor-related apoptosis-inducing ligand (rhTRAIL), or agonistic anti-Fas antibody. E6 siRNA resulted in decreased E6 mRNA levels and enhanced p53 and p21 expression, demonstrating the restoration of p53 functionality in SiHa cells, without inducing high levels of apoptosis (<10%). Cell surface expression of the proapoptotic death receptors (DRs) DR4, DR5, and Fas was not affected by E6 suppression. E6 suppression conferred susceptibility to cisplatin-induced apoptosis but not to irradiation-, rhTRAIL-, or anti-Fas antibody-induced apoptosis. Combining cisplatin with rhTRAIL or anti-Fas antibody induced even higher apoptosis levels in E6-suppressed cells. At the molecular level, cisplatin treatment resulted in elevated p53 levels, enhanced caspase-3 activation, and reduced p21 levels in E6-suppressed cells. Cisplatin in combination with death receptor ligands enhanced caspase-8 and caspase-3 activation and reduced X-linked inhibitor-of-apoptosis protein (XIAP) levels in these cells. We showed using siRNA that the enhanced apoptosis in E6-supressed cells was related to reduced XIAP levels and not due to reduced p21 levels. In conclusion, targeting E6 or XIAP in combination with cisplatin can efficiently potentiate rhTRAIL-induced apoptosis in HPV-positive cervical cancer cells. PMID:22328720

  2. Mixed genotype transmission bodies and virions contribute to the maintenance of diversity in an insect virus

    PubMed Central

    Clavijo, Gabriel; Williams, Trevor; Muñoz, Delia; Caballero, Primitivo; López-Ferber, Miguel

    2010-01-01

    An insect nucleopolyhedrovirus naturally survives as a mixture of at least nine genotypes. Infection by multiple genotypes results in the production of virus occlusion bodies (OBs) with greater pathogenicity than those of any genotype alone. We tested the hypothesis that each OB contains a genotypically diverse population of virions. Few insects died following inoculation with an experimental two-genotype mixture at a dose of one OB per insect, but a high proportion of multiple infections were observed (50%), which differed significantly from the frequencies predicted by a non-associated transmission model in which genotypes are segregated into distinct OBs. By contrast, insects that consumed multiple OBs experienced higher mortality and infection frequencies did not differ significantly from those of the non-associated model. Inoculation with genotypically complex wild-type OBs indicated that genotypes tend to be transmitted in association, rather than as independent entities, irrespective of dose. To examine the hypothesis that virions may themselves be genotypically heterogeneous, cell culture plaques derived from individual virions were analysed to reveal that one-third of virions was of mixed genotype, irrespective of the genotypic composition of the OBs. We conclude that co-occlusion of genotypically distinct virions in each OB is an adaptive mechanism that favours the maintenance of virus diversity during insect-to-insect transmission. PMID:19939845

  3. Evaluation of novel assays for the detection of human papilloma virus in self-collected samples for cervical cancer screening.

    PubMed

    Chen, Q; Du, H; Zhang, R; Zhao, J H; Hu, Q C; Wang, C; Wang, G X; Tang, J L; Wu, R F

    2016-01-01

    The aim of this study was to evaluate the performance of three new high-risk human papillomavirus (HPV) assays for primary cervical cancer screening, by using self-collected samples, and to identify an HPV assay that could overcome the major obstacles faced during large-scale population-based screening. Two hundred and ten women showing abnormal cervical cytology (and referred for a colposcopy) were recruited in this study. Self-collected samples obtained from all women were tested with the Cobas, Seq, and BioPerfectus Multiplex Real Time HPV assays; simultaneously, clinician-collected samples (from the same women) were tested with the gold-standard Cobas HPV assay. The results of all the assays were consistent. The sensitivity, positive predictive value, and negative predictive value for cervical intraepithelial neoplasia 2+ (CIN2+) and CIN3+ were comparable between the self-collected samples tested with the three new assays and the clinician-collected samples tested with the Cobas HPV assay (P > 0.05). The single-genotype HPV load per sample did not differ significantly between the self- and clinician-collected samples (P = 0.195). In conclusion, the results of this study demonstrated the applicability of the three new HPV assays for primary cervical cancer screening based on self-collection. PMID:27420961

  4. Hepatitis C virus infection: Are there still specific problems with genotype 3?

    PubMed Central

    Gondeau, Claire; Pageaux, Georges Philippe; Larrey, Dominique

    2015-01-01

    Hepatitis C virus (HCV) infection is one of the most common causes of chronic liver disease and the main indication for liver transplantation worldwide. As promising specific treatments have been introduced for genotype 1, clinicians and researchers are now focusing on patients infected by non-genotype 1 HCV, particularly genotype 3. Indeed, in the golden era of direct-acting antiviral drugs, genotype 3 infections are no longer considered as easy to treat and are associated with higher risk of developing severe liver injuries, such as cirrhosis and hepatocellular carcinoma. Moreover, HCV genotype 3 accounts for 40% of all HCV infections in Asia and is the most frequent genotype among HCV-positive injecting drug users in several countries. Here, we review recent data on HCV genotype 3 infection/treatment, including clinical aspects and the underlying genotype-specific molecular mechanisms. PMID:26576095

  5. Distribution of hepatitis C virus genotypes in a diverse US integrated health care population.

    PubMed

    Manos, M Michele; Shvachko, Valentina A; Murphy, Rosemary C; Arduino, Jean Marie; Shire, Norah J

    2012-11-01

    Hepatitis C virus (HCV) genotypes influence response to therapy, and recently approved direct-acting antivirals are genotype-specific. Genotype distribution information can help to guide antiviral development and elucidate infection patterns. HCV genotype distributions were studied in a diverse cross-section of patients in the Northern California Kaiser Permanente health plan. Associations between genotype and race/ethnicity, age, and sex were assessed with multivariate logistic regression models. The 10,256 patients studied were median age 56 years, 62% male, 55% White non-Hispanic. Overall, 70% were genotype 1, 16% genotype 2, 12% genotype 3, 1% genotype 4, <1% genotype 5, and 1% genotype 6. Blacks (OR 4.5 [3.8-5.5]) and Asians (OR 1.2 [1.0-1.4]) were more likely to have genotype 1 than 2/3 versus non-Hispanic Whites. Women less likely had genotype 1 versus 2/3 than did men (OR 0.86 [0.78-0.94]). Versus non-Hispanic Whites, Asians (OR 0.38 [0.31-0.46]) and Blacks (OR 0.73 [0.63-0.84]) were less likely genotype1a than 1b; Hispanics (OR 1.3 [1.1-1.5]) and Native Americans (OR 1.9 [1.2-2.8]) more likely had genotype 1a than 1b. Patients age ≥65 years less likely had genotype 1a than 1b versus those age 45-64 (OR 0.34 [0.29-0.41]). The predominance of genotype 1 among all groups studied reinforces the need for new therapies targeting this genotype. Racial/ethnic variations in HCV genotype and subtype distribution must be considered in formulating new agents and novel strategies to successfully treat the diversity of hepatitis C patients. PMID:22997077

  6. Genotypic diversity of beet curly top virus populations in the Western United States.

    PubMed

    Stenger, D C; McMahon, C L

    1997-07-01

    ABSTRACT The genotypic diversity of beet curly top virus (BCTV) present in the western United States has been examined by the analysis of 58 field isolates and eight laboratory or nursery isolates of the virus. Full-length clones for each isolate have been characterized for genotype by restriction endonuclease mapping. The results indicate that most of the genotypes examined may be classified as variants of the CFH, Worland, or Cal/Logan strains of BCTV. Two genotypes were recovered that appear to share certain genotypic markers of both Worland and CFH strains. Genotypic variants of the CFH and Worland strains and the two genotypes sharing markers of both strains were recovered from field isolates collected during 1994 and 1995. In contrast, the Cal/Logan strain was recovered only from isolates maintained in laboratories or nurseries. Comparisons of restriction endonuclease maps of cloned BCTV genomes revealed considerable variability both within and between strains. Although a total of 43 distinct genotypes of BCTV were identified, only 36 (84%) were recovered from field isolates. Of 37 field isolates for which more than a single clone was recovered, 16 (43%) contained more than a single genotype of one strain, whereas 4 (11%) harbored mixed infections of the CFH and Worland strains. A phylogenetic analysis using 43 characters derived from restriction endonuclease mapping data supported the grouping of 41 genotypes into three taxa consistent with the three currently recognized strains of BCTV. The relationships of the two genotypes sharing genotypic markers of both the Worland and CFH strains to other BCTV genotypes was unresolved in the phylogenetic analysis. Based on the mild symptom phenotype of the isolates from which these two genotypes were recovered and the presence of Worland genotypic markers in portions of the genome containing both cis- and trans-acting elements determining replication specificity, these two genotypes were tentatively considered as

  7. Hepatitis B Virus Genotypes and Precore and Core Mutants in Brazilian Patients

    PubMed Central

    Sitnik, Roberta; Pinho, João Renato Rebello; Bertolini, Dennis Armando; Bernardini, Antonio Plinio; da Silva, Luiz Caetano; Carrilho, Flair José

    2004-01-01

    A method for genotyping hepatitis B virus by partial HBsAg gene sequencing with primers common to all known genotypes was developed. Mutations related to anti-HBs resistance are also detected with this method. Samples from 103 Brazilian patients were analyzed. Precore and core region of these viruses were also sequenced in 101 patients. Genotypes A, B, C, D, and F were found with frequencies of 49.5, 2.9, 13.6, 24.3, and 9.7%, respectively. Genotypes B and C were found only in Asian patients, whereas genotypes A, D, and F were more common in patients without an Asian background. Precore mutants were found in 32 (31.7%) of 101 patients, with a higher frequency in those infected with genotype D (22 of 25 [88.0%]). Analysis of nucleotide 1858 showed presence of thymine in all patients with genotypes B, C, and D and in a few patients with genotypes A (10.0%) and F (30.0%), who showed more frequently the presence of cytosine. This nucleotide was closely related to the presence of precore mutants. Mutations in the basal core promoter were found in 64 of 101 (63.4%) samples. These mutations were more frequent in patients infected with genotype F (90.0%) and less frequent in patients infected with genotype B (33.3%). Deletions in this region were found in two genotype C-infected patients. PMID:15184419

  8. The prevalence of the citrus tristeza virus trifoliate resistant breaking genotype among Puerto Rican isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Citrus tristeza virus (CTV) isolates have been grouped previously into five genotypes: T3, T30, T36, VT, B165 based on symptoms, host range and genomic sequence data. A sixth genotype has recently been identified with the novel property of replicating in trifoliate orange trees, a non host for the o...

  9. Emergence of new sub-genotypes of virulent Newcastle disease virus with panzootic features

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Newcastle disease virus (NDV) strains with epizootic characteristics from three new sub-genotypes of genotypes VII and XIII are rapidly spreading through Asia and the Middle East causing outbreaks of Newcastle disease (ND) that are producing significant illness and mortality in vaccinated poultry, s...

  10. Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping

    PubMed Central

    Sariguzel, Fatma Mutlu; Berk, Elife; Gokahmetoglu, Selma; Ercal, Baris Derya; Celik, Ilhami

    2015-01-01

    Objective: The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. Methods: One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Results: Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. Conclusion: The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required. PMID:26649001

  11. Molecular Assay and Genotyping of Hepatitis C Virus among Infected Egyptian and Saudi Arabian Patients

    PubMed Central

    Farag, Mohamed MS; Sofy, Ahmed R; Mousa, Adel A; Ahmed, Mohamed A; Alganzory, Mohamed R

    2015-01-01

    Hepatitis C virus (HCV) infection is a major health problem recognized globally. HCV is a common cause of liver fibrosis that may lead to liver cirrhosis or hepatocellular carcinoma. The aim of this study was to estimate the prevalence of HCV infection and genotyping among Egyptian and Saudi Arabian chronic patients using different molecular techniques. HCV RNA viral load was assessed by real-time polymerase chain reaction (RT-PCR) technology. For HCV genotyping, RT-PCR hybridization fluorescence-based method and reverse hybridization line probe assay (INNO-LiPA) were used. A total of 40 anti-HCV-positive patients with chronic hepatitis C were examined for HCV RNA, genotyping, and different laboratory investigations. In the present study, HCV genotypes 4, mixed 4.1b, and 1 were detected in patients of both countries, while genotype 2 was only detected in Saudi Arabian patients. Genotyping methods for HCV showed no difference in the classification at the genotype level. With regard to HCV subtypes, INNO-LiPA assay was a reliable test in HCV genotyping for the detection of major genotypes and subtypes, while RT-PCR-based assay was a good test at the genotype level only. HCV genotype 4 was found to be the predominant genotype among Egyptian and Saudi Arabian chronic patients. In conclusion, data analysis for detecting and genotyping HCV was an important factor for understanding the epidemiology and treatment strategies of HCV among Egyptian and Saudi Arabian chronic patients. PMID:26512201

  12. Identification of new sub-genotypes of virulent Newcastle disease virus with potential panzootic features

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Strains of virulent Newcastle disease virus (NDV) with epizootic characteristics are rapidly spreading through Asia and the Middle East causing outbreaks of Newcastle disease (ND). Significant illness and mortality in vaccinated poultry caused by highly related viruses of new sub-genotypes within ge...

  13. High prevalence and predominance of hepatitis delta virus genotype 1 infection in Cameroon.

    PubMed

    Foupouapouognigni, Yacouba; Noah, Dominique Noah; Sartre, Michèle Tagni; Njouom, Richard

    2011-03-01

    Antibodies to the hepatitis delta virus (HDV) were found in 17.6% of 233 hepatitis B virus surface antigen-positive subjects in Cameroon. Phylogenetic analyses showed the presence of HDV-1, HDV-5, HDV-6, and HDV-7 genotypes. These results enrich the limited data on HDV prevalence and molecular diversity in Cameroon. PMID:21209162

  14. High Prevalence and Predominance of Hepatitis Delta Virus Genotype 1 Infection in Cameroon▿

    PubMed Central

    Foupouapouognigni, Yacouba; Noah, Dominique Noah; Sartre, Michèle Tagni; Njouom, Richard

    2011-01-01

    Antibodies to the hepatitis delta virus (HDV) were found in 17.6% of 233 hepatitis B virus surface antigen-positive subjects in Cameroon. Phylogenetic analyses showed the presence of HDV-1, HDV-5, HDV-6, and HDV-7 genotypes. These results enrich the limited data on HDV prevalence and molecular diversity in Cameroon. PMID:21209162

  15. Risk Factors for Infection with Different Hepatitis C Virus Genotypes in Southern Brazil

    PubMed Central

    Paraboni, Marisa Lúcia Romani; Sbeghen, Marina Dallagasperina; Wolff, Fernando Herz; Moreira, Leila Beltrami

    2012-01-01

    Objectives. To investigate the proportion of different genotypes in countryside microregions in southern Brazil, and their association with risk factors. Methods. Cross-sectional study including a convenience sample of patients who tested positive for HCV-RNA and were referred to a regional health center for genotyping, from December 2003 to January 2008. Data were obtained through the National Disease Surveillance Data System, from laboratory registers and from patient charts. Identification of genotypes was carried out using the Restriction Fragment Length Polymorphism “in house” technique. Independent associations with genotypes were evaluated in multinomial logistic regression and prevalence rates of genotypes were estimated with modified Poisson regression. Results. The sample consisted of 441 individuals, 41.1 ± 12.0 years old, 56.5% men. Genotype 1 was observed in 41.5% (95% CI 37.9–48.1) of patients, genotype 2 in 19.3% (95% CI 15.0–23.6), and genotype 3 in 39.2% (95% CI 35.6–43.0). HCV genotype was significantly associated with gender and age. Dental procedures were associated with higher proportion of genotype 2 independently of age, education, and patient treatment center. Conclusions. The hepatitis C virus genotype 1 was the most frequent. Genotype 2 was associated with female gender, age, and dental procedure exposition. PMID:22666173

  16. Full coding hepatitis E virus genotype 3 genome amplification method.

    PubMed

    Muñoz-Chimeno, M; Forero, J E; Echevarría, J M; Muñoz-Bellido, J L; Vázquez-López, L; Morago, L; García-Galera, M C; Avellón, A

    2016-04-01

    Hepatitis E virus (HEV) genotype 3 produces zoonotic infection associated with the consumption of infected animals. HEV infections can become chronic in immunocompromised (IC) patients. The viral genome has three well defined open reading frames (ORF1, ORF2 and ORF3) within which various domains and functions have been described. This paper (i) describes a new method of complete sequencing of the HEV coding region through overlapping PCR systems, (ii) establishes a consensus sequence and polymorphic positions (PP) for each domain, and (iii) analyzes the complete coding sequence of an IC patient. With regard to the consensus, a high percentage of PP was observed in protease (PP=19%) and the X domain (PP=22%) within ORF1, the N-terminal region of the S domain (PP=22%) in ORF2, and the P1 (PP=35%) and P2 (PP=25%) domains in ORF3. In contrast, the ORF1 Y, ORF2 S, ORF2 M and ORF3 D1 domains were conserved in the reference sequences (0.40, 1, 0.70 and 0% of PP, respectively). The sequence from the IC patient had more mutations in the RpRp (D1235G, Q1242R, S1454T, V1480I, I1502 V, K1511R, G1373 V, E1442D, V1693 M), the terminal ORF2 S- domain (F10L, S26T, G36S, S70P, A105 V, I113 V), the X domain (T938 M, T856 V, S898A) and the helicase (S1014N, S975T, Q1133 K). PMID:26784284

  17. Genotyping of hepatitis C virus isolates from Basque Country, Spain.

    PubMed Central

    Cilla, G.; García-Bengoechea, M.; Perez-Trallero, E.; Montalvo, I.; Vicente, D.; Arenas, J. I.

    1996-01-01

    The genotype of HCV was determined in 161 chronic HCV-infected patients. The patients were classified into three groups on the basis of the origin of the HCV infection: 50 patients had a history of intravenous drug use (IVDU) but no HIV infection; 41 patients had received blood transfusions, and 70 patients had no known exposure. The distribution of HCV genotypes was associated with the origin of infection and age of patients: genotype 1b was predominant among patients who had received blood transfusions and those without evidence of parenteral exposure (84.6% and 67.7%, respectively), whereas genotype 3a was present in 65.3% of IVDUs. Patients with genotype 1b were older than those with genotypes 1a or 3a: 50.3 +/- 12 vs. 34.1 +/- 9.9 and 31 +/- 5.4 years, respectively. These findings suggest that the pattern of HCV genotypes in our region is changing and that genotype 1b may be substituted by 3a as the dominant genotype in the future. PMID:8972680

  18. Circulation of Mumps Virus Genotypes in Spain from 1996 to 2007▿

    PubMed Central

    Echevarría, J. E.; Castellanos, A.; Sanz, J. C.; Pérez, C.; Palacios, G.; Martínez de Aragón, M. V.; Peña Rey, I.; Mosquera, M.; de Ory, F.; Royuela, E.

    2010-01-01

    Although the WHO recommends the use of genotyping as a tool for epidemiological surveillance for mumps, limited data on mumps virus (MV) genotype circulation that may be used to trace the patterns of virus spread are available. We describe the first complete series of data from Spain. The small hydrophobic region was sequenced from 237 MV-positive samples from several regions of Spain collected between 1996 and 2007. Six different genotypes were identified: A, C, D (D1), G (G1, G2), H (H1, H2), and J. Genotype H1 was predominant during the epidemic that occurred from 1999 to 2003 but was replaced by genotype G1 as the dominant genotype in the epidemic that occurred from 2005 to 2007. The same genotype G1 strain caused concomitant outbreaks in different parts of the world (the United States, Canada, and the United Kingdom). The remaining genotypes (genotypes A, C, D, and J) appeared in sporadic cases or small limited outbreaks. This pattern of circulation seems to reflect continuous viral circulation at the national level, despite the high rates of vaccine coverage. PMID:20107099

  19. Hepatitis B Virus Genotyping: Is the Time Ripe for Routine Clinical Use?

    PubMed Central

    Madan, Kaushal; Tyagi, Pankaj

    2012-01-01

    Hepatitis B is one of the major causes of end-stage liver disease and liver cancer worldwide. A number of host and viral factors influence the disease course and outcomes. One such viral factor is hepatitis B virus (HBV) genotypes. There are eight major HBV genotypes described from various geographic regions of the world. Although direct sequencing appears to be the gold standard for HBV genotyping, it is expensive and laborintensive and therefore cannot be applied for routine clinical use. The newer molecular methods including serotyping have made genotyping easier and simple to apply to large number of samples rapidly. The data collected mainly over the last decade have suggested that HBV genotypes may have a bearing over the natural course of the disease and its response to therapy. This review summarizes the available literature and highlights how genotyping could be incorporated into routine clinical practice in order to improve delivery of care to HBV-infected individuals. PMID:25755425

  20. Novel measles virus genotype, East Timor and Australia.

    PubMed

    Chibo, Doris; Riddell, Michaela; Catton, Michael; Birch, Christopher

    2002-07-01

    Measles outbreaks in 1999 in Queensland and Victoria, Australia, were caused by a novel strain of clade G virus (proposed name g3). Epidemiologic and molecular evidence supports independent circulation of this virus in Queensland, northern Australia, in addition to importation of the virus by East Timor refugees seeking safe haven in Australia. PMID:12095446

  1. Hepatitis C virus (HCV) genotype 2a has a better virologic response to antiviral therapy than HCV genotype 1b

    PubMed Central

    Wang, Meng; Zhang, Yi; Li, Zhiqin; Zhang, Hongyu; Zhang, Zhen; Yue, Dongli; Zhou, Rong; Li, Xiaogang; Wu, Shuhuan; Li, Jiansheng

    2015-01-01

    The standard treatment, pegylated interferon (PEG-IFN) plus ribavirin (RBV), for patients with chronic hepatitis C (CHC), does not provide a sustained virologic response (SVR) in a large majority of patients. In the present study, 211 treatment-naïve patients with the hepatitis C virus (HCV) genotype 1b and 2a were recruited and treated weekly with PEG-IFN plus RBV to determine the response of HCV genotype 1b and 2a patients to standard antiviral treatment. Virologic responses were assessed by TaqMan at week 4, 12, 24, 48 and 24 weeks of treatment. Patients with HCV genotype 2a had a significantly higher rapid virologic response (RVR), early virologic response, end-of-treatment response and SVR, and a lower relapse rate than patients with HCV genotype 1b. Multivariate logistic regression analysis showed that the HCV genotype 2a patients had a HCV RNA level ≤ 5.70 log10 IU/ml, a fibrosis stage < S3, and that HLA-A02 expression and RVR were independent factors of SVR that may improve HCV clearance. PMID:26221288

  2. Structural basis for the neutralization of hepatitis E virus by a cross-genotype antibody

    PubMed Central

    Gu, Ying; Tang, Xuhua; Zhang, Xiao; Song, Cuiling; Zheng, Minghua; Wang, Kaihang; Zhang, Jun; Ng, Mun-Hon; Hew, Choy-Leong; Li, Shaowei; Xia, Ningshao; Sivaraman, J.

    2015-01-01

    Hepatitis E virus (HEV), a non-enveloped, positive-sense, single-stranded RNA virus, is a major cause of enteric hepatitis. Classified into the family Hepeviridae, HEV comprises four genotypes (genotypes 1-4), which belong to a single serotype. We describe a monoclonal antibody (mAb), 8G12, which equally recognizes all four genotypes of HEV, with ∼2.53–3.45 nM binding affinity. The mAb 8G12 has a protective, neutralizing capacity, which can significantly block virus infection in host cells. Animal studies with genotypes 1, 3 and 4 confirmed the cross-genotype neutralizing capacity of 8G12 and its effective prevention of hepatitis E disease. The complex crystal structures of 8G12 with the HEV E2s domain (the most protruded region of the virus capsid) of the abundant genotypes 1 and 4 were determined at 4.0 and 2.3 Å resolution, respectively. These structures revealed that 8G12 recognizes both genotypes through the epitopes in the E2s dimerization region. Structure-based mutagenesis and cell-model assays with virus-like particles identified several conserved residues (Glu549, Lys554 and Gly591) that are essential for 8G12 neutralization. Moreover, the epitope of 8G12 is identified as a key epitope involved in virus-host interactions. These findings will help develop a common strategy for the prevention of the most abundant form of HEV infection. PMID:25793314

  3. Cross-protective immune responses between genotypically distinct lineages of infectious laryngotracheitis viruses.

    PubMed

    Lee, Sang-Won; Markham, Philip F; Coppo, Mauricio J C; Legione, Alistair R; Shil, Niraj K; Quinteros, José A; Noormohammadi, Amir H; Browning, Glenn F; Hartley, Carol A; Devlin, Joanne M

    2014-03-01

    Recent phylogenetic studies have identified different genotypic lineages of infectious laryngotracheitis virus (ILTV), and these lineages can recombine in the field. The emergence of virulent recombinant field strains of ILTV by natural recombination between commercial vaccines belonging to different genotypic lineages has been reported recently. Despite the use of attenuated ILTV vaccines, these recombinant viruses were able to spread and cause disease in commercial poultry flocks, raising the question of whether the different lineages of ILTV can induce cross-protective immune responses. This study examined the capacity of the Australian-origin A20 ILTV vaccine to protect against challenge with the class 8 ILTV recombinant virus, the genome of which is predominantly derived from a heterologous genotypic lineage. Following challenge, birds vaccinated via eyedrop were protected from clinical signs of disease and pathological changes in the tracheal mucosa, although they were not completely protected from viral infection or replication. In contrast, the challenge virus induced severe clinical signs and tracheal pathology in unvaccinated birds. This is the first study to examine the ability of a vaccine from the Australian lineage to protect against challenge with a virus from a heterologous lineage. These results suggest that the two distinct genotypic lineages of ILTV can both induce cross-protection, indicating that current commercial vaccines are still likely to assist in control of ILTV in the poultry industry, in spite of the emergence of novel recombinants derived from different genotypic lineages. PMID:24758128

  4. Molecular identification of Saint Louis encephalitis virus genotype IV in Colombia

    PubMed Central

    Hoyos-López, Richard; Soto, Sandra Uribe; Rúa-Uribe, Guillermo; Gallego-Gómez, Juan Carlos

    2015-01-01

    Saint Louis encephalitis virus (SLEV) is a member of the Japanese-encephalitis virus serocomplex of the genus Flavivirus. SLEV is broadly distributed in the Americas and the Caribbean Islands, where it is usually transmitted by mosquitoes of the genus Culex and primarily to birds and mammalian-hosts. Humans are occasionally infected by the virus and are dead-end hosts. SLEV causes encephalitis in temperate regions, while in tropical regions of the Americas, several human cases and a wide biological diversity of SLEV-strains have been reported. The phylogenetic analysis of the envelope (E) protein genes indicated eight-genotypes of SLEV with geographic overlap. The present paper describes the genotyping of two SLEV viruses detected in mosquito-pools collected in northern Colombia (department of Cordoba). We used reverse transcription-polymerase chain reaction to amplify a fragment of theE-gene to confirm the virus identity and completeE-gene sequencing for phylogenetic analysis and genotyping of the two-SLEV viruses found circulating in Córdoba. This is the first report of SLEV genotype IV in Colombia (Córdoba) in mosquitoes from a region of human inhabitation, implicating the risk of human disease due to SLEV infection. Physicians should consider SLEV as a possible aetiology for undiagnosed febrile and neurologic syndromes among their patients who report exposure to mosquito-bites. PMID:26313538

  5. [Hepatitis B virus genotype E infection in Turkey: the detection of the first case].

    PubMed

    Sayan, Murat; Sanlıdağ, Tamer; Akçalı, Sinem; Arıkan, Ayşe

    2014-10-01

    Hepatitis B virus (HBV) infection is a global major health problem. Currently, 10 genotypes (A-J) of hepatitis B virus (HBV) are identified based on the nucleic acid sequence heterogeneity, and these genotypes have been shown to have distinct geographic distribution. Reports of the previous studies indicated that the genotype D is the predominant type among hepatitis B patients in different regions of Turkey. However, recent studies indicated that other HBV genotypes are also seen with an increasing rate. Although epidemiological and clinical information on genotype E infection is currently limited, it is known that genotype E infection is common in West and Central Africa. In this report, the first case of HBV genotype E infection in Turkey was presented. A 22-year-old Nigerian male employee who resided in Manisa for five years was admitted to Celal Bayar University Hospital Manisa, Turkey, for his routine check-up. Since HBsAg was found positive, other HBV markers were tested with a repeated serum sample. Laboratory findings were as follows; HBsAg (+), anti-HBs (-), HBeAg (-), anti-HBe (+), anti-HBc (+), anti-HCV (-), anti-HIV (-), ALT: 44 U/L and AST: 45 U/L. HBV-DNA level was detected as 700 IU/ml by real-time PCR (Artus HBV QS RGQ Qiagen, Germany). HBV-DNA isolated from the serum sample of the patient was amplified by PCR and polymerase gene segment of HBV was directly sequenced. UPGMA method was used for phylogenetic analysis and Inno-LIPA HBV genotyping method (Innogenetics, Belgium) was performed to determine multiple HBV genotype infection. On the basis of those methods the genotype of the virus was identified as genotype E. The partial sequences of the HBV polymerase gene were loaded to the international DNA data bank (GenBank) for contribution to the global HBV surveillance. This report emphasized that besides genotype D the other HBV genotypes could be found in Turkey. Since the patient was an inactive HBsAg carrier before his residence in Turkey, this

  6. Hepatitis C Virus Genotypes and Association With Viral Load in Yazd, Central Province of Iran

    PubMed Central

    Hadinedoushan, Hossein; Salmanroghani, Hasan; Amirbaigy, Mohammad Kazem; Akhondi-Meybodi, Mohsen

    2014-01-01

    Background: Hepatitis C virus (HCV) is a major cause of liver disease. Infection with HCV is a global public health problem. The virus is classified into 6 genotypes and more than 80 subtypes named as a, b, c, etc. HCV genotyping has been an important parameter for the treatment of HCV infection. Objectives: The main aim of this study was to estimate the prevalence of HCV genotypes in Yazd, central province of Iran. In addition, the study investigated whether there was any association between HCV load and genotypes. Patients and Methods: This descriptive cross-sectional study was performed on samples suspicious of HCV infection from March 2010 to June 2013. Peripheral blood sample was obtained and screened for anti-HCV antibodies using Enzyme-Linked Immunosorbent Assay (ELISA). Then sera of anti-HCV positive samples were analyzed using quantitative polymerase chain reaction method. Plasma samples were used to determine the HCV genotypes of 1a, 1b, 2, 3, and 4 in 191 infected patients. Results: One hundred fifty-two out of 191 (79.6%) samples were from male patients. The mean of the patients’ age was 40.7 ± 11.9 years (range 21-75 years old). Sixty- three (33%) patients were included in 31-40 years group. The mean number of HCV in infected patients was 2.92 × 106 ± 1.85 × 106 copies/mL (Min: 508; Max: 2.75 × 108 copies/mL). HCV genotype 3 was the predominant genotype (50.3%) followed by subtypes 1a (38.7%) and 1b (6.8%). The distribution of other HCV genotypes showed genotype 2 in 1.6% and mixed genotypes in 2.6% of positive samples. Genotype 3 was predominant in all age groups except 21-30 years of age group. We were unable to find any significant difference between mean viral load of the patients infected with genotype 3 and those infected with genotype 1 (1a and 1b). Conclusions: Findings of the present study showed that HCV genotype 3 was the predominant genotype followed by the subtypes 1a and 1b in Yazd, central province of Iran. In addition, there was

  7. [First case of hepatitis B virus genotype H infection in Turkey].

    PubMed

    Ural, Onur; Sayan, Murat; Akhan, Sıla; Sümer, Sua; Simşek, Funda

    2013-07-01

    Clinical studies reported from Turkey indicate that hepatitis B virus (HBV) genotype D is more prevalent than other genotypes. Epidemiological and clinical information on genotype H infection is currently limited. Genotype H infection is most likely due to its regional (Central and South America) prevalence throughout the world. The aim of this report is to present the first HBV genotype H infection in a chronic hepatitis B patient in Turkey. Laboratory findings of a 42 years old male patient admitted to our hospital revealed HBsAg (+), anti-HBs (-), HBeAg (-), anti-HBe (+), anti-HBc IgM (-), anti-HBc IgG (+), anti-HAV IgG (+), HBV-DNA: 5.689.776 IU/ml and high liver enzymes (ALT: 223 U/L, AST: 121 U/L). History of the patient indicated no risk factor (intravenous drug use, blood transfusion, suspicious sexual contact) related to HBV transmission. Since liver ultrasonography showed multiple hemangiomas, biopsy was performed and histologic activity index was found as 6/18 and fibrosis as 2/6, according to modified Knodell score system. HBV DNA isolated from the serum sample of the patient was amplified by polymerase chain reaction and polymerase gene segment of HBV was directly sequenced. UPGMA method was used for phylogenetic analysis, and the genotype of the virus was identified accordingly. The nucleotide sequence was compared to those from the international DNA data bank (GenBank). The genotyping of the patient revealed that the isolated HBV was genotype H. Treatment with tenofovir disoproxil fumarate was initiated and the patient responded to the treatment. This finding suggested that other HBV genotypes, except the predominant genotype D may also be in circulation in Turkey. In conclusion, detection of epidemiologic and molecular characteristics of HBV genotype H which is related to chronic hepatitis, seems to be necessary in order to better understand its circulation and progression around the world. PMID:23971934

  8. Treatment of a patient with genotype 7 hepatitis C virus infection with sofosbuvir and velpatasvir.

    PubMed

    Schreiber, Jonas; McNally, John; Chodavarapu, Krishna; Svarovskaia, Evguenia; Moreno, Christophe

    2016-09-01

    During a phase 3 study evaluating the combination of sofosbuvir-velpatasvir for 12 weeks in patients with genotype 1, 2, 4, 5, and 6 hepatitis C virus (HCV) infection, we enrolled a patient who was subsequently found to be infected with genotype 7 HCV. This patient tolerated the study regimen well and achieved sustained virological response 12 weeks after treatment (SVR12). (Hepatology 2016;64:983-985). PMID:27177605

  9. Detection of bovine leukemia virus and identification of its genotype in Mongolian cattle.

    PubMed

    Ochirkhuu, Nyamsuren; Konnai, Satoru; Odbileg, Raadan; Nishimori, Asami; Okagawa, Tomohiro; Murata, Shiro; Ohashi, Kazuhiko

    2016-04-01

    Epidemiological studies have indicated that bovine leukemia virus (BLV) infection is globally distributed. However, no information regarding the disease and genetic diversity of the virus in the cattle of Mongolia is currently available. In this study, the prevalence of BLV was assessed using PCR, and the genetic diversity was analyzed through DNA sequencing. Of the 517 samples tested, 20 positives were identified. Phylogenetic analysis showed that six, one, and four isolates were classified into genotype 4, 7, and 1, respectively. Most isolates were clustered with isolates from Eastern Europe and Russia. This study is the first to investigate the BLV genotype in Mongolia. PMID:26711456

  10. Hepatitis B virus infection and genotype in asymptomatic people from 10 ethnic groups in Yunnan, China

    PubMed Central

    Shen, Yuan-Ying; Hou, Wei; Yang, Zhan-Qiu; Xiao, Wen

    2015-01-01

    AIM: To evaluate the infection and genotype distribution of hepatitis B virus (HBV) in ethnic groups in Yunnan, China. METHODS: Two thousand five hundred and eighty-four asymptomatic local people from 10 ethnic groups were investigated in Yunnan, China. Infection and genotype distribution were evaluated by serological and genetic methods. Genotyping was verified by sequencing. Ethnic genotype distribution was compared by proportion test. RESULTS: Four types of infection model based on HBV serum markers were identified, and the average HBV infection rate was 5.7% in those asymptomatic local people. The genotype prevalence was 59.6% for B, 21.1% for C and 19.3% BC; subgenotypes Ba, Cs and Ce were identified in this study. Hepatitis B surface antigen-positive rate and the proportion of genotype B were significantly lower in ethnic groups with a northern origin compared to those with a southern origin (50% vs 73.9%, P = 0.037; 4.2% vs 10.5%, P = 0.000). CONCLUSION: Genotype B is dominant and genotype BC has high occurrence in asymptomatic local ethnic groups in Yunnan. HBV infection status and genotype distribution may associate with ethnic origin. PMID:26640334

  11. Assessing Yield Potential of Cowpea Genotypes Grown Under Virus Pressure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cowpea (Vigna unguiculata (L.) Walp) is an important grain legume in many parts of the tropics. However, viral diseases, particularly cucumber mosaic virus (CMV) and blackeye cowpea mosaic virus (BlCMV), can be a limiting factor in cowpea production. We evaluated in replicated field plots and unde...

  12. Hepatitis C virus genotype 3a with phylogenetically distinct origin is circulating in Pakistan

    PubMed Central

    2011-01-01

    Background Hepatitis C virus (HCV) is one of the leading causes of viral hepatitis worldwide and its genotype 3a is predominant in vast areas of Pakistan. Findings The present study reports the first full sequence of HCV 3a isolate PK-1 from Pakistan. This nucleotide sequence was compared with six other HCV genotype 3a full length sequences from different regions of the world by using statistical methods of phylogenetic analysis. Conclusion The nucleotide difference of these seven sequences shows that HCV genotype 3a of phylogenetically distinct origin is circulating in Pakistan. PMID:21211024

  13. [Determination of hepatitis C virus genotypes among hepatitis C patients in Eastern Black Sea Region, Turkey].

    PubMed

    Buruk, Celal Kurtuluş; Bayramoğlu, Gülçin; Reis, Ahu; Kaklıkkaya, Neşe; Tosun, Ilknur; Aydın, Faruk

    2013-10-01

    Hepatitis C virus (HCV), the major cause of transfusion-associated hepatitis, is an important public health problem in the world as well as in Turkey. HCV is grouped as six distinct genotypes and a large number of closely-related subtypes. Genotyping of HCV is an important tool for providing epidemiological data, prediction of prognosis, and optimization of antiviral therapy. This study was carried out to determine the distribution of HCV genotypes in hepatitis C patients residing in different provinces of the Eastern Black Sea Region, Turkey. A total of 304 HCV-RNA positive cases (151 male, 153 female; age range: 11-93 years, mean age: 55.2 ± 13.3 years) who were admitted to the Molecular Microbiology Unit of Department of Medical Microbiology, Karadeniz Technical University Faculty of Medicine, between January 2009 to December 2012, were included in the study. HCV genotypes were detected in plasma samples of the patients by using commercial assays [INNO-LiPA HCV II (Innogenetics, Belgium) or Abbott RealTime HCV Genotype II (Abbott Molecular Inc, USA)]. Due to the ambiguous genotyping results in some samples with these methods, an in-house multiplex polymerase chain reaction (PCR) assay with genotype-specific primers was also used in the study. Similar to the previous reports from Turkey, our results showed that four HCV genotypes (1, 2, 3, and 4) prevailed in the Eastern Black Sea Region and the predominant genotype and subtype were genotype 1 (92.8%) and 1b (87.5%), respectively. Distribution of genotypes were observed to vary according to the province. Prevalences of subtype 1a, genotype 2, 3, and 4 were noted as 5.3%, 1.6%, 4.9%, and 0.7%, respectively. Furthermore, the samples from Giresun, Gumushane and Bayburt provinces, which are relatively less immigrated, had higher genotype 1, and the prevalence rates in the region was affected by the presence of non-citizen residents. This study is the first report on distribution of HCV genotypes in chronic hepatitis

  14. Role of ledipasvir/sofosbuvir combination for genotype 1 hepatitis C virus infection

    PubMed Central

    Sundaram, Vinay; Kowdley, Kris V

    2016-01-01

    Chronic hepatitis C virus (HCV) infection is one of the most common etiologies of liver-related mortality throughout the world. Among the six HCV genotypes, genotype 1 was significantly more aggressive when utilizing the combination of pegylated interferon and ribavirin, as genotype 1-infected patients had the lowest likelihood of achieving cure (40%–50%) and required twice as long duration of treatment, as compared to genotypes 2 and 3. Recently, however, significant advances have been made with the advent of all-oral direct-acting antiviral agents, which have significantly improved the safety, efficacy, and tolerability of the treatment of HCV genotype 1. Among the available treatments for HCV genotype 1, the combination therapy of ledipasvir/sofosbuvir provides several advantages compared to other regimens, including use of a single-pill regimen, possibility to shorten the duration of treatment to 8 weeks, efficacy in patients exposed to protease inhibitors, safety in decompensated cirrhosis, and potential to avoid ribavirin. In this review, we discuss the pharmacotherapy of the combination of ledipasvir/sofosbuvir therapy and summarize the results of the Phase III clinical trials for this treatment in HCV genotype 1 patients. We will also discuss the data for special populations, including decompensated cirrhosis, human immunodeficiency virus (HIV) coinfected patients, African-Americans, the elderly, and those who failed sofosbuvir-containing regimens. PMID:27418860

  15. Role of ledipasvir/sofosbuvir combination for genotype 1 hepatitis C virus infection.

    PubMed

    Sundaram, Vinay; Kowdley, Kris V

    2016-01-01

    Chronic hepatitis C virus (HCV) infection is one of the most common etiologies of liver-related mortality throughout the world. Among the six HCV genotypes, genotype 1 was significantly more aggressive when utilizing the combination of pegylated interferon and ribavirin, as genotype 1-infected patients had the lowest likelihood of achieving cure (40%-50%) and required twice as long duration of treatment, as compared to genotypes 2 and 3. Recently, however, significant advances have been made with the advent of all-oral direct-acting antiviral agents, which have significantly improved the safety, efficacy, and tolerability of the treatment of HCV genotype 1. Among the available treatments for HCV genotype 1, the combination therapy of ledipasvir/sofosbuvir provides several advantages compared to other regimens, including use of a single-pill regimen, possibility to shorten the duration of treatment to 8 weeks, efficacy in patients exposed to protease inhibitors, safety in decompensated cirrhosis, and potential to avoid ribavirin. In this review, we discuss the pharmacotherapy of the combination of ledipasvir/sofosbuvir therapy and summarize the results of the Phase III clinical trials for this treatment in HCV genotype 1 patients. We will also discuss the data for special populations, including decompensated cirrhosis, human immunodeficiency virus (HIV) coinfected patients, African-Americans, the elderly, and those who failed sofosbuvir-containing regimens. PMID:27418860

  16. Distribution of hepatitis C virus genotypes among hemodialysis patients in Tehran--a multicenter study.

    PubMed

    Hosseini-Moghaddam, Seyed Mohammadmehdi; Keyvani, Hossein; Kasiri, Hossein; Kazemeyni, Seyed Mohammad; Basiri, Abbas; Aghel, Nazanin; Alavian, Seyed-Moayed

    2006-05-01

    Hepatitis C virus has substantial heterogeneity of genotypes throughout the world. The aim of this study was to determine the frequency of HCV genotypes, risk factors and clinical implications in cases of hemodialysis living in Tehran. A total of 155 patients treated by hemodialysis, who had been identified to be anti-HCV positive at 45 medical centers in Tehran, were enrolled. Genotyping was using restriction fragment length polymorphism (RFLP) on HCV-RNA positive samples. HCV-RNA was detected in 66 (42.6%) patients. Genotyping of HCV-RNA positive serum samples demonstrated that subtypes 3a and 1a were predominant accounting for 30.3 and 28.8%, respectively. The distribution of other HCV genotypes showed genotype 1b, 18.2%; genotype 4, 16.7%; mixed genotypes 1a and 1b, 3%; and genotype 3b, 3%. Genotype 2 was not detected in this study. Statistically significant differences were identified between HCV infected and non-HCV infected patients regarding history of hemodialysis unit changes more than two times (P = 0.01), and history of hemodialysis for more than 20 years (P = 0.02). However, blood transfusion, mean duration of hemodialysis therapy and the history of solid organ transplantation did not differ between these two groups. This study indicates that the dominant HCV genotypes among patients treated by hemodialysis living in Tehran were 3a and 1a, and considering previous reports from the general population, genotype 4 was strongly associated with hemodialysis. The duration of treatment by hemodialysis and, in turn, more hemodialysis unit changes will lead to more frequent HCV infections. PMID:16555284

  17. Role of hepatitis B virus genotype D & its mutants in occult hepatitis B infection

    PubMed Central

    Sengupta, Sonali; Panda, Subrat Kumar; Acharya, Subrat Kumar; Durgapal, Hemlata

    2013-01-01

    Background & objectives: Non-detection of hepatitis B virus (HBV) envelope protein (hepatitis B surface antigen, HBsAg) in a chronically HBV infected individual has been described as occult infection. One possible reason for this phenotype is alteration in large (L-HBsAg) to small (S-HBsAg) envelope protein ratio associated with reduced or non secretion of HBsAg. This results in quantitative levels of serum HBsAg below the detection limit of enzyme immunoassays. Genotype D of HBV has a characteristic 33 nucleotide (nt) deletion upstream of the pre-S2/S promoter. This deletion may reduce HBsAg secretion in occult infection patients infected with genotype D HBV. Additional deletions in the pre-S2/S promoter may further aggravate reduced HBsAg secretion in patients infected with genotype D HBV. Thus, the aim of the present study was to determine the role of genotype D specific 33nt deletion and additional pre-S2/S promoter deletions in causing reduced or no secretion of HBsAg, in occult infection. Since these deletions overlap virus polymerase, their effect on virus replication was also investigated. Methods: We examined the in vitro expression of HBsAg, ratio of cure and ‘e’ antigen (HBcAg/HBeAg), their secretion and virus replication, using overlength 1.3 mer/1.86 mer genotype A replicons, and genotype D replicons with and without additional pre-S2/S promoter deletions from cases of occult infection. Results: Genotype D replicon showed a decrease in HBsAg secretion compared to the wild-type genotype A. Genotype D replicons carrying additional pre-S2/S promoter deletions, showed further reduction in HBsAg secretion, demonstrated presence of intracellular HBcAg/HBeAg, virus replication intermediates and ‘e’ antigen secretion. Interpretation & conclusions: The characteristic 33 nt deletion of genotype D HBV reduces HBsAg secretion. Additional pre-S2/S promoter deletions may further diminish HBsAg secretion, leading to occult infection. Pre-S2/S promoter

  18. Evolutionary analysis of rubella viruses in mainland China during 2010–2012: endemic circulation of genotype 1E and introductions of genotype 2B

    PubMed Central

    Zhu, Zhen; Rivailler, Pierre; Abernathy, Emily; Cui, Aili; Zhang, Yan; Mao, Naiyin; Xu, Songtao; Zhou, Shujie; Lei, Yue; Wang, Yan; Zheng, Huanying; He, Jilan; Chen, Ying; Li, Chongshan; Bo, Fang; Zhao, Chunfang; Chen, Meng; Lu, Peishan; Li, Fangcai; Gu, Suyi; Gao, Hui; Guo, Yu; Chen, Hui; Feng, Daxing; Wang, Shuang; Tang, Xiaomin; Lei, Yake; Feng, Yan; Deng, Lili; Gong, Tian; Fan, Lixia; Xu, Wenbo; Icenogle, Joseph; Chen, Xia; Tian, Hong; Ma, Yan; Liu, Leng; Liu, Li; Liu, Jianfeng; Fu, Hong; Yang, Yuying; Ma, Yujie; Zhao, Hua; Huang, Fang; Hu, Ying; Zhang, Hong; Tian, Xiaoling; Du, Hui; Ma, Xuemin; Zhang, Zhenying; Xu, Jin; Zhou, Jianhui; Ye, Xufang; Li, Jing; Lu, Yiyu; Liu, Wei; Zhang, Yanni; Zhao, Shengcang; Ba, Zhuoma

    2015-01-01

    Rubella remains a significant burden in mainland China. In this report, 667 viruses collected in 24 of 31 provinces of mainland China during 2010–2012 were sequenced and analyzed, significantly extending previous reports on limited numbers of viruses collected before 2010. Only viruses of genotypes 1E and 2B were found. Genotype 1E viruses were found in all 24 provinces. Genotype 1E viruses were likely introduced into mainland China around 1997 and endemic transmission of primarily one lineage became established. Viruses reported here from 2010–2012 are largely in a single cluster within this lineage. Genotype 2B viruses were rarely detected in China prior to 2010. This report documents a previously undetected 2B lineage, which likely became endemic in eastern provinces of China between 2010 and 2012. Bayesian analyses were performed to estimate the evolutionary rates and dates of appearance of the genotype 1E and 2B viral linages in China. A skyline plot of viral population diversity did not provide evidence of reduction of diversity as a result of vaccination, but should be useful as a baseline for such reductions as vaccination programs for rubella become widespread in mainland China. PMID:25613734

  19. Evolutionary analysis of rubella viruses in mainland China during 2010-2012: endemic circulation of genotype 1E and introductions of genotype 2B.

    PubMed

    Zhu, Zhen; Rivailler, Pierre; Abernathy, Emily; Cui, Aili; Zhang, Yan; Mao, Naiyin; Xu, Songtao; Zhou, Shujie; Lei, Yue; Wang, Yan; Zheng, Huanying; He, Jilan; Chen, Ying; Li, Chongshan; Bo, Fang; Zhao, Chunfang; Chen, Meng; Lu, Peishan; Li, Fangcai; Gu, Suyi; Gao, Hui; Guo, Yu; Chen, Hui; Feng, Daxing; Wang, Shuang; Tang, Xiaomin; Lei, Yake; Feng, Yan; Deng, Lili; Gong, Tian; Fan, Lixia; Xu, Wenbo; Icenogle, Joseph

    2015-01-01

    Rubella remains a significant burden in mainland China. In this report, 667 viruses collected in 24 of 31 provinces of mainland China during 2010-2012 were sequenced and analyzed, significantly extending previous reports on limited numbers of viruses collected before 2010. Only viruses of genotypes 1E and 2B were found. Genotype 1E viruses were found in all 24 provinces. Genotype 1E viruses were likely introduced into mainland China around 1997 and endemic transmission of primarily one lineage became established. Viruses reported here from 2010-2012 are largely in a single cluster within this lineage. Genotype 2B viruses were rarely detected in China prior to 2010. This report documents a previously undetected 2B lineage, which likely became endemic in eastern provinces of China between 2010 and 2012. Bayesian analyses were performed to estimate the evolutionary rates and dates of appearance of the genotype 1E and 2B viral linages in China. A skyline plot of viral population diversity did not provide evidence of reduction of diversity as a result of vaccination, but should be useful as a baseline for such reductions as vaccination programs for rubella become widespread in mainland China. PMID:25613734

  20. Proteome Differences between Hepatitis B Virus Genotype-B- and Genotype-C-Induced Hepatocellular Carcinoma Revealed by iTRAQ-Based Quantitative Proteomics.

    PubMed

    Wei, Dahai; Zeng, Yongyi; Xing, Xiaohua; Liu, Hongzhi; Lin, Minjie; Han, Xiao; Liu, Xiaolong; Liu, Jingfeng

    2016-02-01

    Hepatitis B virus (HBV) is the main cause of hepatocellular carcinoma (HCC) in southeast Asia where HBV genotype B and genotype C are the most prevalent. Viral genotypes have been reported to significantly affect the clinical outcomes of HCC. However, the underlying molecular differences among different genotypes of HBV virus infected HCC have not been revealed. Here, we applied isobaric tags for relative and absolute quantitation (iTRAQ) technology integrated with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify the proteome differences between the HBV genotypes B- and C-induced HCC. In brief, a total of 83 proteins in the surrounding noncancerous tissues and 136 proteins in the cancerous tissues between HBV genotype-B- and genotype-C-induced HCC were identified, respectively. This information revealed that there might be different molecular mechanisms of the tumorigenesis and development of HBV genotypes B- and C-induced HCC. Furthermore, our results indicate that the two proteins ARFIP2 and ANXA1 might be potential biomarkers for distinguishing the HBV genotypes B- and C-induced HCC. Thus, the quantitative proteomic analysis revealed molecular differences between the HBV genotypes B- and C-induced HCC, and might provide fundamental information for further deep study. PMID:26709725

  1. Universal Primers for Detection and Sequencing of Hepatitis B Virus Genomes across Genotypes A to G

    PubMed Central

    Chook, Jack Bee; Teo, Woon Li; Ngeow, Yun Fong; Tee, Kok Keng; Ng, Kee Peng

    2015-01-01

    Hepatitis B virus (HBV) has been divided into 10 genotypes, A to J, based on an 8% nucleotide sequence divergence between genotypes. The conventional practice of using a single set of primers to amplify a near-complete HBV genome is hampered by its low analytical sensitivity. The current practice of using overlapping conserved primer sets to amplify a complete HBV genome in a clinical sample is limited by the lack of pan-primers to detect all HBV genotypes. In this study, we designed six highly conserved, overlapping primer sets to cover the complete HBV genome. We based our design on the sequences of 5,154 HBV genomes of genotypes A to I downloaded from the GenBank nucleotide database. These primer sets were tested on 126 plasma samples from Malaysia, containing genotypes A to D and with viral loads ranging from 20 to >79,780,000 IU/ml. The overall success rates for PCR amplification and sequencing were >96% and >94%, respectively. Similarly, there was 100% amplification and sequencing success when the primer sets were tested on an HBV reference panel of genotypes A to G. Thus, we have established primer sets that gave a high analytical sensitivity for PCR-based detection of HBV and a high rate of sequencing success for HBV genomes in most of the viral genotypes, if not all, without prior known sequence data for the particular genotype/genome. PMID:25788548

  2. Dual daclatasvir and sofosbuvir for treatment of genotype 3 chronic hepatitis C virus infection.

    PubMed

    Sundaram, Vinay; Kowdley, Kris V

    2016-01-01

    Chronic hepatitis C virus (HCV) infection is one of the most common etiologies of liver-related mortality throughout the world. Traditionally, therapy has been focused on pegylated interferon in combination with ribavirin, with clinical trials demonstrating that HCV genotype 1 had the lowest response rate (40-50%), while genotype 3 had an intermediate response rate (60-70%). Recently, significant advances have been made with all-oral direct-acting antiviral (DAA) therapy, which have significantly improved cure rates for HCV genotype 1. Accordingly, HCV genotype 3 is now potentially the most difficult to treat. One of the most potent DAA medications is sofosbuvir, a pan-genotypic nucleotide analogue that inhibits the NS5B polymerase of HCV. Daclatasvir, a pan-genotypic inhibitor of the HCV NS5A replication complex, was recently approved in the United States for treatment of HCV genotype 3 in conjunction with sofosbuvir. This combination may provide a powerful tool in the treatment of HCV genotype 3. PMID:26560449

  3. Incident Hepatitis C Virus Genotype Distribution and Multiple Infection in Australian Prisons.

    PubMed

    Walker, Melanie R; Li, Hui; Teutsch, Suzy; Betz-Stablein, Brigid; Luciani, Fabio; Lloyd, Andrew R; Bull, Rowena A

    2016-07-01

    Hepatitis C virus (HCV) is a highly diverse pathogen that is classified into seven distinct genotypes. Simultaneous or sequential reinfection with multiple HCV genotypes is recognized in high-risk populations, such as injecting drug users (IDUs). Multiple infection is of clinical concern as different genotypes have various sensitivities to current antiviral therapies. Therefore, a better understanding of the frequency of multiple infection and of the genotypes currently being transmitted is clinically relevant. An Australian cohort of IDUs (n = 123), identified with primary incident infection, was followed for multiple infection by regular HCV RNA testing between 2005 and 2013. A total of 354 samples were tested. Sequencing of primary incident infections revealed that genotype 3a was the most common circulating genotype, followed by genotype 1a. Examination of longitudinally collected samples identified complex patterns of multiple infection, including reinfection and superinfection. In those with multiple infection, there was no apparent evidence of homotypic immunity conferring protection against reinfection of the same subtype. This study revealed frequent multiple infection in a high-risk prisoner cohort, illustrating the complex nature of HCV infection and reinfection and highlighting the need for pan-genotypic antiviral therapies. PMID:27170021

  4. Rapid and sensitive genotyping of hepatitis C virus by single-strand conformation polymorphism.

    PubMed

    Lareu, R R; Swanson, N R; Fox, S A

    1997-02-01

    There is an increasing demand for genotyping hepatitis C virus (HCV) isolates due to the rapidly expanding list of distinct HCV genotypes and the mounting evidence of genotype-specific clinical consequences. We describe an SSCP-based assay for determining genotypes in HCV infections. HCV RNA extracted from serum was amplified by a sensitive nested-PCR assay producing a 287 bp fragment of the conserved 5' non-coding region (NCR) and analysed by non-denaturing polyacrylamide gel electrophoresis. Following empirical optimisation of the SSCP assay we identified distinct conformation polymorphisms (characteristic band patterns) corresponding to types 1a, 1b, 2a, 2b, 2c, 3 and 4 found in the Western Australian population. Seventy-three HCV RNA-positive samples were used to evaluate the SSCP genotyping assay for accuracy and efficiency by comparison with the previously established genotyping methods of manual direct sequencing and dideoxy fingerprinting. SSCP genotyping was in concord with control methods while performing more rapidly and at a fraction of the cost. Moreover, SSCP detected two co-infected samples that were not shown by the control methods. The PCR-SSCP assay provides an accurate and rapid method for genotyping of HCV RNA-positive samples at the 5' NCR by type-specific sequence polymorphisms which is applicable to large-scale screening. PMID:9029525

  5. Universal Primers for Detection and Sequencing of Hepatitis B Virus Genomes across Genotypes A to G.

    PubMed

    Chook, Jack Bee; Teo, Woon Li; Ngeow, Yun Fong; Tee, Kok Keng; Ng, Kee Peng; Mohamed, Rosmawati

    2015-06-01

    Hepatitis B virus (HBV) has been divided into 10 genotypes, A to J, based on an 8% nucleotide sequence divergence between genotypes. The conventional practice of using a single set of primers to amplify a near-complete HBV genome is hampered by its low analytical sensitivity. The current practice of using overlapping conserved primer sets to amplify a complete HBV genome in a clinical sample is limited by the lack of pan-primers to detect all HBV genotypes. In this study, we designed six highly conserved, overlapping primer sets to cover the complete HBV genome. We based our design on the sequences of 5,154 HBV genomes of genotypes A to I downloaded from the GenBank nucleotide database. These primer sets were tested on 126 plasma samples from Malaysia, containing genotypes A to D and with viral loads ranging from 20 to >79,780,000 IU/ml. The overall success rates for PCR amplification and sequencing were >96% and >94%, respectively. Similarly, there was 100% amplification and sequencing success when the primer sets were tested on an HBV reference panel of genotypes A to G. Thus, we have established primer sets that gave a high analytical sensitivity for PCR-based detection of HBV and a high rate of sequencing success for HBV genomes in most of the viral genotypes, if not all, without prior known sequence data for the particular genotype/genome. PMID:25788548

  6. Distribution of hepatitis C virus genotypes in volunteer blood donors from Chengdu, China.

    PubMed

    Gong, Tianxiang; Zhao, Xin; Luo, Yijia; Hong, Ying; Li, Shuping; Fu, Xuemei

    2016-07-01

    Hepatitis C virus (HCV) is a significant pathogen of global concern. The virus is usually spread through blood contact, such as transfusion, hemodialysis and injection of illegal drugs. HCV genotypes have a geographic distribution in different areas. In this paper, we focus on the distribution of HCV genotypes from volunteer blood donors in Chengdu. The prevalence of genotypes was analyzed using phylogenetic analysis. Phylogenetic trees were constructed based on the HCV core and NS5B regions from 313 sequences. HCV sequences were classified into six subtypes, and HCV genotypes were determined with the following results: 1b in 283, 2a in 14, 3b in seven, 3a in three, 6a in five and 6u in one. Subtype 1b was the most common and accounted for approximately 90.41 % (283/313), and a virus of subtype 6u was isolated for the first time from the Chengdu area. Genotypes 4 and 5 were not detected. PMID:27101072

  7. Serological Assay and Genotyping of Hepatitis C Virus in Infected Patients in Zanjan Province

    PubMed Central

    Esmaeilzadeh, Abdolreza; Erfanmanesh, Maryam; Ghasemi, Sousan; Mohammadi, Farzaneh

    2014-01-01

    Background: Hepatitis C Virus (HCV), a public health problem, is an enveloped, single-stranded RNA virus and a member of the Hepacivirus genus of the Flaviviridae family. Liver cancer, cirrhosis, and end-stage liver are the outcomes of chronic infection with HCV. HCV isolates show significant heterogeneity in genetics around the world. Therefore, determining HCV genotypes is a vital step in determining prognosis and planning therapeutic strategies. Objectives: As distribution of HCV genotypes is different in various geographical regions and HCV genotyping of patients has not been investigated in Zanjan City, this study was designed for the first time, to determine HCV genotypes in the region and to promote the impact of the treatment. Materials and Methods: Serum samples of 136 patients were collected and analyzed for anti-HCV antibodies using ELISA (The enzyme-linked immunosorbent assay) method. Then, positive samples were exposed to RT-PCR, which was performed under standard condition. Afterwards, they investigated for genotyping using allele-specific PCR (AS-PCR), and HCV genotype 2.0 line probe assay (LiPA). Results: Samples indicated 216 bp bands on 2% agarose gel. Analyses of the results demonstrated that the most dominant subtype was 3a with frequency of 38.26% in Zanjan Province followed by subtypes of 1b, 1a, 2, and 4 with frequencies of 25.73%, 22.05%, 5.14%, and 4.41%, respectively. The frequency of unknown HCV genotypes was 4.41%. Conclusions: According to the results, it was found that HCV high prevalent genotype in Zanjan is subtype 3a. Analysis of the results provides identification of certain HCV genotypes, and these valuable findings could affect the type and duration of the treatment. PMID:25368655

  8. Immortalization of Human Fetal Hepatocyte by Ectopic Expression of Human Telomerase Reverse Transcriptase, Human Papilloma Virus (E7) and Simian Virus 40 Large T (SV40 T) Antigen Towards Bioartificial Liver Support

    PubMed Central

    Giri, Shibashish; Bader, Augustinus

    2014-01-01

    Background Generation of genetically stable and non-tumoric immortalization cell line from primary cells would be enormously useful for research and therapeutic purposes, but progress towards this goal has so far been limited. It is now universal acceptance that immortalization of human fetal hepatocytes based on recent advances of telomerase biology and oncogene, lead to unlimited population doubling could be the possible source for bioartificial liver device. Methods Immortalization of human fetal hepatocytes cell line by ectopic expression of human telomerase reverse transcriptase (hTERT), human papilloma virus gene (E7) and simian virus 40 large T (SV40 T) antigens is main goal of present study. We used an inducible system containing human telomerase and E7, both of which are cloned into responder constructs controlled by doxycycline transactivator. We characterized the immortalized human fetal hepatocyte cells by analysis of green fluorescent cells (GFP) positive cells using flow cytometry (FACs) cell sorting and morphology, proliferative rate and antigen expression by immunohistochemical analysis. In addition to we analysized lactate formation, glucose consumption, albumin secretion and urea production of immortalized human fetal hepatocyte cells. Results After 25 attempts for transfection of adult primary hepatocytes by human telomerase and E7 to immortalize them, none of the transfection systems resulted in the production of a stable, proliferating cell line. Although the transfection efficiency was more than 70% on the first day, the vast majority of the transfected hepatocytes lost their signal within the first 5–7 days. The remaining transfected hepatocytes persisted for 2–4 weeks and divided one or two times without forming a clone. After 10 attempts of transfection human fetal hepatocytes using the same transfection system, we obtained one stable human fetal hepatocytes cell line which was able albumin secretion urea production and glucose

  9. Complete genome sequence of a novel genotype of squash mosaic virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complete genome sequence of a novel genotype of Squash mosaic virus (SqMV) infecting squash plants in Spain was obtained using deep sequencing of small ribonucleic acids and assembly. The low nucleotide sequence identities, with 87-88% on RNA1 and 84-86% on RNA2 to known SqMV isolates, suggest a new...

  10. Identification and complete genome sequence analysis of a genotype XIV Newcastle disease virus from Nigeria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The first complete genome sequence of a strain of Newcastle disease virus from genotype XIV is reported here. Strain duck/Nigeria/NG-695/KG.LOM.11-16/2009 was isolated from an apparently healthy domestic duck from a live bird market in Kogi State, Nigeria, in 2009. This strain is classified as a m...

  11. Detection of east/central/south African genotype of chikungunya virus in Myanmar, 2010.

    PubMed

    Tun, Mya Myat Ngwe; Thant, Kyaw Zin; Inoue, Shingo; Nabeshima, Takeshi; Aoki, Kotaro; Kyaw, Aung Kyaw; Myint, Tin; Tar, Thi; Maung, Kay Thwe Thwe; Hayasaka, Daisuke; Morita, Kouichi

    2014-08-01

    In 2010, chikungunya virus of the East Central South African genotype was isolated from 4 children in Myanmyar who had dengue-like symptoms. Phylogenetic analysis of the E1 gene revealed that the isolates were closely related to isolates from China, Thailand, and Malaysia that harbor the A226V mutation in this gene. PMID:25062511

  12. Phylogenetic Characterization of Genotype 4 Hepatitis C Virus Isolates from Argentina

    PubMed Central

    Alfonso, Victoria; Flichman, Diego; Sookoian, Silvia; Mbayed, Viviana Andrea; Campos, Rodolfo Héctor

    2001-01-01

    Among 114 patients infected with hepatitis C virus, three genotype 4 isolates, unusual in Argentina, were detected by phylogenetic analysis over different genomic regions. The patients were not related. One sample was associated with Egyptian sequences, and the others were associated with a Zairean isolate, a fact which reinforces the idea that they are from independent sources. PMID:11326031

  13. Detection of East/Central/South African Genotype of Chikungunya Virus in Myanmar, 2010

    PubMed Central

    Tun, Mya Myat Ngwe; Thant, Kyaw Zin; Inoue, Shingo; Nabeshima, Takeshi; Aoki, Kotaro; Kyaw, Aung Kyaw; Myint, Tin; Tar, Thi; Maung, Kay Thwe Thwe; Hayasaka, Daisuke

    2014-01-01

    In 2010, chikungunya virus of the East Central South African genotype was isolated from 4 children in Myanmyar who had dengue-like symptoms. Phylogenetic analysis of the E1 gene revealed that the isolates were closely related to isolates from China, Thailand, and Malaysia that harbor the A226V mutation in this gene. PMID:25062511

  14. Complete genome sequence of an emerging genotype of tobacco streak virus in the U.S.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report the complete genome sequence of an emerging genotype of Tobacco streak virus (TSV) infecting zucchini squash in Florida (TSV_FL13-07), through deep sequencing of sRNAs and validation by Sanger sequencing. TSV_FL13-07 only shares less than 90% sequence identity in three genomic ribonucleic...

  15. Hepatitis C virus genotypes in north eastern Algeria: A retrospective study

    PubMed Central

    Rouabhia, Samir; Sadelaoud, Mourad; Chaabna-Mokrane, Karima; Toumi, Wided; Abenavoli, Ludovico

    2013-01-01

    AIM: To determine the frequency of various hepatitis C virus (HCV) genotypes present in patients from north eastern Algeria. METHODS: This is a retrospective cross-sectional study of 435 HCV infected patients from northeast Algeria, detected in the Sadelaoud laboratory and diagnosed between January 2010 and December 2012. The patients were diagnosed with HCV infection in their local hospitals and referred to be assessed for HCV genotype before the antiviral treatment. Demographic information (sex, age and address), genotype, subtype and viral load were retrieved from the patient medical records. The serum samples were tested by the type-specific genotyping assay. RESULTS: The majority of the patients (82.5%) were from the central part of the examined region (P = 0.002). The mean age of the patients studied was 53.6 ± 11.5 years. HCV genotype 1 was the most frequent (88.7%), followed by genotypes 2 (8.5%), 4 (1.1%), 3 (0.9%) and 5 (0.2%). Genotype 6 was not detected in these patients. Mixed infection across the HCV subtypes was detected in twenty patients (4.6%). The genotype distribution was related to age and region. Genotype 1 was significantly less frequent in the ≥ 60 age group than in the younger age group (OR = 0.2; 95%CI: 0.1-0.5, P < 0.001). Furthermore, genotype 1 was more frequent in the central part of the examined region than elsewhere (P < 0.01). CONCLUSION: The HCV genotype (type 1b was dominant) distribution in Algeria is different from those in other northern countries of Africa. PMID:23898373

  16. Rapid fluorescent lateral-flow immunoassay for hepatitis B virus genotyping.

    PubMed

    Song, Liu-Wei; Wang, Ying-Bin; Fang, Lin-Lin; Wu, Yong; Yang, Lin; Chen, Jie-Yu; Ge, Sheng-Xiang; Zhang, Jing; Xiong, You-Zheng; Deng, Xiu-Mei; Min, Xiao-Ping; Zhang, Jun; Chen, Pei-Jer; Yuan, Quan; Xia, Ning-Shao

    2015-01-01

    Hepatitis B virus (HBV) genotyping plays an important role in the clinical management of chronic hepatitis B (CHB) patients. However, the current nucleic acid based techniques are expensive, time-consuming, and inconvenient. Here, we developed a novel DNA-independent HBV genotyping tool based on a one-step fluorescent lateral flow immunoassay (LFIA). Epitope-targeting immunization and screening techniques were used to develop HBV genotype specific monoclonal antibodies (mAbs). These mAbs were used to develop a multitest LFIA with a matched scanning luminoscope for HBV genotyping (named the GT-LFIA). The performance of this novel assay was carefully evaluated in well-characterized clinical cohorts. The GT-LFIA, which can specifically differentiate HBV genotypes A, B, C, and D in a pretreatment-free single test, was successfully developed using four genotype specific mAbs. The detection limits of the GT-LFIA for HBV genotypes A, B, C, and D were 2.5-10.0 IU HBV surface antigen/mL, respectively. Among the sera from 456 CHB patients, 439 (96.3%; 95% confidence interval (CI), 94.1-97.8%) were genotype-differentiable by the GT-LFIA and 437 (99.5%; 95% CI, 98.4-99.9%) were consistent with viral genome sequencing. In the 21 patients receiving nucleos(t)ide analogue therapy, for end-of-treatment specimens that were HBV DNA undetectable and were not applicable for DNA-dependent genotyping, the GT-LFIA presented genotyping results that were consistent with those obtained in pretreatment specimens by viral genome sequencing and the GT-LFIA. In conclusion, the novel GT-LFIA is a convenient, fast, and reliable tool for differential HBV genotyping, especially in patients with low or undetectable HBV DNA levels. PMID:25892477

  17. Prevalence and genotype of hepatitis C virus infection in pregnant women and blood donors in Ghana.

    PubMed

    Wansbrough-Jones, M H; Frimpong, E; Cant, B; Harris, K; Evans, M R; Teo, C G

    1998-01-01

    The seroprevalence of hepatitis C virus was evaluated in blood donors and antenatal clinic attenders in Kumasi, Ghana and seropositive subjects were tested for hepatitis C virus ribonucleic acid by the polymerase chain reaction (PCR). The overall seroprevalence among Ghanaians was 2.8% but there was a significantly higher prevalence in males (4.6%) than in females (1.0%). No risk factor for infection was identified by a questionnaire. Among those who showed evidence of active infection with a positive PCR, the most common genotype was type 2 but the subtype could not be specifically determined; these type 2 hepatitis C viruses may be indigenous to Africa. PMID:9861360

  18. Genotype characterization of occult hepatitis B virus strains among Egyptian chronic hepatitis C patients.

    PubMed

    Kishk, R; Atta, H Aboul; Ragheb, M; Kamel, M; Metwally, L; Nemr, N

    2014-02-01

    Chronic hepatitis C virus (HCV) infection combined with occult hepatitis B virus (HBV) infection has been associated with increased risk of hepatitis, cirrhosis and hepatocellular carcinoma. This study aimed to determine the prevalence of occult HBV infection among Egyptian chronic HCV patients, the genotype and occurrence of surface gene mutations of HBV and the impact of co-infection on early response to treatment. The study enrolled 162 chronic HCV patients from Ismailia Fever Hospital, Egypt, who were HBV surface antigen-negative. All patients were given clinical assessment and biochemical, histological and virological examinations. HBV-DNA was detectable in sera from 3 patients out of the 40 patients who were positive for hepatitis B core antibody. These 3 patients were responsive to combination therapy at treatment week 12; only 1 of them had discontinued therapy by week 24. HBV genotype D was the only detectable genotype in those patients, with absence of "a" determinant mutations among those isolates. PMID:24945562

  19. Genotype-specific variation in West Nile virus dispersal in California.

    PubMed

    Duggal, Nisha K; Reisen, William K; Fang, Ying; Newman, Ruchi M; Yang, Xiao; Ebel, Gregory D; Brault, Aaron C

    2015-11-01

    West Nile virus (WNV) is an arbovirus that was first reported in North America in New York in 1999 and, by 2003, had spread more than 4000 km to California. However, variation in viral genetics associated with spread is not well understood. Herein, we report sequences for more than 100 WNV isolates made from mosquito pools that were collected from 2003 to 2011 as part of routine surveillance by the California Mosquito-borne Virus Surveillance System. We performed phylogeographic analyses and demonstrated that 5 independent introductions of WNV (1 WN02 genotype strain and 4 SW03 genotype strains) occurred in California. The SW03 genotype of WNV was constrained to the southwestern U.S. and had a more rapid rate of spread. In addition, geographic constraint of WNV strains within a single region for up to 6 years suggest viral maintenance has been driven by resident, rather than migratory, birds and overwintering in mosquitoes. PMID:26210076

  20. New genotypes of white spot syndrome virus (WSSV) and Taura syndrome virus (TSV) from the Kingdom of Saudi Arabia.

    PubMed

    Tang, Kathy F J; Navarro, Solangel A; Pantoja, Carlos R; Aranguren, Fernando L; Lightner, Donald V

    2012-07-25

    White spot syndrome virus (WSSV) and Taura syndrome virus (TSV) are highly pathogenic to penaeid shrimp and have caused significant economic losses in the shrimp culture industry around the world. During 2010 and 2011, both WSSV and TSV were found in Saudi Arabia, where they caused severe mortalities in cultured Indian white shrimp Penaeus indicus. Most outbreaks of shrimp viruses in production facilities can be traced to the importation of infected stocks or commodity shrimp. In an attempt to determine the origins of these viral outbreaks in Saudi Arabia, we performed variable number of tandem repeat (VNTR) analyses for WSSV isolates and a phylogenetic analysis for TSV isolates. From the WSSV genome, the VNTR in open reading frames (ORFs) 125 and 94 were investigated with PCR followed by DNA sequence analysis. The genotypes were categorized as {N125, N94} where N is the number of repeat units in a specific ORF, and the subscript indicates the ORF (i.e. ORFs 125 and 94 in this case). From 15 Saudi Arabia WSSV isolates, we detected 3 genotypes: {6125, 794}, {7125, del94}, and {8125, 1394}. The WSSV genotype of {7125, del94} appears to be a new variant with a 1522 bp deletion encompassing complete coding regions of ORF 94 and ORF 95 and the first 82 bp of ORF 93. For TSV genotyping, we used a phylogenetic analysis based on the amino acid sequence of TSV capsid protein 2 (CP2). We analyzed 8 Saudi Arabian isolates in addition to 36 isolates from other areas: SE Asia, Mexico, Venezuela and Belize. The Saudi Arabian TSV clustered into a new, distinct group. Based on these genotyping analyses, new WSSV and TSV genotypes were found in Saudi Arabia. The data suggest that they have come from wild shrimp Penaeus indicus from the Red Sea that are used for broodstock. PMID:22832716

  1. [The genotyping and molecular evolution of varicella-zoster virus].

    PubMed

    Jiang, Long-Feng; Gan, Lin; Chen, Jing-Xian; Wang, Ming-Li

    2012-09-01

    Varicella-zoster virus (VZV, Human herpesvirus 3) is a member of the family Herpesviridae, and is classified as alpha-subfamily along with HSV-1 and HSV-2. VZV is the causative agent of chicken pox (varicella) mostly in children, after which it establishes latency in the sensory ganglia with the potential to reactivate at a later time to cause shingles (zoster). Increasing molecular epidemiological studies in recent years have been performed to monitor the mutations in VZV genome, discriminate vaccine virus from wild type virus, study the phylogeny of VZV strains throughout the world, and understand the evolution of the different clades of VZV. The progress has great impact on the fields of epidemiology, virology and bioinformatics. In this review, the currently available data concerning the geographic distribution and molecular evolution of VZV clades are discussed. PMID:23233938

  2. Simultaneous circulation of genotypes I and III of dengue virus 3 in Colombia

    PubMed Central

    Usme-Ciro, Jose A; Mendez, Jairo A; Tenorio, Antonio; Rey, Gloria J; Domingo, Cristina; Gallego-Gomez, Juan C

    2008-01-01

    Background Dengue is a major health problem in tropical and subtropical regions. In Colombia, dengue viruses (DENV) cause about 50,000 cases annually, 10% of which involve Dengue Haemorrhagic Fever/Dengue Shock Syndrome. The picture is similar in other surrounding countries in the Americas, with recent outbreaks of severe disease, mostly associated with DENV serotype 3, strains of the Indian genotype, introduced into the Americas in 1994. Results The analysis of the 3'end (224 bp) of the envelope gene from 32 DENV-3 strains recently recovered in Colombia confirms the circulation of the Indian genotype, and surprisingly the co-circulation of an Asian-Pacific genotype only recently described in the Americas. Conclusion These results have important implications for epidemiology and surveillance of DENV infection in Central and South America. Molecular surveillance of the DENV genotypes infecting humans could be a very valuable tool for controlling/mitigating the impact of the DENV infection. PMID:18764951

  3. Isolation of Genotype V St. Louis Encephalitis Virus in Florida

    PubMed Central

    Ambrose, Jason H.; White, Gregory S.; Unnasch, Thomas R.; Stark, Lillian M.

    2009-01-01

    We isolated and characterized St. Louis encephalitis virus (SLEV) from cloacal swabs of naturally exposed adult sentinel chickens in 2006. Phylogenetic analysis of SLEV strains isolated in Florida indicated that Brazilian SLEV circulated in 1972 and 2006; lineages were VA and VB. PMID:19331744

  4. Two distinct human parainfluenza virus type 1 genotypes detected during the 1991 Milwaukee epidemic.

    PubMed Central

    Henrickson, K J; Savatski, L L

    1996-01-01

    The extent of genetic and antigenic variation found in a population of human parainfluenza virus type 1 (HPIV-1) during a single local epidemic was investigated. Fifteen HPIV-1 strains isolated from children in 1991 were analyzed. Nucleotide sequence variation in the hemagglutinin-neuraminidase protein (HN) gene demonstrated two distinct genotypes (genotypes C and D). Unique patterns were identified involving 62 nucleotide and 10 amino acid positions. These patterns represented 40% of all mutations within the HN gene. The remaining mutations were randomly distributed, and 74% involved only one (55%) or two isolates. Genotypes were statistically different from each other at both the nucleotide (P = 0.001) and amino acid (P = 0.001) levels and demonstrated unique potential N-linked glycosylation patterns. Thirty-eight monoclonal antibodies (MAbs) made to four different viral proteins (22 HN, 2 fusion [F], 1 phosphoprotein, and 13 nucleoprotein) (originating from two different genotypes [genotypes A and D]) were compared for their ability to bind to the clinical isolates in enzyme-linked immunosorbent assays (ELISAs) and hemagglutinin-inhibition (HI) assays. Twenty-one MAbs bound well to all clinical isolates in ELISAs and HI assays. The remaining 17 MAbs showed variation in all four structural proteins. Three HN MAbs demonstrated genotype C- and D-specific antigenic and neutralization differences. Evolutionary analysis using parsimony methods confirmed the differences between the two genotypes. No differences in either clinical presentation or disease severity between the two genotypes were found. Geographically localized HPIV-1 epidemics can be caused by at least two distinct genotypes with minor but specific antigenic changes. The clinical and immunologic roles of HPIV-1 genotypes have not been determined. PMID:8904440

  5. Genotypic distribution of hepatitis C virus in Thailand and Southeast Asia.

    PubMed

    Wasitthankasem, Rujipat; Vongpunsawad, Sompong; Siripon, Nipaporn; Suya, Chutima; Chulothok, Phrutsada; Chaiear, Kasemporn; Rujirojindakul, Pairaya; Kanjana, Sawan; Theamboonlers, Apiradee; Tangkijvanich, Pisit; Poovorawan, Yong

    2015-01-01

    The majority of hepatitis C virus (HCV) infection results in chronic infection, which can lead to liver cirrhosis and hepatocellular carcinoma. Global burden of hepatitis C virus (HCV) is estimated at 150 million individuals, or 3% of the world's population. The distribution of the seven major genotypes of HCV varies with geographical regions. Since Asia has a high incidence of HCV, we assessed the distribution of HCV genotypes in Thailand and Southeast Asia. From 588 HCV-positive samples obtained throughout Thailand, we characterized the HCV 5' untranslated region, Core, and NS5B regions by nested PCR. Nucleotide sequences obtained from both the Core and NS5B of these isolates were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results were compared to the epidemiological data of HCV genotypes identified within Southeast Asian. Among the HCV subtypes characterized in the Thai samples, subtype 3a was the most predominant (36.4%), followed by 1a (19.9%), 1b (12.6%), 3b (9.7%) and 2a (0.5%). While genotype 1 was prevalent throughout Thailand (27-36%), genotype 3 was more common in the south. Genotype 6 (20.9%) constituted subtype 6f (7.8%), 6n (7.7%), 6i (3.4%), 6j and 6m (0.7% each), 6c (0.3%), 6v and 6xa (0.2% each) and its prevalence was significantly lower in southern Thailand compared to the north and northeast (p = 0.027 and p = 0.030, respectively). Within Southeast Asia, high prevalence of genotype 6 occurred in northern countries such as Myanmar, Laos, and Vietnam, while genotype 3 was prevalent in Thailand and Malaysia. Island nations of Singapore, Indonesia and Philippines demonstrated prevalence of genotype 1. This study further provides regional HCV genotype information that may be useful in fostering sound public health policy and tracking future patterns of HCV spread. PMID:25962112

  6. Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

    PubMed Central

    Waman, Vaishali P.; Kolekar, Pandurang; Ramtirthkar, Mukund R.; Kale, Mohan M.

    2016-01-01

    Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis revealed that the

  7. Genotypic Distribution of Hepatitis C Virus in Thailand and Southeast Asia

    PubMed Central

    Wasitthankasem, Rujipat; Vongpunsawad, Sompong; Siripon, Nipaporn; Suya, Chutima; Chulothok, Phrutsada; Chaiear, Kasemporn; Rujirojindakul, Pairaya; Kanjana, Sawan; Theamboonlers, Apiradee; Tangkijvanich, Pisit; Poovorawan, Yong

    2015-01-01

    The majority of hepatitis C virus (HCV) infection results in chronic infection, which can lead to liver cirrhosis and hepatocellular carcinoma. Global burden of hepatitis C virus (HCV) is estimated at 150 million individuals, or 3% of the world’s population. The distribution of the seven major genotypes of HCV varies with geographical regions. Since Asia has a high incidence of HCV, we assessed the distribution of HCV genotypes in Thailand and Southeast Asia. From 588 HCV-positive samples obtained throughout Thailand, we characterized the HCV 5’ untranslated region, Core, and NS5B regions by nested PCR. Nucleotide sequences obtained from both the Core and NS5B of these isolates were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results were compared to the epidemiological data of HCV genotypes identified within Southeast Asian. Among the HCV subtypes characterized in the Thai samples, subtype 3a was the most predominant (36.4%), followed by 1a (19.9%), 1b (12.6%), 3b (9.7%) and 2a (0.5%). While genotype 1 was prevalent throughout Thailand (27–36%), genotype 3 was more common in the south. Genotype 6 (20.9%) constituted subtype 6f (7.8%), 6n (7.7%), 6i (3.4%), 6j and 6m (0.7% each), 6c (0.3%), 6v and 6xa (0.2% each) and its prevalence was significantly lower in southern Thailand compared to the north and northeast (p = 0.027 and p = 0.030, respectively). Within Southeast Asia, high prevalence of genotype 6 occurred in northern countries such as Myanmar, Laos, and Vietnam, while genotype 3 was prevalent in Thailand and Malaysia. Island nations of Singapore, Indonesia and Philippines demonstrated prevalence of genotype 1. This study further provides regional HCV genotype information that may be useful in fostering sound public health policy and tracking future patterns of HCV spread. PMID:25962112

  8. Persistent infection and promiscuous recombination of multiple genotypes of an RNA virus within a single host generate extensive diversity.

    PubMed

    Weng, Ziming; Barthelson, Roger; Gowda, Siddarame; Hilf, Mark E; Dawson, William O; Galbraith, David W; Xiong, Zhongguo

    2007-01-01

    Recombination and reassortment of viral genomes are major processes contributing to the creation of new, emerging viruses. These processes are especially significant in long-term persistent infections where multiple viral genotypes co-replicate in a single host, generating abundant genotypic variants, some of which may possess novel host-colonizing and pathogenicity traits. In some plants, successive vegetative propagation of infected tissues and introduction of new genotypes of a virus by vector transmission allows for viral populations to increase in complexity for hundreds of years allowing co-replication and subsequent recombination of the multiple viral genotypes. Using a resequencing microarray, we examined a persistent infection by a Citrus tristeza virus (CTV) complex in citrus, a vegetatively propagated, globally important fruit crop, and found that the complex comprised three major and a number of minor genotypes. Subsequent deep sequencing analysis of the viral population confirmed the presence of the three major CTV genotypes and, in addition, revealed that the minor genotypes consisted of an extraordinarily large number of genetic variants generated by promiscuous recombination between the major genotypes. Further analysis provided evidence that some of the recombinants underwent subsequent divergence, further increasing the genotypic complexity. These data demonstrate that persistent infection of multiple viral genotypes within a host organism is sufficient to drive the large-scale production of viral genetic variants that may evolve into new and emerging viruses. PMID:17878952

  9. Single endemic genotype of measles virus continuously circulating in China for at least 16 years.

    PubMed

    Zhang, Yan; Xu, Songtao; Wang, Huiling; Zhu, Zhen; Ji, Yixin; Liu, Chunyu; Zhang, Xiaojie; Sun, Liwei; Zhou, Jianhui; Lu, Peishan; Hu, Ying; Feng, Daxing; Zhang, Zhenying; Wang, Changyin; Fang, Xueqiang; Zheng, Huanying; Liu, Leng; Sun, Xiaodong; Tang, Wei; Wang, Yan; Liu, Yan; Gao, Hui; Tian, Hong; Ma, Jiangtao; Gu, Suyi; Wang, Shuang; Feng, Yan; Bo, Fang; Liu, Jianfeng; Si, Yuan; Zhou, Shujie; Ma, Yuyan; Wu, Shengwei; Zhou, Shunde; Li, Fangcai; Ding, Zhengrong; Yang, Zhaohui; Rota, Paul A; Featherstone, David; Jee, Youngmee; Bellini, William J; Xu, Wenbo

    2012-01-01

    The incidence of measles in China from 1991 to 2008 was reviewed, and the nucleotide sequences from 1507 measles viruses (MeV) isolated during 1993 to 2008 were phylogenetically analyzed. The results showed that measles epidemics peaked approximately every 3 to 5 years with the range of measles cases detected between 56,850 and 140,048 per year. The Chinese MeV strains represented three genotypes; 1501 H1, 1 H2 and 5 A. Genotype H1 was the predominant genotype throughout China continuously circulating for at least 16 years. Genotype H1 sequences could be divided into two distinct clusters, H1a and H1b. A 4.2% average nucleotide divergence was found between the H1a and H1b clusters, and the nucleotide sequence and predicted amino acid homologies of H1a viruses were 92.3%-100% and 84.7%-100%, H1b were 97.1%-100% and 95.3%-100%, respectively. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Cluster H1a and H1b viruses were co-circulating during 1993 to 2005, while no H1b viruses were detected after 2005 and the transmission of that cluster has presumably been interrupted. Analysis of the nucleotide and predicted amino acid changes in the N proteins of H1a and H1b viruses showed no evidence of selective pressure. This study investigated the genotype and cluster distribution of MeV in China over a 16-year period to establish a genetic baseline before MeV elimination in Western Pacific Region (WPR). Continuous and extensive MeV surveillance and the ability to quickly identify imported cases of measles will become more critical as measles elimination goals are achieved in China in the near future. This is the first report that a single endemic genotype of measles virus has been found to be continuously circulating in one country for at least 16 years. PMID:22532829

  10. Comparison of the antigenic relationship between Japanese encephalitis virus genotypes 1 and 3

    PubMed Central

    2016-01-01

    Purpose The Japanese encephalitis virus (JEV) genotype circulating in Korea has changed from G3 to G1. Therefore, the purpose of this study was to compare the antigenic relationship between the two genotypes by using antibody tests. Materials and Methods Blood samples from 42 sows and 216 horses were collected, and their seroprevalence was monitored using the hemagglutination inhibition and virus neutralization tests. Antisera against JEV G1 and G3 were isolated and prepared from guinea pigs. The cross-reactivity of these two viruses was then compared using the neutralizing antibody test. Results We found that there was a difference in the seropositive ratios of JEV G1 and G3. However, the difference was dependent on the antibody test used. There was also an observed difference in the antigenicity between the two genotypes, as ascertained using the neutralizing antibody test. Conclusion There is an evident difference in JEV antigenicity between the genotypes G1 and G3. Therefore, we propose monitoring of the seroprevalence of JEV, and reevaluating the antigenicity of the current vaccine by using the relevant tests. PMID:26866021

  11. Genotypic evolution and antigenicity of H9N2 influenza viruses in Shanghai, China.

    PubMed

    Ge, Feifei; Li, Xin; Ju, Houbin; Yang, Dequan; Liu, Jian; Qi, Xinyong; Wang, Jian; Yang, Xianchao; Qiu, Yafeng; Liu, Peihong; Zhou, Jinping

    2016-06-01

    H9N2 influenza viruses have been circulating in China since 1994, but a systematic investigation of H9N2 in Shanghai has not previously been undertaken. Here, using 14 viruses we isolated from poultry and pigs in Shanghai during 2002 and 2006-2014, together with the commercial vaccine A/chicken/Shanghai/F/1998 (Ck/SH/F/98), we analyzed the evolution of H9N2 influenza viruses in Shanghai and showed that all 14 isolates originated from Ck/SH/F/98 antigenically. We evaluated the immune protection efficiency of the vaccine. Our findings demonstrate that H9N2 viruses in Shanghai have undergone extensive reassortment. Various genotypes emerged in 2002, 2006 and 2007, while during 2009-2014 only one genotype was found. Four antigenic groups, A-D, could be identified among the 14 isolates and a variety of antigenically distinct H9N2-virus-derived avian influenza viruses (AIVs) circulated simultaneously in Shanghai during this period. Challenge experiments using vaccinated chickens indicated that the vaccine prevented shedding of antigenic group A and B viruses, but not those of the more recent groups C and D. Genetic analysis showed that compared to the vaccine strain, representative viruses of antigenic groups C and D possess greater numbers of amino acid substitutions in the hemagglutinin (HA) protein than viruses in antigenic groups A and B. Many of these substitutions are located in antigenic sites. Our results indicate that the persistence of H9N2 AIV in China might be due to incomplete vaccine protection and that the avian influenza vaccine should be regularly evaluated and updated to maintain optimal protection. PMID:26935915

  12. Clinical Features and Outcomes of Patients With Genotype 3 Hepatitis C Virus Infection in Korea

    PubMed Central

    Cha, Ra Ri; Lee, Sang Soo; Lee, Chang Min; Ji, Sung Bok; Jung, Hee Cheul; Cho, Hyun Chin; Kim, Jin Joo; Lee, Jae Min; Kim, Hong Jun; Ha, Chang Yoon; Kim, Hyun Jin; Kim, Tae-Hyo; Jung, Woon Tae; Lee, Ok-Jae

    2016-01-01

    Abstract Hepatitis C virus (HCV) genotype 3 infection is very rare in high-income Asia Pacific. The aim of our retrospective observational study was to evaluate the incidence, clinical features, and treatment outcomes of patients with a genotype 3 HCV infection in the Gyeongnam Province of Korea. Ninety-eight consecutive patients diagnosed with a genotype 3 HCV infection at Gyeongsang National University Hospital, between January 2005 and December 2014, were enrolled into the study. Relevant characteristics of the study group included: 80.6% men, mean age of 41.8 years, and including 69 patients with chronic hepatitis, 25 with liver cirrhosis, and 4 with hepatocellular carcinoma (HCC). Risk factors for HCV infection, sustained virologic response rate, development of HCC, and mortality in patients with genotype 3 were retrospectively analyzed. Among all patients diagnosed with a HCV infection during the study period, the prevalence of genotype 3 was 7.3%. The incidence of genotype 3 was higher in young patients with a risk factor of IVDU (54.0%) and tattooing (62.3%). Among 45 treatment-naive genotype 3 patients, sustained virologic response was achieved with a combination of pegylated-interferon alpha and ribavirin in 75.6%. The cumulative 5-year incidence of HCC was 13.6%, and 8.9% for overall mortality. Liver cirrhosis at enrollment was an independent risk factor for HCC development. This is the first study to elucidate the clinical features and outcomes among the patients with HCV genotype 3 infection in Korea. Further prospective studies are needed to investigate transmission routes and outcomes for HCV genotype 3 infections. PMID:26871824

  13. Detection of mumps virus genotype H in two previously vaccinated patients from Mexico City.

    PubMed

    Del Valle, Alberto; García, Alí A; Barrón, Blanca L

    2016-06-01

    Infections caused by mumps virus (MuV) have been successfully prevented through vaccination; however, in recent years, an increasing number of mumps outbreaks have been reported within vaccinated populations. In this study, MuV was genotyped for the first time in Mexico. Saliva samples were obtained from two previously vaccinated patients in Mexico City who had developed parotitis. Viral isolation was carried out in Vero cells, and the SH and HN genes were amplified by RT-PCR. Amplicons were sequenced and compared to a set of reference sequences to identify the MuV genotype. PMID:26935913

  14. Genotypic characterization of symptomatic hepatitis E virus (HEV) infections in Egypt

    PubMed Central

    Blackard, Jason T.; Rouster, Susan D.; Nady, Soad; Galal, Gehan; Marzuuk, Naglaa; Rafaat, Marwaa M.; Daef, Enas; Din, Salwa Seif El; Purcell, Robert H.; Emerson, Suzanne U.; Sherman, Kenneth E.; Shata, M. Tarek

    2009-01-01

    Background Hepatitis E virus (HEV) is a common cause of acute viral hepatitis (AVH) in many developing countries. In Egypt, HEV seroprevalence is among the highest in the world; however, only a very limited number of Egyptian HEV sequences are currently available. Objectives The objectives were to determine the HEV genotype(s) currently circulating in Egypt. Study Design AVH patients without serologic evidence of hepatitis A, B, and C viruses were evaluated for possible HEV infection using serologic assays for anti-HEV IgM and anti-HEV IgG and real-time PCR for HEV RNA. Stool suspensions from suspected cases were inoculated into rhesus macaques to confirm the presence of HEV. Sequence analysis was utilized to determine HEV genotype. Results Of 287 subjects with AVH enrolled, 58 had serologic evidence of acute HEV infection. Stool samples for two of these patients were repeatedly positive for HEV RNA by real-time PCR. Macaques experimentally inoculated with these human stools also developed viremia. Sequence analysis of open reading frame (ORF) 1 demonstrated that these isolates belonged to HEV genotype 1 and were 3.9% – 9.5% divergent from other genotype 1 isolates. ORF2 was 5.3% – 8.7% divergent from previously reported Egyptian isolates. Conclusions This study strongly suggests that genotype 1 HEV related to other North African isolates is circulating in acute symptomatic patients in Egypt. Further evaluation of genotypic variability is underway in this highly endemic cohort and is considered an important component of our increased understanding of HEV pathogenesis. PMID:19651539

  15. Evaluation of Interferon Resistance in Newly Established Genotype 1b Hepatitis C Virus Cell Culture System

    PubMed Central

    Taniguchi, Miki; Tasaka-Fujita, Megumi; Nakagawa, Mina; Watanabe, Takako; Kawai-Kitahata, Fukiko; Otani, Satoshi; Goto, Fumio; Nagata, Hiroko; Kaneko, Shun; Nitta, Sayuri; Murakawa, Miyako; Nishimura-Sakurai, Yuki; Azuma, Seishin; Itsui, Yasuhiro; Mori, Kenichi; Yagi, Shintaro; Kakinuma, Sei; Asahina, Yasuhiro; Watanabe, Mamoru

    2016-01-01

    Background and Aims: The hepatitis C virus (HCV) genotype 1b is known to exhibit treatment resistance with respect to interferon (IFN) therapy. Substitution of amino acids 70 and 91 in the core region of the 1b genotype is a significant predictor of liver carcinogenesis and poor response to pegylated-IFN-α and ribavirin therapy. However, the molecular mechanism has not yet been clearly elucidated because of limitations of the HCV genotype 1b infectious model. Recently, the TPF1-M170T HCV genotype 1b cell culture system was established, in which the clone successfully replicates and infects Huh-7-derived Huh7-ALS32.50 cells. Therefore, the purpose of this study was to compare IFN resistance in various HCV clones using this system. Methods: HCV core amino acid substitutions R70Q and L91M were introduced to the TPF1-M170T clone and then transfected into Huh7-ALS32.50 cells. To evaluate the production of each virus, intracellular HCV core antigens were measured. Results were confirmed with Western blot analysis using anti-NS5A antibodies, and IFN sensitivity was subsequently measured. Results: Each clone was transfected successfully compared with JFH-1, with a significant difference in intracellular HCV core antigen (p < 0.05), an indicator of continuous HCV replication. Among all clones, L91M showed the highest increase in the HCV core antigen and HCV protein. There was no significant resistance against IFN treatment in core substitutions; however, IFN sensitivity was significantly different between the wildtype core and JFH-1 (p < 0.05). Conclusions: A novel genotype 1b HCV cell culture was constructed with core amino acid substitutions, which demonstrated IFN resistance of genotype 1b. This system will be useful for future analyses into the mechanisms of HCV genotype 1b treatment. PMID:27047766

  16. Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions

    PubMed Central

    Pourkarim, Mahmoud Reza; Amini-Bavil-Olyaee, Samad; Kurbanov, Fuat; Van Ranst, Marc; Tacke, Frank

    2014-01-01

    The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term “recombino-subgenotype”. Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term “immigro-subgenotype” to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment. PMID:24966586

  17. Molecular Identification of Mumps Virus Genotypes from Clinical Samples: Standardized Method of Analysis

    PubMed Central

    Palacios, G.; Jabado, O.; Cisterna, D.; de Ory, F.; Renwick, N.; Echevarria, J. E.; Castellanos, A.; Mosquera, M.; Freire, M. C.; Campos, R. H.; Lipkin, W. I.

    2005-01-01

    A sensitive nested reverse transcription-PCR assay, targeting a short fragment of the gene encoding the small hydrophobic protein (SH gene), was developed to allow rapid characterization of mumps virus in clinical samples. The sensitivity and specificity of the assay were established using representative genotypes A, B, C, D, E, and F. Mumps virus RNA was characterized directly from cerebrospinal fluid (CSF) samples and in extracts of mumps virus isolates from patients with various clinical syndromes. Direct sequencing of products and subsequent phylogenetic analysis enabled genetic classification. A simple web-based system of sequence analysis was established. The study also allowed characterization of mumps virus strains from Argentina as part of a new subgenotype. This PCR assay for characterization of mumps infections coupled to a web-based analytical program provides a rapid method for identification of known and novel strains. PMID:15815011

  18. Injecting drug use: A vector for the introduction of new hepatitis C virus genotypes.

    PubMed

    Ruta, Simona; Cernescu, Costin

    2015-10-14

    Hepatitis C virus (HCV) genotypes' monitoring allows real-time insight into the dynamic changes that occur in the global epidemiological picture of HCV infection. Intravenous drug use is currently the primary driver for HCV transmission in developed and developing countries. The distribution of HCV genotypes/subtypes differs significantly between people who inject drugs (PWID) and the general population. HCV genotypes that previously exhibited a limited geographical distribution (3a, 4) are becoming more prevalent in this high-risk group. Immigration from HCV-endemic countries and the evolving networks of HCV transmission in PWID influence HCV genotypes distribution in Europe. Social vulnerabilities (e.g., unemployment, homelessness, and limited access to social and healthcare insurances systems) are important triggers for illicit drug use, which increases the associated risks of HCV infection and the frequent emergence of less prevalent genotypes. Genotype/subtype determination bears important clinical consequences in the progression of liver disease, susceptibility to antiviral therapies and the emergence of resistance-associated variants. An estimated half of the chronically HCV-infected PWID are unaware of their infection, and only one in ten of those diagnosed enter treatment. Nevertheless, PWID exhibit high response rates to new antiviral regimens, and the level of HCV reinfection is unexpectedly low. The focus of the healthcare system must be on the early detection and treatment of infection, to avoid late presentations that are associated with high levels of viremia and liver fibrosis, which may diminish the therapeutic success rate. PMID:26478672

  19. Evaluation of Mungbean Genotypes Based on Yield Stability and Reaction to Mungbean Yellow Mosaic Virus Disease

    PubMed Central

    Alam, AKM Mahbubul; Somta, Prakit; Jompuk, Choosak; Chatwachirawong, Prasert; Srinives, Peerasak

    2014-01-01

    This work was conducted to identify mungbean genotypes showing yield stability and resistance to mungbean yellow mosaic virus (MYMV) disease. Sixteen genotypes were evaluated in a randomized complete block design with two replications for two years (2011 and 2012) at three locations (Gazipur, Ishurdi and Madaripur) of the Bangladesh Agricultural Research Institute. An analysis of variance exhibited significant effects of genotype (G), environment (E), and genotype × environment (G×E) on grain yield. Among eight agronomic characters, the principal component 1 (PC1) was always higher than the PC2. Considering G×E interaction, BM6 was the best genotype at all three locations in both years. Based on grain yield and stability performance, BM6 ranked first while the worst performing genotypes were BM1 and G10. Based on discrimination and representation, Gazipur was identified as an ideal environment for these mungbeans. Relationship between soil-plant analysis developments (SPAD) value was positive with yield but negative with MYMV severity. BM6, G1 and G2 were considered as promising sources of resistance for low disease score and stable response across the environments. The environment proved to have an influence on MYMV infection under natural infestation. A positive correlation was observed between disease score and the temperature under natural growing condition. PMID:25289012

  20. Phylogenetic Analysis of Hepatitis B Virus Genotypes Circulating in Different Risk Groups of Panama, Evidence of the Introduction of Genotype A2 in the Country

    PubMed Central

    Martínez, Alexander A.; Zaldívar, Yamitzel; Arteaga, Griselda; de Castillo, Zoila; Ortiz, Alma; Mendoza, Yaxelis; Castillero, Omar; Castillo, Juan A.; Cristina, Juan; Pascale, Juan M.

    2015-01-01

    The Hepatitis B Virus (HBV) can cause acute or chronic infection it is also associated with the development of liver cancer, thousands of new infections occur on a yearly basis, and many of these cases are located in certain areas of the Caribbean and Latin America. In these areas, the HBV prevalence is still high which makes this virus a serious public health concern to the entire region. Studies performed in Panama suggest a complex pattern in the distribution of HBV among the country’s different risk groups. We use phylogenetic analysis in order to determine which HBV genotypes were circulating in these specific groups; for this we used a fragment of the PreS2/2 region of the HBV genome. Subsequently whole HBV genome sequences were used for Bayesian analysis of phylodynamics and phylogeography. Two main genotypes were found: genotype A (54.5%) and genotype F (45.5%). There was a difference in the distribution of genotypes according to risk groups: 72.9% of high risk groups were associated to genotype A, and 55.0% of samples of genotype F were associated to the low risk group (p<0.002). The Bayesian analysis of phylogeny-traits association revealed a statistically significant geographical association (p<0.0001) with both genotypes and different regions of the country. The Bayesian time of most recent common ancestor analysis (tMRCA) revealed a recent tMRCA for genotype A2 circulating in Panama (1997, 95% HPD: 1986—2005), when it is compared with Panamanian genotype F1c sequences (1930, 95% HPD: 1810 – 2005). These results suggest a possible change in the distribution of HBV genotypes in Panama and Latin America as a whole. They also serve to encourage the implementation of vaccination programs in high-risk groups, in order to prevent an increase in the number of new HBV cases in Latin America and worldwide. PMID:26230260

  1. The Hepatitis B Virus Genotype Affects the Persistence of Viral Replication in Immunodeficient NOG Mice

    PubMed Central

    Yokoyama, Yoshinobu; Miyagi, Takuya; Hikita, Hayato; Yoshioka, Teppei; Mukai, Kaori; Nawa, Takatoshi; Sakamori, Ryotaro; Ohkawa, Kazuyoshi; Hiramatsu, Naoki; Takahashi, Takeshi; Suemizu, Hiroshi; Ryo, Akihide; Tatsumi, Tomohide; Takehara, Tetsuo

    2015-01-01

    Background & Aims At least eight genotypes of Hepatitis B virus (HBV) have been identified. HBV genotype C is the most common genotype in Japan, although the incidence of HBV genotype A is increasing. The reason underlying the differences in viral multiplication of the HBV genotypes is unclear, especially in vivo. The purpose of this study was to elucidate the differences in HBV load and the persistence of viremia in vivo between genotypes A and C. Methods Immunodeficient NOG mice were transfected by hydrodynamic injection with the HBV expression plasmids pHBA1.2 or pHBC1.2, which contain overlength (1.2-mer) copies of the genomes of HBV genotype A or C, respectively. Results One day after transfection, the number of HBcAg-positive hepatocytes and serum HBV DNA levels were similar between mice transfected with pHBA1.2 and pHBC1.2. Serum levels of HBV DNA, HBsAg and HBeAg in mice transfected with pHBA1.2 were maintained over 5 months. In contrast, those in mice with pHBC1.2 gradually decreased over time and reached undetectable levels within 3 months after transfection. HBcAg-stained hepatocytes were detected in mice transfected with pHBA1.2, but not pHBC1.2, 5 months post-transfection. Double-staining immunohistochemistry revealed that the number of cleaved caspase3-stained, HBcAg-positive hepatocytes in the pHBC1.2-transfected mice was higher than in the pHBA1.2-transfected mice 3 days post-transfection. Moreover, the plasmid DNA and covalently closed circular DNA levels were decreased in the livers of pHBC1.2-transfected mice. These results suggested that hepatocytes expressing HBV genotype C were eliminated by apoptosis in the absence of immune cells more often than in hepatocytes expressing HBV genotype A. Conclusions Immunodeficient mice transfected with HBV genotype A develop persistent viremia, whereas those transfected with HBV genotype C exhibit transient viremia accompanied by apoptosis of HBV-expressing hepatocytes. This differences may affect the

  2. [Determination of hepatitis B virus genotypes by DNA sequence analysis in patients from Ankara, Turkey].

    PubMed

    Külah, Canan; Cirak, Meltem Yalinay

    2010-04-01

    Hepatitis B virus (HBV) genotypes vary depending on the geographical region. The HBV genotype determined in Turkey has been genotype D which is found as the homogenously disseminated single genotype. The aim of this study was to determine HBV genotypes in a group of HBV infected patients who were admitted to a university hospital in Ankara, Turkey. Serum samples from HBsAg positive and anti-HBs negative 84 (52 male, 32 female) patients with HBV infection were included into the study. Anti-HBc was positive in 95.2%, HBeAg was positive in 47.6% and anti-HBe was positive in 11.9% of the patients. Mean HBV-DNA levels of the patients were 5.7 x 10(7) +/- 4.6 x 10(7) IU/ml; mean ALT levels were 131 +/- 171 IU/ml and mean AST levels were 98 +/- 170 IU/ml. HBV-DNA was extracted from serum by the phenol-chloroform method and PCR was performed to amplify the S gene region of HBV-DNA. Cycle sequencing of PCR products was performed by a commercial "Cy5/Cy5.5 Dye Primer Cycle Sequencing Kit" (Visible Genetics, Canada) based on dideoxy chain termination method. The sequences were read and analyzed in an automated fluorescence-based DNA-sequencing system (Long-Read Tower System, Visible Genetics, Canada). The nucleotide sequences of the patient samples were compared with the previously reported sequences in gene bank for each genotype. According to the comparative analysis of S-sequences of all patient samples with the published sequences of the genotypes in gene bank, all of the 84 hepatitis B strains (100%) were shown to be related to D genotypic group, subtype ayw. A phylogenetic analysis was performed and phylogenetic trees were constructed using programs in the PHYLIP phylogeny inference package. The patient samples clustered within the genotypic group D. According to these results, the main HBV genotype in our patients was genotype D in accordance with the previous molecular epidemiologic information on HBV in this geographic area. HBV genotype determination may help to

  3. Evolutionary history of Dengue virus type 4: insights into genotype phylodynamics.

    PubMed

    Villabona-Arenas, Christian Julián; Zanotto, Paolo Marinho de Andrade

    2011-07-01

    Dengue virus type 4 (DENV-4) circulates in tropical and subtropical countries from Asia and the Americas. Despite the importance of dengue virus distribution, little is known about the worldwide viral spread. Following a Bayesian phylogenetic approach we inferred the evolutionary history of 310 isolates sampled from 37 countries during the time period 1956-2008 and the spreading dynamics for genotypes I and II. The region (tropical rainforest biome) comprised by Malaysia-Thailand was the most likely ancestral area from which the serotype has originated and spread. Interestingly, cross-correlation analysis on demographic time series with the Asian sequences showed a statistically significant negative correlation that could be suggestive of competition among genotypes within the same serotype. PMID:21335103

  4. Hepatitis C Virus Genotype 5a Subgenomic Replicons for Evaluation of Direct-Acting Antiviral Agents

    PubMed Central

    Wose Kinge, Constance N.; Espiritu, Christine; Prabdial-Sing, Nishi; Sithebe, Nomathamsaqa Patricia

    2014-01-01

    Hepatitis C virus (HCV) exists as six major genotypes that differ in geographical distribution, pathogenesis, and response to antiviral therapy. In vitro replication systems for all HCV genotypes except genotype 5 have been reported. In this study, we recovered genotype 5a full-length genomes from four infected voluntary blood donors in South Africa and established a G418-selectable subgenomic replicon system using one of these strains. The replicon derived from the wild-type sequence failed to replicate in Huh-7.5 cells. However, the inclusion of the S2205I amino acid substitution, a cell culture-adaptive change originally described for a genotype 1b replicon, resulted in a small number of G418-resistant cell colonies. HCV RNA replication in these cells was confirmed by quantification of viral RNA and detection of the nonstructural protein NS5A. Sequence analysis of the viral RNAs isolated from multiple independent cell clones revealed the presence of several nonsynonymous mutations, which were localized mainly in the NS3 protein. These mutations, when introduced back into the parental backbone, significantly increased colony formation. To facilitate convenient monitoring of HCV RNA replication levels, the mutant with the highest replication level was further modified to express a fusion protein of firefly luciferase and neomycin phosphotransferase. Using such replicons from genotypes 1a, 1b, 2a, 3a, 4a, and 5a, we compared the effects of various HCV inhibitors on their replication. In conclusion, we have established an in vitro replication system for HCV genotype 5a, which will be useful for the development of pan-genotype anti-HCV compounds. PMID:24982066

  5. Complete Genome Sequence of Hepatitis B Virus Genotype E: The First Molecular Characterization from an Imported Case in Mexico

    PubMed Central

    Escobar-Escamilla, Noé; Fragoso-Fonseca, David Esaú; Arreguín-Porras, Dulce María; Esteban-Valencia, María del Carmen; Corona-Valdespino, Estela; Falcón-Acosta, Jaime Israel; Vázquez-Campuzano, Roberto; Garcés-Ayala, Fabiola; Ortiz-Alcantara, Joanna María; López-Martinez, Irma

    2016-01-01

    Hepatitis B virus infection is currently a global public health problem. Here, we present the first characterization and complete genome sequence of a strain belonging to genotype E in Mexico, obtained from a foreign carrier with chronic infection. PMID:27034495

  6. Complete Genome Sequence of Genotype VI Newcastle Disease Viruses Isolated from Pigeons in Pakistan

    PubMed Central

    Wajid, Abdul; Rehmani, Shafqat Fatima; Sharma, Poonam; Goraichuk, Iryna V.; Dimitrov, Kiril M.

    2016-01-01

    Two complete genome sequences of Newcastle disease virus (NDV) are described here. Virulent isolates pigeon/Pakistan/Lahore/21A/2015 and pigeon/Pakistan/Lahore/25A/2015 were obtained from racing pigeons sampled in the Pakistani province of Punjab during 2015. Phylogenetic analysis of the fusion protein genes and complete genomes classified the isolates as members of NDV class II, genotype VI. PMID:27540069

  7. Identification and Complete Genome Sequence Analysis of a Genotype XIV Newcastle Disease Virus from Nigeria.

    PubMed

    Shittu, Ismaila; Sharma, Poonam; Volkening, Jeremy D; Solomon, Ponman; Sulaiman, Lanre K; Joannis, Tony M; Williams-Coplin, Dawn; Miller, Patti J; Dimitrov, Kiril M; Afonso, Claudio L

    2016-01-01

    The first complete genome sequence of a strain of Newcastle disease virus (NDV) from genotype XIV is reported here. Strain duck/Nigeria/NG-695/KG.LOM.11-16/2009 was isolated from an apparently healthy domestic duck from a live bird market in Kogi State, Nigeria, in 2009. This strain is classified as a member of subgenotype XIVb of class II. PMID:26823576

  8. Identification and Complete Genome Sequence Analysis of a Genotype XIV Newcastle Disease Virus from Nigeria

    PubMed Central

    Shittu, Ismaila; Sharma, Poonam; Volkening, Jeremy D.; Solomon, Ponman; Sulaiman, Lanre K.; Joannis, Tony M.; Williams-Coplin, Dawn; Miller, Patti J.; Dimitrov, Kiril M.

    2016-01-01

    The first complete genome sequence of a strain of Newcastle disease virus (NDV) from genotype XIV is reported here. Strain duck/Nigeria/NG-695/KG.LOM.11-16/2009 was isolated from an apparently healthy domestic duck from a live bird market in Kogi State, Nigeria, in 2009. This strain is classified as a member of subgenotype XIVb of class II. PMID:26823576

  9. Complete genome sequence of an emerging genotype of tobacco streak virus in the United States.

    PubMed

    Padmanabhan, Chellappan; Gao, Shan; Li, Rugang; Zhang, Shouan; Fei, Zhangjun; Ling, Kai-Shu

    2014-01-01

    We report here the complete genome sequence of an emerging genotype of tobacco streak virus (TSV) infecting zucchini squash in Florida (TSV_FL13-07), obtained using deep sequencing of short RNAs (sRNAs) and validation by Sanger sequencing. TSV_FL13-07 shares only <90% sequence identity in all three genomic RNAs to several known U.S. isolates. PMID:25377714

  10. Complete Genome Sequence of Genotype VI Newcastle Disease Viruses Isolated from Pigeons in Pakistan.

    PubMed

    Wajid, Abdul; Rehmani, Shafqat Fatima; Sharma, Poonam; Goraichuk, Iryna V; Dimitrov, Kiril M; Afonso, Claudio L

    2016-01-01

    Two complete genome sequences of Newcastle disease virus (NDV) are described here. Virulent isolates pigeon/Pakistan/Lahore/21A/2015 and pigeon/Pakistan/Lahore/25A/2015 were obtained from racing pigeons sampled in the Pakistani province of Punjab during 2015. Phylogenetic analysis of the fusion protein genes and complete genomes classified the isolates as members of NDV class II, genotype VI. PMID:27540069

  11. Virulence correlates with fitness in vivo for two M group genotypes of Infectious hematopoietic necrosis virus (IHNV).

    USGS Publications Warehouse

    Wargo, Andrew R.; Garver, Kyle A.; Kurath, Gael

    2010-01-01

    The nature of the association between viral fitness and virulence remains elusive in vertebrate virus systems, partly due to a lack of in vivo experiments using statistically sufficient numbers of replicate hosts. We examined the relationship between virulence and fitness in Infectious hematopoietic necrosis virus (IHNV), in vivo, in intact living rainbow trout. Trout were infected with a high or low virulence genotype of M genogroup IHNV, or a mixture of the two genotypes, so as to calculate relative fitness and the effect of a competition environment on fitness. Fitness was measured as total viral load in the host at time of peak viral density, quantified by genotype-specific quantitative RT-PCR (qRT-PCR). The more virulent IHNV genotype reached higher densities in both single and mixed infections. There was no effect of competition on the performance of either genotype. Our results suggest a positive link between IHNV genotype fitness and virulence.

  12. Production and characterization of a Brazilian candidate antigen for Hepatitis E Virus genotype 3 diagnosis.

    PubMed

    de Almeida Ramos, Denise; Miani, Michela; Pandolfi, Rafael; Tondo, Luis; Colli, Maikel L; Rosado Spilki, Fernando; Rovaris Gardinali, Noemi; Alves Pinto, Marcelo; Kreutz, Luiz C; Frandoloso, Rafael

    2016-03-01

    Hepatitis E, caused by hepatitis E virus (HEV), is a viral infectious pathology of great importance in the public health. Hepatitis E outbreaks were registered in developing countries with poor or no sanitation, where drinking water was contaminated with fecal material, but also in many industrialized countries probably due to consumption of HEV-positive swine meat. In this study, we present the development and characterization of a recombinant antigen from ORF2 HEV genotype 3. Viral RNA was extracted from swine feces infected with the native virus. A total of 267 residues from the C-terminal ORF2((394-661)) coding sequence were cloned into the pET20a vector and expressed in Escherichia coli ER2566. Recombinant protein was purified by liquid chromatography and the fragment obtained a 98% homology against other human or swine HEV genotype 3 ORF2 sequences. Wistar rats were inoculated with ORF2p, developing antibodies able to recognize both the homologous antigen and the native HEV genotype 3 ORF2 present in infected stool. In parallel, HEV-negative swine were experimentally challenged with HEV genotype 3. ORF2 was detected by PCR 14 days post-inoculation in three-fourth piglets' feces and one week later by dot blot. In conclusion, this study proved the immunogenic and antigenic properties of the recombinant protein ORF2p. PMID:26832642

  13. Human papillomavirus genotypes in human immunodeficiency virus-positive patients with anal pathology in Madrid, Spain

    PubMed Central

    2013-01-01

    Background We studied anal specimens to determine the distribution of human papillomavirus (HPV) genotypes and co-infection occurrence. This information will contribute to the knowledge of HPV genotype distributions and provide an estimate of the prevalence of different oncogenic HPV genotypes found in patients in Madrid (Spain). Methods We studied a total of 82 anal biopsies from the Hospital General Universitario Gregorio Marañón of Madrid. These included 4 specimens with benign lesions, 52 specimens with low-grade anal squamous intraepithelial lesion, 24 specimens with high-grade anal squamous intraepithelial lesions and 2 specimens with invasive anal carcinoma. HPV genotyping was performed with PCR amplification and reverse dot blot hybridization. Results We detected 33 different HPV genotypes, including 16 HPVs associated with a high risk of carcinogenesis, 3 HPVs associated with a highly likely risk of carcinogenesis and 14 HPVs associated with a low-risk of carcinogenesis. In two specimens, an uncharacterized HPV genotype was detected. The most frequent HPV genotypes found were HPV-16 (10.3%; 95% CI: 6.6%-15.1%), HPV-52 (8.5%; 95% CI: 5.2%-13%) and HPV-43/44 (7.6%; 95% CI: 4.5%-11.9%). HPV-18 was only detected in 0.9% (95% CI: 0.1%-3.2%) of the total viruses detected in all lesions. HPV co-infections were found in 83.9% of all types of lesions. The majority of cases (90.2%) were concomitantly infected with the human immunodeficiency virus (HIV). Conclusion The prevalence of high-risk carcinogenic genotypes in anal pathological samples was remarkable. Therefore, further studies that include a greater number of samples, particularly invasive carcinoma cases are needed to evaluate the potential influence of these HPV genotypes in the appearance of anal carcinomas. Also, the influence of other accompanying infections should be evaluated clarify the appearance of this type of carcinoma. Virtual slides The virtual slide(s) for this article can be found here

  14. Persistent infection and promiscuous recombination of multiple genotypes of an RNA virus within a single host generate extensive diversity.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recombination and reassortment of viral genomes are major processes contributing to emerging viruses. These processes are especially significant in long-term persistent infections where multiple viral genotypes co-replicate in a single host, generating abundant genotypic variants, some of which may ...

  15. Complete Nucleotide Sequence of a New Genotype of Citrus Tristeza Virus from an Isolate Having a Mixed Infection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An isolate of Citrus tristeza virus (CTV) that causes severe stem pitting in grapefruits (# 3800) was used for sequencing. Analysis of the isolate revealed the presence of at least three different populations, one belonging to T30 genotype and the other two belonging to new genotypes, designated T2K...

  16. Replication of a chronic hepatitis B virus genotype F1b construct.

    PubMed

    Hernández, Sergio; Jiménez, Gustavo; Alarcón, Valentina; Prieto, Cristian; Muñoz, Francisca; Riquelme, Constanza; Venegas, Mauricio; Brahm, Javier; Loyola, Alejandra; Villanueva, Rodrigo A

    2016-03-01

    Genotype F is one of the less-studied genotypes of human hepatitis B virus, although it is widely distributed in regions of Central and South American. Our previous studies have shown that HBV genotype F is prevalent in Chile, and phylogenetic analysis of its full-length sequence amplified from the sera of chronically infected patients identified it as HBV subgenotype F1b. We have previously reported the full-length sequence of a HBV molecular clone obtained from a patient chronically infected with genotype F1b. In this report, we established a system to study HBV replication based on hepatoma cell lines transfected with full-length monomers of the HBV genome. Culture supernatants were analyzed after transfection and found to contain both HBsAg and HBeAg viral antigens. Consistently, fractionated cell extracts revealed the presence of viral replication, with both cytoplasmic and nuclear DNA intermediates. Analysis of HBV-transfected cells by indirect immunofluorescence or immunoelectron microscopy revealed the expression of viral antigens and cytoplasmic viral particles, respectively. To test the functionality of the ongoing viral replication further at the level of chromatinized cccDNA, transfected cells were treated with a histone deacetylase inhibitor, and this resulted in increased viral replication. This correlated with changes posttranslational modifications of histones at viral promoters. Thus, the development of this viral replication system for HBV genotype F will facilitate studies on the regulation of viral replication and the identification of new antiviral drugs. PMID:26620585

  17. Injecting drug use: A vector for the introduction of new hepatitis C virus genotypes

    PubMed Central

    Ruta, Simona; Cernescu, Costin

    2015-01-01

    Hepatitis C virus (HCV) genotypes’ monitoring allows real-time insight into the dynamic changes that occur in the global epidemiological picture of HCV infection. Intravenous drug use is currently the primary driver for HCV transmission in developed and developing countries. The distribution of HCV genotypes/subtypes differs significantly between people who inject drugs (PWID) and the general population. HCV genotypes that previously exhibited a limited geographical distribution (3a, 4) are becoming more prevalent in this high-risk group. Immigration from HCV-endemic countries and the evolving networks of HCV transmission in PWID influence HCV genotypes distribution in Europe. Social vulnerabilities (e.g., unemployment, homelessness, and limited access to social and healthcare insurances systems) are important triggers for illicit drug use, which increases the associated risks of HCV infection and the frequent emergence of less prevalent genotypes. Genotype/subtype determination bears important clinical consequences in the progression of liver disease, susceptibility to antiviral therapies and the emergence of resistance-associated variants. An estimated half of the chronically HCV-infected PWID are unaware of their infection, and only one in ten of those diagnosed enter treatment. Nevertheless, PWID exhibit high response rates to new antiviral regimens, and the level of HCV reinfection is unexpectedly low. The focus of the healthcare system must be on the early detection and treatment of infection, to avoid late presentations that are associated with high levels of viremia and liver fibrosis, which may diminish the therapeutic success rate. PMID:26478672

  18. Ledipasvir/sofosbuvir fixed-dose combination for treatment of hepatitis C virus genotype 4 infection.

    PubMed

    Nehra, V; Tan, E M; Rizza, S A; Temesgen, Z

    2016-02-01

    Hepatitis C virus (HCV) genotype 4 accounts for 8-13% of all chronic HCV infections worldwide. Patients with HCV genotype 4 have been reported to have poor treatment responses to PEGylated interferon and ribavirin regimens. Recently a single tablet, fixed-dose combination of sofosbuvir, an RNA-directed RNA polymerase (NS5B) inhibitor, and ledipasvir, a nonstructural protein 5A (NS5A) inhibitor, has been approved for treatment of chronic HCV infection. Two studies using the fixed-dose combination in chronic HCV genotype 4 for 12 weeks reported sustained virologic response rates at 12 weeks (SVR12) of 93-95%. Data also support the use of ledipasvir/sofosbuvir in chronic HCV genotype 4 and HIV co-infection. Administered as a single once-daily oral regimen, this ribavirin- and interferon-free regimen is well tolerated, with low potential for adverse effects and represents a significant advancement in the treatment of chronic HCV genotype 4 infection. PMID:27092340

  19. Hepatitis C virus: epidemiology and genotypes in the north east of England.

    PubMed Central

    Watson, J P; Brind, A M; Chapman, C E; Bates, C L; Gould, F K; Johnson, S J; Burt, A D; Ferguson, J; Simmonds, P; Bassendine, M F

    1996-01-01

    The epidemiology of hepatitis C virus (HCV) infection was studied in an English teaching hospital over an 18 month period. A total of 104 HCV antibody positive patients were referred for further investigation. They were divided into those diagnosed through screening (blood donors and intravenous drug abusers) and those diagnosed for other reasons, and their mean ages, known risk factors for HCV transmission, genotypes, and liver biopsy histology were analysed. Screened patients were significantly younger than the others. No significant difference in age was found between genotypes. Most patients genotyped (69%) were genotype 1. Intravenous drug abusers had a higher proportion of subtype 1a, and patients who acquired HCV through blood transfusion had a higher proportion of subtype 1b. Liver biopsy specimens were scored using a histological activity index for liver inflammation and fibrosis. Patients with subtype 1b had significantly more severe liver disease than other genotypes when the histological activity index scores for fibrosis were analysed (p < 0.05). Liver disease worsened significantly with age according to all three histological activity index scores (portal activity: p < 0.01, acinar activity: p < 0.001, fibrosis: p < 0.0001). Liver disease worsened with increased duration of infection (p < 0.002), and patients who also abused alcohol presented at a significantly younger age (cirrhosis, p < 0.05, hepatocellular carcinoma, p < 0.02). PMID:8801210

  20. Heminested PCR assay for detection of six genotypes of rabies and rabies-related viruses.

    PubMed Central

    Heaton, P R; Johnstone, P; McElhinney, L M; Cowley, R; O'Sullivan, E; Whitby, J E

    1997-01-01

    A heminested reverse transcriptase PCR (hnRT-PCR) protocol which is rapid and sensitive for the detection of rabies virus and rabies-related viruses is described. Sixty isolates from six of the seven genotypes of rabies and rabies-related viruses were screened successfully by hnRT-PCR and Southern blot hybridization. Of the 60 isolates, 93% (56 of 60) were positive by external PCR, while all isolates were detected by heminested PCR and Southern blot hybridization. We also report on a comparison of the sensitivity of the standard fluorescent-antibody test (FAT) for rabies antigen and that of hnRT-PCR for rabies viral RNA with degraded tissue infected with a genotype 1 virus. Results indicated that FAT failed to detect viral antigen in brain tissue that was incubated at 37 degrees C for greater than 72 h, while hnRT-PCR detected viral RNA in brain tissue that was incubated at 37 degrees C for 360 h. PMID:9350729

  1. Genotype Characterization of Commonly Used Newcastle Disease Virus Vaccine Strains of India

    PubMed Central

    Gaikwad, Satish; Kataria, Jag Mohan; Vakharia, Vikram N.

    2014-01-01

    Newcastle disease is an avian pathogen causing severe economic losses to the Indian poultry industry due to recurring outbreaks in vaccinated and unvaccinated flocks. India being an endemic country, advocates vaccination against the virus using lentogenic and mesogenic strains. Two virus strains which are commonly used for vaccination are strain F (a lentogenic virus) and strain R2B (a mesogenic virus). Strain F is given to 0–7 days old chicks and R2B is given to older birds which are around 6–8 weeks old. To understand the genetic makeup of these two strains, a complete genome study and phylogenetic analysis of the F, HN genes of these vaccine strains were carried out. Both the viral strains had a genome length of 15,186 nucleotides and consisted of six genes with conserved complimentary 3' leader and 5' trailer regions. The fusion protein cleavage site of strain F is GGRQGRL and strain R2B is RRQKRF. Although both the viral strains had different virulence attributes, the length of the HN protein was similar with 577 amino acids. Phylogenetic analysis of F, HN and complete genome sequences grouped these two strains in genotype II category which are considered as early genotypes and corroborated with their years of isolation. PMID:24897503

  2. Hepatitis C Virus Genotype Diversity among Intravenous Drug Users in Yunnan Province, Southwestern China

    PubMed Central

    Wu, Wenlong; Feng, Ruilin; Wu, Zhongxiang; Cun, Wei; Dong, Shaozhong

    2013-01-01

    Background Recently, high proportions (15.6%–98.7%) of intravenous drug users (IDUs) in China were found to be positive for hepatitis C virus (HCV). Yunnan Province is located in southwestern China and borders one of the world's most important opium-producing regions, thus it is an important drug trafficking route to other regions of China. Methodology/Principal Findings Here, we assessed 100 HCV-positive plasma samples from IDUs who were enrolled through the Kunming Center for Disease Control and Prevention in 2012. HCV C/E1 fragments were PCR-amplified and sequenced. We identified eight HCV subtypes (1a, 1b, 3a, 3b, 6a, 6n, 6u and 6v), of which genotype 6 was most predominant (frequency, 47%) followed by genotypes 3 (41%) and 1 (12%). HCV subtypes 6n (30%) and 3b (29%) were most common and were identified in 59% of the IDUs. We compared HCV genotypes among IDUs in Yunnan Province with those from other regions and found that the distribution patterns of HCV genotypes in Yunnan Province were similar to those in southern China, but different from those in eastern China. However, the distribution patterns of HCV subtypes varied among Yunnan Province and southern China, despite the shared similar genotypes. A comparison of the current data with those previously reported showed that the frequency of HCV genotype 6 increased from 25% to 47% within 5 years, especially subtypes 6a (5% to 15%) and 6n (11.2% to 30%). In contrast, the frequencies of subtypes 3b and 1b decreased by almost 50% within 5 years. Conclusion/Significance Our results provided further information to support the assertion that drug trafficking routes influence HCV transmission patterns among IDUs in Yunnan Province. The frequency of HCV genotypes and subtypes changed rapidly among IDUs in Yunnan Province and subtypes 6a and 6n may have originated in Vietnam and Myanmar, respectively. PMID:24358211

  3. Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015.

    PubMed

    Seger, Waleed; GhalyanchiLangeroudi, Arash; Karimi, Vahid; Madadgar, Omid; Marandi, Mehdi Vasfi; Hashemzadeh, Masoud

    2016-05-01

    Infectious bronchitis virus (IBV) is one of the most critical pathogens in the poultry industry, causing serious economic losses in all countries including Iraq. IBV has many genotypes that do not confer any cross-protection. This virus has been genotyped by sequence analysis of the S1 glycoprotein gene. A total of 100 tracheal and kidney tissue specimens from different commercial broiler flocks in the middle and south of Iraq were collected from September 2013 to September 2014. Thirty-two IBV-positive samples were selected from among the total and were further characterized by nested PCR. Phylogenetic analysis revealed that isolates belong to four groups (group I, variant 2 [IS/1494-like]; group II, 793/B-like; group III, QX-like; group IV, DY12-2-like). Sequence analysis revealed nucleotide sequence identities within groups I, II, and III of 99.68 %-100 %, 99.36 %-100 %, and 96.42 %-100 %, respectively. Group I (variant 2) was the dominant IBV genotype. One Chinese-like recombinant virus (DY12-2-like) that had not been reported in the Middle East was detected. In addition, the presence of QX on broiler chicken farms in the area studied was confirmed. This is the first comprehensive study on the genotyping of IBV in Iraq with useful information regarding the molecular epidemiology of IBV. The phylogenetic relationship of the strains with respect to different time sequences and geographical regions displayed complexity and diversity. Further studies are needed and should include the isolation and full-length molecular characterization of IBV in this region. PMID:26887967

  4. Phenotypic and genotypic characterization of influenza virus mutants selected with the sialidase fusion protein DAS181

    PubMed Central

    Triana-Baltzer, Gallen B.; Sanders, Rebecca L.; Hedlund, Maria; Jensen, Kellie A.; Aschenbrenner, Laura M.; Larson, Jeffrey L.; Fang, Fang

    2011-01-01

    Background Influenza viruses (IFVs) frequently achieve resistance to antiviral drugs, necessitating the development of compounds with novel mechanisms of action. DAS181 (Fludase®), a sialidase fusion protein, may have a reduced potential for generating drug resistance due to its novel host-targeting mechanism of action. Methods IFV strains B/Maryland/1/59 and A/Victoria/3/75 (H3N2) were subjected to >30 passages under increasing selective pressure with DAS181. The DAS181-selected IFV isolates were characterized in vitro and in mice. Results Despite extensive passaging, DAS181-selected viruses exhibited a very low level of resistance to DAS181, which ranged between 3- and 18-fold increase in EC50. DAS181-selected viruses displayed an attenuated phenotype in vitro, as exhibited by slower growth, smaller plaque size and increased particle to pfu ratios relative to wild-type virus. Further, the DAS181 resistance phenotype was unstable and was substantially reversed over time upon DAS181 withdrawal. In mice, the DAS181-selected viruses exhibited no greater virulence than their wild-type counterparts. Genotypic and phenotypic analysis of DAS181-selected viruses revealed mutations in the haemagglutinin (HA) and neuraminidase (NA) molecules and also changes in HA and NA function. Conclusions Results indicate that resistance to DAS181 is minimal and unstable. The DAS181-selected IFV isolates exhibit reduced fitness in vitro, likely due to altered HA and NA functions. PMID:21097900

  5. Novel Cell Culture-Adapted Genotype 2a Hepatitis C Virus Infectious Clone

    PubMed Central

    Date, Tomoko; Kato, Takanobu; Kato, Junko; Takahashi, Hitoshi; Morikawa, Kenichi; Akazawa, Daisuke; Murayama, Asako; Tanaka-Kaneko, Keiko; Sata, Tetsutaro; Tanaka, Yasuhito; Mizokami, Masashi

    2012-01-01

    Although the recently developed infectious hepatitis C virus system that uses the JFH-1 clone enables the study of whole HCV viral life cycles, limited particular HCV strains have been available with the system. In this study, we isolated another genotype 2a HCV cDNA, the JFH-2 strain, from a patient with fulminant hepatitis. JFH-2 subgenomic replicons were constructed. HuH-7 cells transfected with in vitro transcribed replicon RNAs were cultured with G418, and selected colonies were isolated and expanded. From sequencing analysis of the replicon genome, several mutations were found. Some of the mutations enhanced JFH-2 replication; the 2217AS mutation in the NS5A interferon sensitivity-determining region exhibited the strongest adaptive effect. Interestingly, a full-length chimeric or wild-type JFH-2 genome with the adaptive mutation could replicate in Huh-7.5.1 cells and produce infectious virus after extensive passages of the virus genome-replicating cells. Virus infection efficiency was sufficient for autonomous virus propagation in cultured cells. Additional mutations were identified in the infectious virus genome. Interestingly, full-length viral RNA synthesized from the cDNA clone with these adaptive mutations was infectious for cultured cells. This approach may be applicable for the establishment of new infectious HCV clones. PMID:22787209

  6. Evolutionary genetics of genotype H1 measles viruses in China from 1993 to 2012

    PubMed Central

    Xu, Songtao; Zhang, Yan; Rivailler, Pierre; Wang, Huiling; Ji, Yixin; Zhen, Zhu; Mao, Naiying; Li, Chongshan; Bellini, William J.

    2014-01-01

    Virologic surveillance is a critical component of measles management. One of the criteria for verification of elimination of endemic measles is genetic analysis of wild-type viruses to demonstrate lack of an indigenous genotype. Measles is yet to be eliminated in China, and genotype H1 has been detected continuously since virologic surveillance was initiated in 1993. Virologic surveillance has been very active in China, providing a unique opportunity to conduct a detailed study of the evolution of a single, endemic genotype over a timespan of nearly two decades. Phylogenetic analysis performed on the 450 nt coding sequence for the C-terminal 150 amino acids of the nucleoprotein (N-450), fusion (F) gene and haemagglutinin (H) gene confirmed the continued circulation of genotype H1 viruses for 19 years. No evidence of selective pressure for the H protein was found. The substitution rates ranged from 0.75×10−3 substitutions site−1 year−1 for H to 1.65×10−3 substitutions site−1 year−1 for N-450. The time of most recent common ancestor (TMRCA) for genotype H1 was estimated as approximately 1985 (95 % highest probability density, 1979–1989). Finally, the overall diversity of measles sequences from China decreased from 2005 to 2012, coincident with a substantial decrease in measles cases. The results suggest that detailed evolutionary analyses should facilitate the documentation of eventual measles elimination in China. Moreover, the molecular approaches used in this study can be applied in other countries approaching measles elimination. PMID:24914068

  7. Pepino mosaic virus genotype shift in North America and development of a loop-mediated isothermal amplification for rapid genotype identification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pepino mosaic, once an emerging disease a decade ago, has become endemic on greenhouse tomatoes worldwide in recent years. Three distinct genotypes of Pepino mosaic virus (PepMV), including EU, US1 and CH2 have been recognized. Our earlier study conducted in 2006-2007 demonstrated a predominant EU...

  8. A Genetic Variant of Hepatitis B Virus Divergent from Known Human and Ape Genotypes Isolated from a Japanese Patient and Provisionally Assigned to New Genotype J▿ †

    PubMed Central

    Tatematsu, Kanako; Tanaka, Yasuhito; Kurbanov, Fuat; Sugauchi, Fuminaka; Mano, Shuhei; Maeshiro, Tatsuji; Nakayoshi, Tomokuni; Wakuta, Moriaki; Miyakawa, Yuzo; Mizokami, Masashi

    2009-01-01

    Hepatitis B virus (HBV) of a novel genotype (J) was recovered from an 88-year-old Japanese patient with hepatocellular carcinoma who had a history of residing in Borneo during the World War II. It was divergent from eight human (A to H) and four ape (chimpanzee, gorilla, gibbon, and orangutan) HBV genotypes, as well as from a recently proposed ninth human genotype I, by 9.9 to 16.5% of the entire genomic sequence and did not have evidence of recombination with any of the nine human genotypes and four nonhuman genotypes. Based on a comparison of the entire nucleotide sequence against 1,440 HBV isolates reported, HBV/J was nearest to the gibbon and orangutan genotypes (mean divergences of 10.9 and 10.7%, respectively). Based on a comparison of four open reading frames, HBV/J was closer to gibbon/orangutan genotypes than to human genotypes in the P and large S genes and closest to Australian aboriginal strains (HBV/C4) and orangutan-derived strains in the S gene, whereas it was closer to human than ape genotypes in the C gene. HBV/J shared a deletion of 33 nucleotides at the start of preS1 region with C4 and gibbon genotypes, had an S-gene sequence similar to that of C4, and expressed the ayw subtype. Efficient infection, replication, and antigen expression by HBV/J were experimentally established in two chimeric mice with the liver repopulated for human hepatocytes. The HBV DNA sequence recovered from infected mice was identical to that in the inoculum. Since HBV/J is positioned phylogenetically in between human and ape genotypes, it may help to trace the origin of HBV and merits further epidemiological surveys. PMID:19640977

  9. New insights into the hepatitis E virus genotype 3 phylodynamics and evolutionary history.

    PubMed

    Mirazo, Santiago; Mir, Daiana; Bello, Gonzalo; Ramos, Natalia; Musto, Héctor; Arbiza, Juan

    2016-09-01

    Hepatitis E virus (HEV) is an emergent hepatotropic virus endemic mainly in Asia and other developing areas. However, in the last decade it has been increasingly reported in high-income countries. Human infecting HEV strains are currently classified into four genotypes (1-4). Genotype 3 (HEV-3) is the prevalent virus genotype and the mostly associated with autochthonous and sporadic cases of HEV in developed areas. The evolutionary history of HEV worldwide remains largely unknown. In this study we reconstructed the spatiotemporal and population dynamics of HEV-3 at global scale, but with particular emphasis in South America, where case reports have increased dramatically in the last years. To achieve this, we applied a Bayesian coalescent-based approach to a comprehensive data set comprising 97 GenBank HEV-3 sequences for which the location and sampling date was documented. Our phylogenetic analyses suggest that the worldwide genetic diversity of HEV-3 can be grouped into two main Clades (I and II) with a Ƭmrca dated in approximately 320years ago (95% HPD: 420-236years) and that a unique independent introduction of HEV-3 seems to have occurred in Uruguay, where most of the human HEV cases in South America have been described. The phylodynamic inference indicates that the population size of this virus suffered substantial temporal variations after the second half of the 20th century. In this sense and conversely to what is postulated to date, we suggest that the worldwide effective population size of HEV-3 is not decreasing and that frequently sources of error in its estimates stem from assumptions that the analyzed sequences are derived from a single panmictic population. Novel insights on the global population dynamics of HEV are given. Additionally, this work constitutes an attempt to further describe in a Bayesian coalescent framework, the phylodynamics and evolutionary history of HEV-3 in the South American region. PMID:27264728

  10. Middle ear squamous papilloma: A report of four cases analyzed by HPV and EBV in situ hybridization

    PubMed Central

    ZHOU, HAN; CHEN, ZHIBIN; ZHANG, WEIMING; XING, GUANGQIAN

    2014-01-01

    Squamous papilloma involving the middle ear as a primary lesion is an extremely rare occurrence. The aims of the present study were to investigate the presence of human papilloma virus (HPV) and Epstein-Barr virus (EBV) infections in primary middle ear squamous papilloma and to describe the clinical and pathological features of the disease along with therapeutic strategies. A retrospective review was conducted of four patients with clinical and pathological diagnoses of middle ear squamous papilloma. In situ hybridization (ISH) for a wide range of HPV DNA subtypes and EBV-encoded RNA was performed in the tissue samples obtained from these patients. Only two cases of primary squamous papilloma in the middle ear have been previously reported in the English literature. These papillomas developed in males of ~60-years of age and otorrhea was the most frequent complaint. Premalignant changes were observed in two of the present cases and ISH of HPV and EBV was negative in all four cases. The results of the present study indicated that chronic inflammatory stimulation, not HPV and EBV infection, is involved in the occurrence of middle ear squamous papilloma and its malignant transformation. Radical surgery and long-term postoperative follow-up are recommended due to its malignant and recurrent potential. Further genetic investigations with additional new cases are required to clarify the pathogenesis of squamous papilloma involving the middle ear. PMID:24348817

  11. Phylogeography and molecular epidemiology of hepatitis C virus genotype 2 in Africa.

    PubMed

    Markov, Peter V; Pepin, Jacques; Frost, Eric; Deslandes, Sylvie; Labbé, Annie-Claude; Pybus, Oliver G

    2009-09-01

    Understanding the origin and nature of hepatitis C virus (HCV) genetic diversity is critical for improving treatment and vaccine design, and such diversity is the sole source of information about the virus' epidemic history prior to its identification 20 years ago. In this paper, we study the molecular epidemiology of HCV genotype 2 in its region of endemic origin, west and central Africa. Our analysis includes 56 new and highly diverse HCV isolates sampled from infected individuals in Guinea-Bissau. By combining phylogenetic, geographical and epidemiological information, we find a previously unappreciated geographical structure in the diversity of HCV genotype 2, pointing to a history of eastwards spatial spread from the west African coast to Cameroon that took place over several centuries. Molecular clock analysis dates the common ancestor of HCV in Guinea-Bissau to 1470 (1414-1582). The phylogenetic position of isolates from Madagascar and Martinique suggests a role for the historical slave trade in the global dissemination of HCV and of the epidemic subtypes 2a and 2c. Coalescent-based estimates of epidemic growth indicate a rapid 20th-century spread of HCV genotype 2 in Cameroon that is absent in Guinea-Bissau. We discuss this contrast in the context of possible parenteral HCV exposure during public-health campaigns undertaken during the colonial era. PMID:19474244

  12. Imported Genotype 2B Rubella Virus Caused the 2012 Outbreak in Anqing City, China

    PubMed Central

    Dai, Jingjing; Chen, Xia; Tang, Jihai; Chen, Shuping; Zheng, Yilun; Song, Jie; Xu, Wenbo

    2015-01-01

    A rubella outbreak occurred in Anqing city of Anhui province, China, from February to July of 2012, and a total of 241 clinically diagnosed or lab-confirmed patients were reported. The highest number of rubella cases during this outbreak was recorded in teenagers between 10 and 19 years of age who had not previously received the rubella vaccine. Genotyping results indicated that the genotype 2B rubella virus (RV) was responsible for the outbreak. However, a phylogenetic analysis showed that the genotype 2B RVs isolated in Anqing City were not related to 2B RVs found in other cities of Anhui province and in other provinces of China, thus providing evidence for importation. After importation, the transmission of Anqing RVs was interrupted owing to an effective immunization campaign against rubella, suggesting the timeliness and effectiveness of contingency vaccination. Strengthening rubella surveillance, including the integration of epidemiologic information and laboratory data, is a vital strategy for rubella control and elimination. In addition, except for routine immunization, targeted supplementary immunization activities aimed at susceptible groups according to sero-epidemiological surveillance data also play a key role in stopping the continuous transmission of rubella viruses and in preventing further congenital rubella syndrome cases. PMID:26402467

  13. The clinical implications of hepatitis B virus genotypes and HBeAg in pediatrics.

    PubMed

    Kramvis, Anna

    2016-07-01

    Although a successful vaccine against HBV has been implemented in 184 countries, eradication of hepatitis B virus (HBV) is still not on the horizon. There are over 240 million chronic carriers of HBV globally. The risk of developing chronic hepatitis ranges from >90% in newborns of hepatitis Be antigen (HBeAg)-positive mothers, 25%-35% in children under 5 years of age and <5% in adults. HBeAg, a non-particulate viral protein, is a marker of HBV replication. This is the only HBV antigen to cross the placenta, leading to specific unresponsiveness of helper T cells to the capsid protein and HBeAg in newborns. HBeAg is tolerated in utero and acts as a tolerogen after birth. Perinatal transmission is frequent when mothers are HBeAg-positive, whereas it occurs less frequently when mothers are HBeAg-negative. Sequence heterogeneity is a feature of HBV. Based on an intergroup divergence >7.5% across the complete genome, HBV is classified phylogenetically into at least nine genotypes. With between ~4% and 8% intergroup nucleotide divergence, genotypes A-D, F, H and I are classified further into subgenotypes. HBV genotypes/subgenotypes may have distinct geographical distribution and can develop different mutations in the regions of the HBV genome that code for HBeAg. These differences can be related to the role of HBV genotypes to the natural history of infection and mode of transmission. Thus genotypes/subgenotypes of HBV can be responsible for the different natural history of infection and modes of transmission in children, found in various regions of the world, where different genotypes/subgenotypes prevail. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27139263

  14. Comparison of Genotypes I and III in Japanese Encephalitis Virus Reveals Distinct Differences in Their Genetic and Host Diversity

    PubMed Central

    Han, Na; Adams, James; Chen, Ping; Guo, Zhen-yang; Zhong, Xiang-fu; Fang, Wei; Li, Na; Wen, Lei; Tao, Xiao-yan; Yuan, Zhi-ming

    2014-01-01

    ABSTRACT Japanese encephalitis (JE) is an arthropod-borne disease associated with the majority of viral encephalitis cases in the Asia-Pacific region. The causative agent, Japanese encephalitis virus (JEV), has been phylogenetically divided into five genotypes. Recent surveillance data indicate that genotype I (GI) is gradually replacing genotype III (GIII) as the dominant genotype. To investigate the mechanism behind the genotype shift and the potential consequences in terms of vaccine efficacy, human cases, and virus dissemination, we collected (i) all full-length and partial JEV molecular sequences and (ii) associated genotype and host information comprising a data set of 873 sequences. We then examined differences between the two genotypes at the genetic and epidemiological level by investigating amino acid mutations, positive selection, and host range. We found that although GI is dominant, it has fewer sites predicted to be under positive selection, a narrower host range, and significantly fewer human isolates. For the E protein, the sites under positive selection define a haplotype set for each genotype that shows striking differences in their composition and diversity, with GIII showing significantly more variety than GI. Our results suggest that GI has displaced GIII by achieving a replication cycle that is more efficient but is also more restricted in its host range. IMPORTANCE Japanese encephalitis is an arthropod-borne disease associated with the majority of viral encephalitis cases in the Asia-Pacific region. The causative agent, Japanese encephalitis virus (JEV), has been divided into five genotypes based on sequence similarity. Recent data indicate that genotype I (GI) is gradually replacing genotype III (GIII) as the dominant genotype. Understanding the reasons behind this shift and the potential consequences in terms of vaccine efficacy, human cases, and virus dissemination is important for controlling the spread of the virus and reducing human

  15. Rescue of a genotype 4 human hepatitis E virus from cloned cDNA and characterization of intergenotypic chimeric viruses in cultured human liver cells and in pigs

    PubMed Central

    Córdoba, Laura; Feagins, Alicia R.; Opriessnig, Tanja; Cossaboom, Caitlin M.; Dryman, Barbara A.; Huang, Yao-Wei

    2012-01-01

    Hepatitis E virus (HEV) is an important but extremely understudied human pathogen. Genotypes 1 and 2 are restricted to humans, whereas genotypes 3 and 4 are zoonotic, infecting both humans and pigs. This report describes, for the first time, the successful rescue of infectious HEV in vitro and in vivo from cloned cDNA of a genotype 4 human HEV (strain TW6196E). The complete genomic sequence of the TW6196E virus was determined and a full-length cDNA clone (pHEV-4TW) was assembled. Capped RNA transcripts from the pHEV-4TW clone were replication competent in Huh7 cells and infectious in HepG2/C3A cells. Pigs inoculated intrahepatically with capped RNA transcripts from pHEV-4TW developed an active infection, as evidenced by faecal virus shedding and seroconversion, indicating the successful rescue of infectious genotype 4 HEV and cross-species infection of pigs by a genotype 4 human HEV. To demonstrate the utility of the genotype 4 HEV infectious clone and to evaluate the potential viral determinant(s) for species tropism, four intergenotypic chimeric clones were constructed by swapping various genomic regions between genotypes 1 and 4, and genotypes 1 and 3. All four chimeric clones were replication competent in Huh7 cells, but only the two chimeras with sequences swapped between genotypes 1 and 4 human HEVs produced viruses capable of infecting HepG2/C3A cells. None of the four chimeras was able to establish a robust infection in pigs. The availability of a genotype 4 HEV infectious clone affords an opportunity to delineate the molecular mechanisms of HEV cross-species infection in the future. PMID:22837416

  16. First isolation and genotyping of viruses from recent outbreaks of viral haemorrhagic septicaemia (VHS) in Slovenia.

    PubMed

    Toplak, Ivan; Hostnik, Peter; Rihtaric, Danijela; Olesen, Niels Jørgen; Skall, Helle Frank; Jencic, Vlasta

    2010-10-26

    In November and December 2007, the virus causing viral haemorrhagic septicaemia (VHS) was detected in rainbow trout Oncorhynchus mykiss from 2 fish farms in Slovenia. During 2008 and 2009 the infection spread only among rainbow trout farms and 4 new outbreaks were confirmed. High mortality and clinical signs of VHS were observed among the diseased fish. VHSV was confirmed by virus isolation, immunoperoxidase test, reverse transcriptase polymerase chain reaction (RT-PCR) and phylogenetic analysis. Based on 1 complete (1524 nucleotides [nt]) and 9 partial (600 nt) glycoprotein gene nucleotide sequences, 9 VHSV isolates from the 6 VHS outbreaks were genetically closely related (99 to 100% identity), and were classified into the Subgroup I-a of Genotype I, most closely related to the German isolates Dstg21-07, Dstg36-06, and Dstg54-1-07 (99 to 100% identity). Phylogenetic analysis and epidemiological investigations confirmed that the VHS virus had been (re)introduced with imported live fish, and that subsequent outbreaks were linked to the initial infection. Our study shows that direct nucleotide sequencing of RT-PCR products, amplified from the tissue of VHSV-infected fish, represents a reliable tool for fast routine genotyping in diagnostic laboratories. This is the first report of a natural epidemic associated with VHSV infection in Slovenia since the eradication of the disease in 1977. PMID:21166311

  17. Specific Polymorphisms in Hepatitis C Virus Genotype 3 Core Protein Associated with Intracellular Lipid Accumulation

    PubMed Central

    Jhaveri, Ravi; McHutchison, John; Patel, Keyur; Qiang, Guan; Diehl, Anna Mae

    2008-01-01

    Background Steatosis is a common histological finding and a poor prognostic indicator in patients with hepatitis C virus (HCV) infection. In HCV genotype 3–infected patients, the etiology of steatosis appears to be closely correlated with unknown viral factors that increase intracellular lipid levels. We hypothesize that specific sequence polymorphisms in HCV genotype 3 core protein may be associated with hepatic intracellular lipid accumulation. Methods Using selected serum samples from 8 HCV genotype 3–infected patients with or without steatosis, we sequenced the HCV core gene to identify candidate polymorphisms associated with increased intracellular lipid levels. Results Two polymorphisms at positions 182 and 186 of the core protein correlated with the presence (P = .03) and absence (P = .005) of intrahepatic steatosis. Transfected liver cell lines expressing core protein with steatosis-associated polymorphisms had increased intracellular lipid levels compared with non–steatosis-associated core isolates, as measured by oil red O staining (P = .02). Site-specific mutagenesis performed at positions 182 and 186 in steatosis-associated core genes yielded proteins that had decreased intracellular lipid levels in transfected cells (P = .03). Conclusions We have identified polymorphisms in HCV core protein genotype 3 that produce increased intracellular lipid levels and thus may play a significant role in lipid metabolism or trafficking, contributing to steatosis. PMID:18177246

  18. The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing

    PubMed Central

    Linnstaedt, Sarah D.; Kasprzak, Wojciech K.; Shapiro, Bruce A.; Casey, John L.

    2006-01-01

    RNA editing plays a critical role in the life cycle of hepatitis delta virus (HDV). The host editing enzyme ADAR1 recognizes specific RNA secondary structure features around the amber/W site in the HDV antigenome and deaminates the amber/W adenosine. A previous report suggested that a branched secondary structure is necessary for editing in HDV genotype III. This branched structure, which is distinct from the characteristic unbranched rod structure required for HDV replication, was only partially characterized, and knowledge concerning its formation and stability was limited. Here, we examine the secondary structures, conformational dynamics, and amber/W site editing of HDV genotype III RNA using a miniaturized HDV genotype III RNA in vitro. Computational analysis of this RNA using the MPGAfold algorithm indicated that the RNA has a tendency to form both metastable and stable unbranched secondary structures. Moreover, native polyacrylamide gel electrophoresis demonstrated that this RNA forms both branched and unbranched rod structures when transcribed in vitro. As predicted, the branched structure is a metastable structure that converts readily to the unbranched rod structure. Only branched RNA was edited at the amber/W site by ADAR1 in vitro. The structural heterogeneity of HDV genotype III RNA is significant because not only are both conformations of the RNA functionally important for viral replication, but the ratio of the two forms could modulate editing by determining the amount of substrate RNA available for modification. PMID:16790843

  19. Hepatitis E Virus Genotype 3 in Colombia: Survey in Patients with Clinical Diagnosis of Viral Hepatitis

    PubMed Central

    Rendon, Julio; Hoyos, Maria Cristina; di Filippo, Diana; Cortes-Mancera, Fabian; Mantilla, Carolina; Velasquez, Maria Mercedes; Sepulveda, Maria Elsy; Restrepo, Juan Carlos; Jaramillo, Sergio; Arbelaez, Maria Patricia; Correa, Gonzalo; Navas, Maria-Cristina

    2016-01-01

    Background Hepatitis E virus is a major cause of outbreaks as well as sporadic hepatitis cases worldwide. The epidemiology of this enterically transmitted infection differs between developing and developed countries. The aims of this study were to describe HEV infection in Colombian patients and to characterize the genotype. Methods A prospective study was carried out on 40 patients aged over 15 with a clinical diagnosis of viral hepatitis, recruited from five primary health units in the city of Medellin, Colombia. Fecal samples obtained from the 40 consecutives cases were analyzed for HEV RNA using nested reverse transcription PCR for both ORF1 and ORF2-3. The amplicons were sequenced for phylogenetic analyses. Results Nine (22.5%) cases of HEV infection were identified in the study population. Three HEV strains obtained from patients were classified as genotype 3. No significant association was found between cases of Hepatitis E and the variables water drinking source, garbage collection system and contact with pigs. Conclusions This is the first prospective study of hepatitis E in Colombian patients. The circulation of the genotype 3 in this population is predictable considering the reports of the region and the identification of this genotype from pigs in the state of Antioquia, of which Medellin is the capital. Further studies are necessary to establish whether zoonotic transmission of HEV is important in Colombia. PMID:26886728

  20. Hepatitis B virus genotypes in southwest Iran: Molecular, serological and clinical outcomes

    PubMed Central

    Mojiri, Anahita; Behzad-Behbahani, Abbas; Saberifirozi, Mehdei; Ardabili, Maryam; Beheshti, Mahmood; Rahsaz, Marjan; Banihashemi, Mehrdad; Azarpira, Negar; Geramizadeh, Bita; Khadang, Baharak; Moaddeb, Afsaneh; Ghaedi, Mojgan; Heidari, Tahereh; Torab, Ardeshir; Salah, Alireza; Amirzadeh, Saeid; Jowkar, Zahra; Mehrabani, Davood; Amini-Bavil-Olyaee, Samad; Dehyadegari, Mohammad Ali

    2008-01-01

    AIM: To investigate the associations of hepatitis B virus (HBV) genotype with HBeAg and anti-HBe status, alanine aminotransferase (ALT) levels and HBV-DNA detection in different groups of HBV-infected patients in southwest Iran. METHODS: A total of 89 HBsAg-positive serum samples were collected from the same number of patients. All sera were then investigated to determine HBV DNA and serological markers. For all the polymerase chain reaction (PCR)-positive samples, biochemical, histopathological assays and genotyping were also performed. RESULTS: Genotype D was the only type of HBV found in different clinical forms of acute and chronic infections. There was a high prevalence of HBeAg-negative HBV-infected patients with chronic hepatitis (52.7%). Out of 55 patients with chronic hepatitis, seven (12.7%) were diagnosed with cirrhosis. A significant association between the presence of anti-HBe antibody and an increase in ALT level, among either HBeAg-negative (P = 0.01) or HBeAg-positive (P = 0.026) patients, was demonstrated. No significant differences were observed between the clinical outcomes of HBeAg-positive and -negative individuals (P = 0.24). CONCLUSION: Genotype D has been recognized as the only type of HBV found in different clinical forms of HBV infections, including cirrhosis, among the residents of southwest Iran. Anti-HBe possibly plays a role in disease progression in some patients with chronic hepatitis, at least for a period of disease. PMID:18330939

  1. Hepatitis C virus genotype 6: Virology, epidemiology, genetic variation and clinical implication

    PubMed Central

    Thong, Vo Duy; Akkarathamrongsin, Srunthron; Poovorawan, Kittiyod; Tangkijvanich, Pisit; Poovorawan, Yong

    2014-01-01

    Hepatitis C virus (HCV) is a serious public health problem affecting 170 million carriers worldwide. It is a leading cause of chronic hepatitis, cirrhosis, and liver cancer and is the primary cause for liver transplantation worldwide. HCV genotype 6 (HCV-6) is restricted to South China, South-East Asia, and it is also occasionally found in migrant patients from endemic countries. HCV-6 has considerable genetic diversity with 23 subtypes (a to w). Although direct sequencing followed by phylogenetic analysis is the gold standard for HCV-6 genotyping and subtyping, there are also now rapid genotyping tests available such as the reverse hybridization line probe assay (INNO-LiPA II; Innogenetics, Zwijnaarde, Belgium). HCV-6 patients present with similar clinical manifestations as patients infected with other genotypes. Based on current evidence, the optimal treatment duration of HCV-6 with pegylated interferon/ribavirin should be 48 wk, although a shortened treatment duration of 24 wk could be sufficient in patients with low pretreatment viral load who achieve rapid virological response. In addition, the development of direct-acting antiviral agents is ongoing, and they give high response rate when combined with standard therapy. Herein, we review the epidemiology, classification, diagnosis and treatment as it pertain to HCV-6. PMID:24659883

  2. Genotyping of clinical varicella-zoster virus isolates collected from Yunnan in Southwestern China

    PubMed Central

    LI, YUNLONG; ZHU, BAOSHENG

    2016-01-01

    Varicella-zoster virus (VZV) belongs to the α-herpesvirus family. Genetically, it is stable and is divided into several genotypes based upon the genetic variations. The genotypes of VZV are rarely studied in the Southwestern region of China. In the present study, the common genetic variations in the VZV genes were examined in 42 VZV isolates collected from the patients with herpes zoster in the Yunnan province (Southwestern China). The restriction fragment length polymorphism analysis of open reading frames (ORFs) 38, 54 and 62 in the VZV genes showed that all the collected VZV isolates were PstI, BglI and SmaI positive. The R5 variable-repeat region in these isolates was variable (R5A: 46.4%; R5B: 53.6%). The sequencing data of ORFs 1, 21, 22 and 54 indicated that 41 of the 42 collected VZV isolates could be grouped into genotype J or J1. Only one VZV isolate was identified as genotype A1 or M2. No new substitutions in the sequenced fragments were found in the collected VZV isolates. The results of the present study provided a preliminary genetic characterization of the VZV strains in the Yunnan province of Southwestern China. PMID:26893840

  3. Effects of challenge with a virulent genotype II strain of porcine reproductive and respiratory syndrome virus on piglets vaccinated with an attenuated genotype I strain vaccine.

    PubMed

    Roca, M; Gimeno, M; Bruguera, S; Segalés, J; Díaz, I; Galindo-Cardiel, I J; Martínez, E; Darwich, L; Fang, Y; Maldonado, J; March, R; Mateu, E

    2012-07-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) is endemic in most parts of Asia, where genotype I and II strains of diverse virulence may coexist. This study evaluated the outcome of infection with a highly virulent Asian genotype II PRRSV isolate in piglets vaccinated with a genotype I vaccine. Twenty-one 3-week-old piglets were divided in three groups: Pigs in group V (n=8) were vaccinated with an attenuated genotype I commercial PRRSV vaccine, while pigs in group U (n=8) and a control group (group C; n=5) were unvaccinated; 6 weeks later, pigs in groups V and U were challenged intranasally with a highly virulent strain of genotype II PRRSV (1×10(5) 50% tissue culture infectious doses/mL), while pigs in group C received a placebo. Over a period of 21 days after challenge, vaccinated pigs had significantly lower mortality (0/8 versus 2/8), fewer days of fever, a lower frequency of catarrhal bronchopneumonia, higher weight gains (13.4 versus 6.6 kg) and lower levels of viraemia compared to unvaccinated challenged pigs. Immunisation with a genotype I attenuated PRRSV vaccine provided partial protection against challenge with a highly virulent genotype II strain. PMID:22264642

  4. Genotyping of classical swine fever virus using high-resolution melt analysis.

    PubMed

    Titov, Ilya; Tsybanov, Sodnom; Malogolovkin, Alexander

    2015-11-01

    Discrimination between different field and vaccine strains of classical swine fever virus (CSFV) is crucial for meaningful disease diagnosis and epidemiological investigation. In this study, a rapid method for differentiating vaccine strains and outbreak CSFV isolates by combined RT-PCR and high-resolution melt (HRM) analysis has been developed. The assay is based on PCR amplification of short fragments from the most variable region of CSFVgene E2, followed by HRM analysis of amplicons. Real-Time PCR/HRM for CSFV detection and differentiation analysis has sensitivity comparable to RT-qPCR and genotyping resolution comparable to E2 nucleotide sequencing. This assay in one step enables rapid and sensitive identification and genotype discrimination of CSFV in field samples, and thus will be valuable for CSF outbreak response and disease control. PMID:26300371

  5. The relevance of dengue virus genotypes surveillance at country level before vaccine approval.

    PubMed

    Usme-Ciro, José A; Méndez, Jairo A; Laiton, Katherine D; Páez, Andrés

    2014-01-01

    Dengue is a major threat for public health in tropical and subtropical countries around the world. In the absence of a licensed vaccine and effective antiviral therapies, control measures have been based on education activities and vector elimination. Current efforts for developing a vaccine are both promising and troubling. At the advent of the introduction of a tetravalent dengue vaccine, molecular surveillance of the circulating genotypes in different geographical regions has gained considerable importance. A growing body of in vitro, preclinical, and clinical phase studies suggest that vaccine conferred protection in a geographical area could depends on the coincidence of the dengue virus genotypes included in the vaccine and those circulating. In this review we present the state-of-the-art in this field, highlighting the need of deeper knowledge on neutralizing immune response for making decisions about future vaccine approval and the potential need for different vaccine composition for regional administration. PMID:25483495

  6. The relevance of dengue virus genotypes surveillance at country level before vaccine approval

    PubMed Central

    Usme-Ciro, José A; Méndez, Jairo A; Laiton, Katherine D; Páez, Andrés

    2014-01-01

    Dengue is a major threat for public health in tropical and subtropical countries around the world. In the absence of a licensed vaccine and effective antiviral therapies, control measures have been based on education activities and vector elimination. Current efforts for developing a vaccine are both promising and troubling. At the advent of the introduction of a tetravalent dengue vaccine, molecular surveillance of the circulating genotypes in different geographical regions has gained considerable importance. A growing body of in vitro, preclinical, and clinical phase studies suggest that vaccine conferred protection in a geographical area could depends on the coincidence of the dengue virus genotypes included in the vaccine and those circulating. In this review we present the state-of-the-art in this field, highlighting the need of deeper knowledge on neutralizing immune response for making decisions about future vaccine approval and the potential need for different vaccine composition for regional administration. PMID:25483495

  7. Detection of Hepatitis E Virus Genotype 1 Among Blood Donors From Southwest of Iran

    PubMed Central

    Parsa, Rahil; Adibzadeh, Setare; Behzad Behbahani, Abbas; Farhadi, Ali; Yaghobi, Ramin; Rafiei Dehbidi, Gholam Reza; Hajizamani, Saeideh; Rahbar, Sanaz; Nikouyan, Negin; Okhovat, Mohammad Ali; Naderi, Samaneh; Salehi, Saeede; Alizadeh, Marzieh; Ranjbaran, Reza; Zarnegar, Golnoosh; Alavi, Parnian

    2016-01-01

    Background Infection with hepatitis E virus (HEV) is endemic in developing countries and reveals significant regional differences. Several studies have reported virus transmission via blood transfusion. To date, however, no cases of HEV RNA detection in blood donors have been reported from Iran. Objectives The aim of this study was to determine the presence of HEV RNA in plasma samples of blood donors referred to a blood transfusion center in Shiraz in the southwest of Iran. The HEV genotypes were also investigated using nucleotide sequencing. Patients and Methods Blood samples were collected from 700 blood donors who were referred to Fars blood transfusion organization from January to March 2014. Plasma samples were screened for the presence of HEV IgG and IgM antibodies by standard enzyme immunoassay. Samples seroreactive to anti-HEV were further tested for the presence of HEV RNA using nested polymerase chain reaction (PCR) with universal primers for detection of all four HEV genotypes. Positive PCR samples were then subjected to DNA sequencing for further analysis. Results Fifty (50, 7.1%) out of 700 plasma samples tested positive for anti-HEV antibodies. HEV RNA was detected in 7/50 (12%) of the antibody-positive samples, the majority of which were IgM positive. Sequence analysis of seven isolates of the HEV RNA ORF 2 gene region revealed > 80% similarity with genotype 1. Conclusions The analysis indicates that the HEV isolated from blood donors in the southwest of Iran belongs to genotype 1. However, more samples from other geographic regions of Iran are needed to confirm these findings. Because transmission of HEV by administration of blood or blood components is likely to occur, it may be sensible to screen donor blood for HEV to eliminate transfusion-transmitted HEV infection when the recipient is immunocompromised.

  8. Hepatitis B virus in Pakistan: A systematic review of prevalence, risk factors, awareness status and genotypes

    PubMed Central

    2011-01-01

    In Pakistan, there are estimated 7-9 million carriers of hepatitis B virus (HBV) with a carrier rate of 3-5%. This article reviews the available literature about the prevalence, risk factors, awareness status and genotypes of the HBV in Pakistan by using key words; HBV prevalence, risk factors, awareness status and genotypes in Pakistani population in PubMed, PakMediNet, Directory of Open Access Journals (DOAJ) and Google Scholar. One hundred and six different studies published from 1998 to 2010 were included in this study. Weighted mean and standard deviation were determined for each population group. The percentage of hepatitis B virus infection in general population was 4.3318% ± 1.644%, healthy blood donors (3.93% ± 1.58%), military recruits (4.276% ± 1.646%), healthcare persons (3.25% ± 1.202%), pregnant women (5.872% ± 4.984), prisoners (5.75% ± 0.212%), surgical patients (7.397% ± 2.012%), patients with cirrhosis (28.87% ± 11.90%), patients with HCC (22% ± 2.645%), patients with hepatitis (15.896% ± 14.824%), patients with liver diseases (27.54% ± 6.385%), multiple transfused patients (6.223% ± 2.121%), opthalmic patients (3.89% ± 1.004%) and users of injectable drugs (14.95% ± 10.536%). Genotype D (63.71%) is the most prevalent genotype in Pakistani population. Mass vaccination and awareness programs should be initiated on urgent basis especially in populations with HBV infection rates of more than 5%. PMID:21375760

  9. Hepatitis B virus in Pakistan: a systematic review of prevalence, risk factors, awareness status and genotypes.

    PubMed

    Ali, Muhammad; Idrees, Muhammad; Ali, Liaqat; Hussain, Abrar; Ur Rehman, Irshad; Saleem, Sana; Afzal, Samia; Butt, Sadia

    2011-01-01

    In Pakistan, there are estimated 7-9 million carriers of hepatitis B virus (HBV) with a carrier rate of 3-5%. This article reviews the available literature about the prevalence, risk factors, awareness status and genotypes of the HBV in Pakistan by using key words; HBV prevalence, risk factors, awareness status and genotypes in Pakistani population in PubMed, PakMediNet, Directory of Open Access Journals (DOAJ) and Google Scholar. One hundred and six different studies published from 1998 to 2010 were included in this study. Weighted mean and standard deviation were determined for each population group. The percentage of hepatitis B virus infection in general population was 4.3318% ± 1.644%, healthy blood donors (3.93% ± 1.58%), military recruits (4.276% ± 1.646%), healthcare persons (3.25% ± 1.202%), pregnant women (5.872% ± 4.984), prisoners (5.75% ± 0.212%), surgical patients (7.397% ± 2.012%), patients with cirrhosis (28.87% ± 11.90%), patients with HCC (22% ± 2.645%), patients with hepatitis (15.896% ± 14.824%), patients with liver diseases (27.54% ± 6.385%), multiple transfused patients (6.223% ± 2.121%), opthalmic patients (3.89% ± 1.004%) and users of injectable drugs (14.95% ± 10.536%). Genotype D (63.71%) is the most prevalent genotype in Pakistani population. Mass vaccination and awareness programs should be initiated on urgent basis especially in populations with HBV infection rates of more than 5%. PMID:21375760

  10. HAVCR1 Gene Haplotypes and Infection by Different Viral Hepatitis C Virus Genotypes

    PubMed Central

    Abad-Molina, Cristina; Garcia-Lozano, José-Raúl; Montes-Cano, Marco-Antonio; Torres-Cornejo, Almudena; Torrecillas, Fuensanta; Aguilar-Reina, José; Romero-Gómez, Manuel; López-Cortés, Luis-Fernando; Núñez-Roldan, Antonio

    2012-01-01

    The hepatitis A virus cellular receptor 1 (HAVCR1) gene is highly polymorphic, and several variants have been associated with susceptibility to allergic and autoimmune diseases. The HAVCR1 gene region was identified as a candidate for hepatitis C virus (HCV) natural clearance in a genotyping study of selected immune response genes in both European-American and African-American populations. The aim of the present study was to explore the influence of HAVCR1 in the outcome of HCV infection in the Spanish population. Three cohorts, consisting of 354 subjects with persistent HCV infection (285 with persistent HCV monoinfection and 69 with natural clearance), 182 coinfected HIV/HCV patients, and 320 controls, were included. Samples were genotyped in several polymorphic positions, insertion/deletion variants in exon 4 and tag single nucleotide polymorphisms (SNPs), in order to define previously described HAVCR1 haplotypes (haplotypes A to D). No statistically significant differences were observed with spontaneous resolution of infection or with viral clearance after treatment. Nevertheless, different rates of infection by viral genotypes (G's) were observed among the HAVCR1 haplotypes. Individuals bearing haplotype C had the highest viral G1 infection rate when compared to individuals bearing other haplotypes (75.82% versus 57.72%, respectively; corrected P value [Pc], 3.2 × 10−4; odds ratio [OR], 2.30; 95% confidence interval [CI], 1.51 to 3.47). Thus, HAVCR1 could be involved in susceptibility or resistance to infection by a particular HCV genotype. PMID:22190394

  11. Laser treatment of an oral squamous papilloma in a pediatric patient: a case report.

    PubMed

    Misir, Ahmet Ferhat; Demiriz, Levent; Barut, Figen

    2013-01-01

    Oral squamous papilloma is a benign proliferation of the stratified squamous epithelium, which results in a papillary or verrucous exophytic mass induced by human papilloma virus (HPV). These oral mucosa lesions are most often asymptomatic and have small progression. Laser assisted surgery is common nowadays with several advantages including successful hemostasis, devoid of sutures, wound sterilization and minimal post-operative pain and edema. The aim of this report is to present the oral squamous papilloma in a pediatric patient and its treatment with soft tissue laser. The lesion was excised with diode laser and the healing was uneventful in follow-up visit after one year. Oral squamous papillomas can be found in child's oral cavity and laser dentistry can be used by dental clinicians to treat these kinds of oral lesions and should be considered as an alternative to conventional surgery. PMID:24262405

  12. Identification of a natural intergenotypic recombinant hepatitis delta virus genotype 1 and 2 in Vietnamese HBsAg-positive patients.

    PubMed

    Sy, B T; Nguyen, H M; Toan, N L; Song, L H; Tong, H V; Wolboldt, C; Binh, V Q; Kremsner, P G; Velavan, T P; Bock, C-T

    2015-01-01

    Hepatitis D virus (HDV) infection is acquired as a co- /superinfection of Hepatitis B virus (HBV) and can modulate the pathophysiology of chronic hepatitis B and related liver diseases including hepatocellular carcinoma. Among the eight distinct HDV genotypes reported, relatively few studies have attempted to investigate the prevalence of HDV mixed genotypes and RNA recombination of HDV. With a recorded prevalence of 10-20% HBV infection in Vietnam, this study investigated the HDV variability, HDV genotypes and HDV recombination among twenty-one HDV isolates in Vietnamese HBsAg-positive patients. HDV subgenomic and full-length genome sequences were obtained using newly established HDV-specific RT-PCR techniques. The nucleotide homology was observed from 74.6% to 99.4% among the investigated full-length genome of the HDV isolates. We observed HDV genotype 1 and HDV genotype 2 in the investigated Vietnamese patients. Although no HDV genotype mixtures were observed, we report here a newly identified recombinant of HDV genotypes (HDV 1 and HDV 2). The identified recombinant HDV isolate C03 revealed sequence homology to both HDV genotype 1 (nt1 to nt907) and HDV genotype 2 (nt908 to nt1675; HDAg coding region) with a breakpoint at nt908. Our findings demonstrate the prevalence of intergenotypic recombination between HDV genotypes 1 and 2 in a Vietnamese HBsAg-positive patient. Extended investigation on the distribution and prevalence of HDV, HDV mixed genotypes and recombinant HDV genotypes in a larger Vietnamese population offers vital insights into understanding of the micro-epidemiology of HDV and subsequent pathophysiology in chronic HBV- /HDV-related liver diseases. PMID:24548489

  13. High Diversity of Hepatitis B Virus Genotypes in Panamanian Blood Donors: A Molecular Analysis of New Variants

    PubMed Central

    Martínez, Alexander A.; Zaldivar, Yamitzel Y.; De Castillo, Zoila; Ortiz, Alma Y.; Mendoza, Yaxelis; Cristina, Juan; Pascale, Juan M.

    2014-01-01

    Hepatitis B Virus (HBV) is an infectious agent that causes more than half of the cases of liver disease and cancer in the world. Globally there are around 250 million people chronically infected with this virus. Despite 16% of the cases of liver disease in Central America are caused by HBV, the information regarding its genetic diversity, genotypes and circulation is scarce. The purpose of this study was to evaluate the genetic variability of the HBV genotypes from HBV-DNA positive samples obtained from screening blood donors at the Social Security System of Panama and to estimate its possible origin. From 59,696 blood donors tested for HBV infection during 2010–2012, there were 74 HBV-DNA positive subjects. Analysis of the partial PreS2-S region of 27 sequences shows that 21% of the infections were caused by genotype A, 3% by genotype D and 76% by genotype F. In addition, we were able to confirm circulation of six sub-genotypes A1, A2, A3, D4, F3, F1 and a proposed new sub-genotype denominated F5pan. We found a confinement of sub-genotypes F1 and F5pan to the western area of Panama. The tMRCA analysis suggests a simultaneous circulation of previously described sub-genotypes rather than recent introductions of the Panamanian sub-genotypes in the country. Moreover, these results highlight the need of more intensive research of the HBV strains circulating in the region at the molecular level. In conclusion, Panama has a high HBV genotype diversity that includes a new proposed sub-genotype, an elevated number of PreCore-Core mutations, and confinement of these variants in a specific geographical location. PMID:25093674

  14. High diversity of hepatitis B virus genotypes in Panamanian blood donors: a molecular analysis of new variants.

    PubMed

    Martínez, Alexander A; Zaldivar, Yamitzel Y; De Castillo, Zoila; Ortiz, Alma Y; Mendoza, Yaxelis; Cristina, Juan; Pascale, Juan M

    2014-01-01

    Hepatitis B Virus (HBV) is an infectious agent that causes more than half of the cases of liver disease and cancer in the world. Globally there are around 250 million people chronically infected with this virus. Despite 16% of the cases of liver disease in Central America are caused by HBV, the information regarding its genetic diversity, genotypes and circulation is scarce. The purpose of this study was to evaluate the genetic variability of the HBV genotypes from HBV-DNA positive samples obtained from screening blood donors at the Social Security System of Panama and to estimate its possible origin. From 59,696 blood donors tested for HBV infection during 2010-2012, there were 74 HBV-DNA positive subjects. Analysis of the partial PreS2-S region of 27 sequences shows that 21% of the infections were caused by genotype A, 3% by genotype D and 76% by genotype F. In addition, we were able to confirm circulation of six sub-genotypes A1, A2, A3, D4, F3, F1 and a proposed new sub-genotype denominated F5pan. We found a confinement of sub-genotypes F1 and F5pan to the western area of Panama. The tMRCA analysis suggests a simultaneous circulation of previously described sub-genotypes rather than recent introductions of the Panamanian sub-genotypes in the country. Moreover, these results highlight the need of more intensive research of the HBV strains circulating in the region at the molecular level. In conclusion, Panama has a high HBV genotype diversity that includes a new proposed sub-genotype, an elevated number of PreCore-Core mutations, and confinement of these variants in a specific geographical location. PMID:25093674

  15. Hepatitis B Virus Genotypes Distribution with HBsAg Positive in the North of Iran (Mazandaran) During 2011-2014

    PubMed Central

    Mousavi, Tahoora; Haghshenas, Mohammad Reza; Rafiei, Alireza; Navaei, Reza Alizadeh; khah, Zahra Hosseini

    2014-01-01

    Background: HBV infection is a major global health problem and ten genotypes (A to J) and multiples subtypes of HBV have been identified, and they show some distinct geographic distributions. The available data on HBV genotype in Iran are very heterogeneous and limited. Therefore in this study, we tried to identify the HBV genotypes by using polymerase chain reaction. Methods: In this cross-sectional study, HBV- positive serum samples of 122 patients with chronic hepatitis from 2011 to 2014 were studied. HBV-DNA was extracted from plasma samples using QIAamp® MiniElute® Virus Spin Kit (Qiagen). Plasma samples from HBsAg positive were confirmed the presence of HBV nucleic acid and determined the genotypes of HBV genome by PCR using the DNA PCR kit (Cinagene) with Taq-DNA polymerase enzyme and type of specific primers. All samples were examined in the virology laboratory of Sari Medical School. Results: The mean age of patients were 45 ± 25 (range, 20 to 70) year that 70 (57.37%) patients were male and 52 (42.62%) were female. The majority of HBV positive patients had a major surgery (44% patients) and then 32% patients followed by intra familial of hepatitis B virus infected and 11% of HBV positive patients had a history of blood transfusions. In this study, 91(74.59%) had genotype D, 7(5.73%) genotype B and 24(19.67%) genotype D and B. Conclusion: This study indicates that the genotype D is the most frequent followed by the mixed genotypes D and B and genotype B in our region. Prevalence and incidence of HBV genotypes are with distributed among of areas and different genotypes may show different responses with antiviral therapy. PMID:25648402

  16. Hepatitis B and D viruses replication interference: Influence of hepatitis B genotype

    PubMed Central

    Madejón, Antonio; Romero, Míriam; Hernández, Ángela; García-Sánchez, Araceli; Sánchez-Carrillo, Marta; Olveira, Antonio; García-Samaniego, Javier

    2016-01-01

    AIM: To study the hepatitis B virus (HBV) and hepatitis D virus (HDV) replication interferences in patients with chronic hepatitis delta infected with different HBV genotypes. METHODS: We conducted a transversal study including 68 chronic hepatitis delta (CHD) (37 HIV-positive) patients and a control group of 49 chronic hepatitis B (CHB) (22 HIV-positive) patients. In addition, a dynamic follow-up was performed in 16 CHD patients. In all the samples, the surface antigen of hepatitis B (HBsAg) serum titers were analyzed with the Monolisa HBsAg Ultra system (Bio-Rad), using as quantification standard a serial dilution curve of an international HBsAg standard. Serum HBV-DNA titers were analyzed using the Roche Cobas TaqMan (Roche, Barcelona, Spain), and the serum HDV-RNA using an in-house real-time qRT-PCR method, with TaqMan probes. HBV genotype was determined with the line immunoassay LiPA HBV genotyping system (Innogenetics, Ghent, Belgium). In those patients negative for LiPA assay, a nested PCR method of complete HBsAg coding region, followed by sequence analysis was applied. RESULTS: No differences in the HBV-DNA levels were found in CHB patients infected with different HBV genotypes. However, in CHD patients the HBV-DNA levels were lower in those infected with HBV-A than in those with HBV-D, both in HIV negative [median (IQR): 1.25 (1.00-1.35) vs 2.95 (2.07-3.93) log10 (copies/mL), P = 0.013] and HIV positive patients [2.63 (1.24-2.69) vs 7.25 (4.61-7.55) log10 (copies/mL), P < 0.001]. This was confirmed in the dynamic study of the HBV/HDV patients. These differences induce an under-estimation of HBV-A incidence in patients with CHD analyzed with LiPA assay. Finally, the HBsAg titers reflected no significant differences in CHD patients infected with HBV-A or D. CONCLUSION: Viral replication interference between HBV and HDV is HBV-genotype dependent, and more evident in patients infected with HBV-genotype A, than with HBV-D or E. PMID:27003993

  17. The effects of female sex, viral genotype and IL28B genotype on spontaneous clearance of acute hepatitis C virus infection

    PubMed Central

    Grebely, Jason; Page, Kimberly; Sacks-Davis, Rachel; van der Loeff, Maarten Schim; Rice, Thomas M.; Bruneau, Julie; Morris, Meghan D.; Hajarizadeh, Behzad; Amin, Janaki; Cox, Andrea L.; Kim, Arthur Y.; McGovern, Barbara H.; Schinkel, Janke; George, Jacob; Shoukry, Naglaa H.; Lauer, Georg M.; Maher, Lisa; Lloyd, Andrew R.; Hellard, Margaret; Dore, Gregory J.; Prins, Maria

    2014-01-01

    Although 20–40% of persons with acute HCV infection demonstrate spontaneous clearance, the time-course and factors associated with clearance remain poorly understood. We investigated the time to spontaneous clearance and predictors among participants with acute HCV using Cox proportional hazards analyses. Data for this analysis were drawn from an international collaboration of nine prospective cohorts evaluating outcomes following acute HCV infection. Among 632 participants with acute HCV, 35% were female, 82% were Caucasian, 49% had IL28B CC genotype (rs12979860), 96% had injected drugs ever, 47% were infected with HCV genotype 1 and 5% had HIV co-infection. Twenty-eight percent were HCV antibody negative/RNA positive at the time of acute HCV detection (early acute HCV). During follow-up, spontaneous clearance occurred in 173 of 632 and at one year following infection, 25% (95%CI: 21%, 29%) had cleared virus. Among those with clearance, the median time to clearance was 16.5 weeks (IQR: 10.5, 33.4 weeks), with 34%, 67% and 83% demonstrating clearance at three, six and twelve months. Adjusting for age, factors independently associated with time to spontaneous clearance included female sex [adjusted hazards ratio (AHR) 2.16; 95%CI 1.48, 3.18], IL28B CC genotype (vs. CT/TT, AHR 2.26; 95%CI 1.52, 3.34), and HCV genotype 1 (vs. non-genotype 1, AHR 1.56; 95%CI 1.06, 2.30). The effect of IL28B genotype and HCV genotype on spontaneous clearance was greater among females compared to males. Conclusions Female sex, favorable IL28B genotype and HCV genotype 1 are independent predictors of spontaneous clearance. Further research is required to elucidate the observed sex-based differences in HCV control. PMID:23908124

  18. Molecular virology of hepatitis B virus, sub-genotype C4 in northern Australian Indigenous populations.

    PubMed

    Littlejohn, M; Davies, J; Yuen, L; Edwards, R; Sozzi, T; Jackson, K; Cowie, B; Tong, S; Davis, J; Locarnini, S

    2014-04-01

    Indigenous Australians experience a significant health burden from chronic hepatitis B infection; however, the strain of hepatitis B virus (HBV) found among Indigenous Australians has not been well characterized. Blood samples were collected from 65 Indigenous Australians with chronic HBV infection from across the Top End of Australia's Northern Territory. Phylogenetic analysis of HBV from these samples revealed that 100% of the isolates were genotype C, sub-genotype C4, expressing the serotype ayw3. This strain is a divergent group within the HBV/C genotype, and has only been described in Indigenous Australians. Evidence of recombination was suggested by discordant phylogenetic clustering of the C4 sequences when comparing the full genome to the surface region and confirmed by recombination analysis which showed the surface gene region to be most closely related to genotype J, while the remaining regions of the genome were most similar to genotype C sequences. Mutational analysis revealed the presence of multiple mutations that have been linked with more rapid liver disease progression and an increased risk of hepatocellular carcinoma. These mutations were detected in the majority of sequences examined. Variants associated with vaccine failure were detected as the predominant viral quasi-species in 3/35 samples. In summary, the HBV C4 variant found in this population has a high potential to cause advanced liver disease and to escape vaccination programs. Further in vitro functional and natural history studies are warranted in order to determine the clinical and public health consequences of infection with the HBV C4 variant in these communities. PMID:24497078

  19. Evidence of Experimental Vertical Transmission of Emerging Novel ECSA Genotype of Chikungunya Virus in Aedes aegypti

    PubMed Central

    Agarwal, Ankita; Dash, Paban Kumar; Singh, Anil Kumar; Sharma, Shashi; Gopalan, Natarajan; Rao, Putcha Venkata Lakshmana; Parida, Man Mohan; Reiter, Paul

    2014-01-01

    Background Chikungunya virus (CHIKV) has emerged as one of the most important arboviruses of public health significance in the past decade. The virus is mainly maintained through human-mosquito-human cycle. Other routes of transmission and the mechanism of maintenance of the virus in nature are not clearly known. Vertical transmission may be a mechanism of sustaining the virus during inter-epidemic periods. Laboratory experiments were conducted to determine whether Aedes aegypti, a principal vector, is capable of vertically transmitting CHIKV or not. Methodology/Principal Findings Female Ae. aegypti were orally infected with a novel ECSA genotype of CHIKV in the 2nd gonotrophic cycle. On day 10 post infection, a non-infectious blood meal was provided to obtain another cycle of eggs. Larvae and adults developed from the eggs obtained following both infectious and non-infectious blood meal were tested for the presence of CHIKV specific RNA through real time RT-PCR. The results revealed that the larvae and adults developed from eggs derived from the infectious blood meal (2nd gonotrophic cycle) were negative for CHIKV RNA. However, the larvae and adults developed after subsequent non-infectious blood meal (3rd gonotrophic cycle) were positive with minimum filial infection rates of 28.2 (1∶35.5) and 20.2 (1∶49.5) respectively. Conclusion/Significance This study is the first to confirm experimental vertical transmission of emerging novel ECSA genotype of CHIKV in Ae. aegypti from India, indicating the possibilities of occurrence of this phenomenon in nature. This evidence may have important consequence for survival of CHIKV during adverse climatic conditions and inter-epidemic periods. PMID:25080107

  20. Development of a reverse genetics system based on RNA polymerase II for Newcastle disease virus genotype VII.

    PubMed

    Wang, Jianzhong; Wang, Chunfeng; Feng, Na; Wang, Hualei; Zheng, Xuexing; Yang, Songtao; Gao, Yuwei; Xia, Xianzhu; Yin, Renfu; Liu, Xiufan; Hu, Shunlin; Ding, Chan; Yu, Shengqing; Cong, Yanlong; Ding, Zhuang

    2015-02-01

    Newcastle disease virus (NDV) has only a single serotype but diversified genotypes. Genotype VII strains are the prevalent currently circulating genotype worldwide, and in particular, these strains cause outbreaks in waterfowl. In this study, a reverse genetics system for highly virulent NDV isolated from goose flocks was developed independent of conventional T7 RNA polymerase. Infectious virus was successfully generated by an RNA polymerase II promoter to drive transcription of the full-length virus antigenome. A green fluorescent protein (GFP)-expressing virus was generated by inserting an additional transcription cassette coding for the enhanced GFP between the P and M genes of the genome. The expression of GFP was confirmed by western blotting and fluorescence microscopy. The replication kinetics and pathogenicity of the recombinant viruses are indistinguishable from the parental wild-type virus. This reverse genetics system will provide a powerful tool for the analysis of goose-origin NDV dissemination and pathogenesis, as well as preparation for genotype-matched NDV attenuated vaccines. PMID:25384536

  1. Dynamics of the Emergence and Establishment of a Newly Dominant Genotype of Japanese Encephalitis Virus throughout Asia

    PubMed Central

    Schuh, Amy J.; Ward, Melissa J.; Leigh Brown, Andrew J.

    2014-01-01

    ABSTRACT In recent years, genotype I (GI) of Japanese encephalitis virus (JEV) has displaced genotype III (GIII) as the dominant virus genotype throughout Asia. In this study, the largest collection of GIII and GI envelope gene-derived viral sequences assembled to date was used to reconstruct the spatiotemporal chronology of genotype displacement throughout Asia and to determine the evolutionary and epidemiological dynamics underlying this significant event. GI consists of two clades, GI-a and GI-b, with the latter being associated with displacement of GIII as the dominant JEV genotype throughout Asia in the 1990s. Phylogeographic analysis indicated that GI-a diverged in Thailand or Cambodia and has remained confined to tropical Asia, whereas GI-b diverged in Vietnam and then dispersed northwards to China, where it was subsequently dispersed to Japan, Korea, and Taiwan. Molecular adaptation was detected by more than one method at one site (residue 15), and coevolution was detected at two pairs of sites (residues 89 to 360 and 129 to 141) within the GI E gene protein alignment. Viral multiplication and temperature sensitivity analyses in avian and mosquito cells revealed that the GI-b isolate JE-91 had significantly higher infectivity titers in mosquito cells from 24 to 48 h postinfection than did the GI-a and GIII isolates. If the JE-91 isolate is indeed representative of GI-b, an increased multiplicative ability of GI-b viruses compared to that of GIII viruses early in mosquito infection may have resulted in a shortened extrinsic incubation period that led to an increased number of GI enzootic transmission cycles and the subsequent displacement of GIII. IMPORTANCE Japanese encephalitis virus (JEV), a mosquito-borne flavivirus, represents the most significant etiology of childhood viral neurological infection in Asia. Despite the existence of effective vaccines, JEV is responsible for an estimated 68,000 human cases and a reported 10,000 to 15,000 deaths annually

  2. Endoplasmic Reticulum Stress Induced Synthesis of a Novel Viral Factor Mediates Efficient Replication of Genotype-1 Hepatitis E Virus

    PubMed Central

    Nair, Vidya P.; Madhvi, Abhilasha; Bakshi, Karishma; Srivastava, Akriti; Shalimar; Nayak, Baibaswata; CT, Ranjith Kumar; Surjit, Milan

    2016-01-01

    Hepatitis E virus (HEV) causes acute hepatitis in many parts of the world including Asia, Africa and Latin America. Though self-limiting in normal individuals, it results in ~30% mortality in infected pregnant women. It has also been reported to cause acute and chronic hepatitis in organ transplant patients. Of the seven viral genotypes, genotype-1 virus infects humans and is a major public health concern in South Asian countries. Sporadic cases of genotype-3 and 4 infection in human and animals such as pigs, deer, mongeese have been reported primarily from industrialized countries. Genotype-5, 6 and 7 viruses are known to infect animals such as wild boar and camel, respectively. Genotype-3 and 4 viruses have been successfully propagated in the laboratory in mammalian cell culture. However, genotype-1 virus replicates poorly in mammalian cell culture and no other efficient model exists to study its life cycle. Here, we report that endoplasmic reticulum (ER) stress promotes genotype-1 HEV replication by inducing cap-independent, internal initiation mediated translation of a novel viral protein (named ORF4). Importantly, ORF4 expression and stimulatory effect of ER stress inducers on viral replication is specific to genotype-1. ORF4 protein sequence is mostly conserved among genotype-1 HEV isolates and ORF4 specific antibodies were detected in genotype-1 HEV patient serum. ORF4 interacted with multiple viral and host proteins and assembled a protein complex consisting of viral helicase, RNA dependent RNA polymerase (RdRp), X, host eEF1α1 (eukaryotic elongation factor 1 isoform-1) and tubulinβ. In association with eEF1α1, ORF4 stimulated viral RdRp activity. Furthermore, human hepatoma cells that stably express ORF4 or engineered proteasome resistant ORF4 mutant genome permitted enhanced viral replication. These findings reveal a positive role of ER stress in promoting genotype-1 HEV replication and pave the way towards development of an efficient model of the

  3. Early predictive efficacy of core antigen on antiviral outcomes in genotype 1 hepatitis C virus infected patients.

    PubMed

    Feng, Bo; Yang, Rui-Feng; Zhang, Hai-Ying; Luo, Bi-Fen; Kong, Fan-Yun; Rao, Hui-Ying; Jin, Qian; Cong, Xu; Wei, Lai

    2015-01-01

    Response-guided therapy is of limited use in developing countries because hepatitis C virus RNA detection by sensitive molecular methods is time- and labor-consuming and expensive. We evaluated early predictive efficacy of serum hepatitis C virus core antigen kinetics on sustained virologic response in patients with genotype 1 hepatitis C virus during pegylated interferon plus ribavirin treatment. For 478 patients recruited, hepatitis C virus RNAs were detected at baseline, and at weeks 4, 12, 24, 48, and 72 using Cobas TaqMan. Architect hepatitis C virus core antigen was performed at baseline, and weeks 4 and 12. Predictive values of hepatitis C virus core antigen on sustained virologic response were compared to hepatitis C virus RNA. In the first 12 weeks after treatment initiation the dynamic patterns of serum hepatitis C virus core antigen and hepatitis C virus RNA levels were similar in sustained virologic response, relapse, and null response patients groups. Although areas under the receiver operating characteristics curves of hepatitis C virus core antigen were lower than those of hepatitis C virus RNA at the same time points, modeling analysis showed that undetectable hepatitis C virus core antigen (rapid virological response based on hepatitis C virus core antigen) had similar positive predictive value on sustained virologic response to hepatitis C virus RNA at week 4 (90.4% vs 93.3%), and hepatitis C virus core antigen decrease greater than 1log10IU/mL (early virological response based on hepatitis C virus core antigen) had similar negative predictive value to hepatitis C virus RNA at week 12 (94.1% vs 95.2%). Analysis on the validation group demonstrated a positive predictive value of 97.5% in rapid virological response based on hepatitis C virus core antigen and a negative predictive value of 100% in early virological response based on hepatitis C virus core antigen. In conclusion, hepatitis C virus core antigen is comparable to hepatitis C virus RNA in

  4. Virulence of viral hemorrhagic septicemia virus (VHSV) genotypes Ia, IVa, IVb, and IVc in five fish species.

    USGS Publications Warehouse

    Emmenegger, Eveline J.; Moon, Chang Hoon; Hershberger, Paul K.; Kurath, Gael

    2013-01-01

    The susceptibility of yellow perch Perca flavescens, rainbow trout Oncorhynchus mykiss, Chinook salmon O. tshawytscha, koi Cyprinus carpio koi, and Pacific herring Clupea pallasii to 4 strains of viral hemorrhagic septicemia virus (VHSV) was assessed. Fish were challenged via intraperitoneal injection with high (1 × 106 plaque-forming units, PFU) and low (1 × 103 PFU) doses of a European strain (genotype Ia), and North American strains from the West coast (genotype IVa), Great Lakes (genotype IVb), and the East coast (genotype IVc). Pacific herring were exposed to the same VHSV strains, but at a single dose of 5 × 103 PFU ml-1 by immersion in static seawater. Overall, yellow perch were the most susceptible, with cumulative percent mortality (CPM) ranging from 84 to 100%, and 30 to 93% in fish injected with high or low doses of virus, respectively. Rainbow trout and Chinook salmon experienced higher mortalities (47 to 98% CPM) after exposure to strain Ia than to the other virus genotypes. Pacific herring were most susceptible to strain IVa with an average CPM of 80% and moderately susceptible (42 to 52% CPM) to the other genotypes. Koi had very low susceptibility (≤5.0% CPM) to all 4 VHSV strains. Fish tested at 7 d post challenge were positive for all virus strains, with yellow perch having the highest prevalence and concentrations of virus, and koi the lowest. While genotype Ia had higher virulence in salmonid species, there was little difference in virulence or host-specificity between isolates from subtypes IVa, IVb, and IVc.  

  5. Complete Genome Sequence of a Genotype XVII Newcastle Disease Virus, Isolated from an Apparently Healthy Domestic Duck in Nigeria.

    PubMed

    Shittu, Ismaila; Sharma, Poonam; Joannis, Tony M; Volkening, Jeremy D; Odaibo, Georgina N; Olaleye, David O; Williams-Coplin, Dawn; Solomon, Ponman; Abolnik, Celia; Miller, Patti J; Dimitrov, Kiril M; Afonso, Claudio L

    2016-01-01

    The first complete genome sequence of a strain of Newcastle disease virus (NDV) of genotype XVII is described here. A velogenic strain (duck/Nigeria/903/KUDU-113/1992) was isolated from an apparently healthy free-roaming domestic duck sampled in Kuru, Nigeria, in 1992. Phylogenetic analysis of the fusion protein gene and complete genome classified the isolate as a member of NDV class II, genotype XVII. PMID:26847901

  6. Complete Genome Sequence of a Genotype XVII Newcastle Disease Virus, Isolated from an Apparently Healthy Domestic Duck in Nigeria

    PubMed Central

    Shittu, Ismaila; Sharma, Poonam; Joannis, Tony M.; Volkening, Jeremy D.; Odaibo, Georgina N.; Olaleye, David O.; Williams-Coplin, Dawn; Solomon, Ponman; Abolnik, Celia; Miller, Patti J.; Dimitrov, Kiril M.

    2016-01-01

    The first complete genome sequence of a strain of Newcastle disease virus (NDV) of genotype XVII is described here. A velogenic strain (duck/Nigeria/903/KUDU-113/1992) was isolated from an apparently healthy free-roaming domestic duck sampled in Kuru, Nigeria, in 1992. Phylogenetic analysis of the fusion protein gene and complete genome classified the isolate as a member of NDV class II, genotype XVII. PMID:26847901

  7. North American West Nile virus genotype isolates demonstrate differential replicative capacities in response to temperature

    PubMed Central

    Andrade, Christy C.; Maharaj, Payal D.; Reisen, William K.

    2011-01-01

    The presence of West Nile virus (WNV) was first documented in California, USA, during the summer of 2003, and subsequently the virus has become endemic throughout the state. Sequence analysis has demonstrated that the circulating strains are representative of the North American (WN02) genotype that has displaced the East Coast genotype (NY99). A recent study has indicated that enhanced vector competence at elevated temperatures may have played a role in the displacement of the East Coast genotype by WN02. In the current study, four WN02 strains from California, including an initial 2003 isolate (COAV997), were compared to strain NY99 in growth curve assays in mosquito and duck embryonic fibroblast (DEF) cell lines at differing, biologically relevant temperatures to assess the relative temperature sensitivities of these natural isolates. COAV997 was significantly debilitated in viral replication in DEF cells at 44 °C. Full-length sequence comparison of COAV997 against the NY99 reference strain revealed non-synonymous mutations in the envelope glycoprotein (V159A), non-structural protein 1 (NS1) (K110N) and non-structural protein 4A (NS4A) (F92L), as well as two mutations in the 3′ UTR: C→T at nt 10 772 and A→G at nt 10 851. These non-synonymous mutations were introduced into the NY99 viral backbone by site-directed mutagenesis. A mutant containing the NS1-K110N and NS4A-F92L mutations exhibited a debilitated growth phenotype in DEF cells at 44 °C, similar to that of COAV997. One explanation for the subsistence of this genotype is that COAV997 was obtained from an area of California where avian host species might not present elevated temperatures. These data indicate that the NS1 and NS4A mutations identified in some WN02 isolates could reduce thermal stability and impede replication of virus at temperatures observed in febrile avian hosts. PMID:21775581

  8. Current status and emerging challenges in the treatment of hepatitis C virus genotypes 4 to 6

    PubMed Central

    Papastergiou, Vasilios; Karatapanis, Stylianos

    2015-01-01

    Hepatitis C virus (HCV) genotypes 4, 5 and 6 are mainly present in Africa, the Middle East and Asia and they have been less extensively studied with respect to epidemiology, natural disease history and therapeutic endpoints. Response rates to a 48-wk combined peginterferon/ribavirin treatment range to 40%-69% for HCV 4, 55%-60% for HCV 5 and 60%-90% for HCV 6. Response-guided schedules are recommended to optimize the outcomes of peginterferon/ribavirin treatment in HCV 4 and, in form of preliminary data, for HCV 6, but no data are yet available to support such an individualization of therapy for HCV 5. Recently, the direct-acting antivirals (DAAs) with pan-genotypic activities simeprevir, sofosbuvir and daclatasvir have been recommended in triple regimens with peginterferon/ribavirin for the treatment of HCV genotypes 4 to 6 infections. In the future, DAA-based interferon-free therapies are awaited to drastically improve treatment outcomes in HCV. However, efforts to improve treatment outcomes with peginterferon/ribavirin should continue, as the HCV 4-6 infected population is mainly based in resource-limited settings with restricted access to the costly DAAs. PMID:25789294

  9. Current status and emerging challenges in the treatment of hepatitis C virus genotypes 4 to 6.

    PubMed

    Papastergiou, Vasilios; Karatapanis, Stylianos

    2015-03-16

    Hepatitis C virus (HCV) genotypes 4, 5 and 6 are mainly present in Africa, the Middle East and Asia and they have been less extensively studied with respect to epidemiology, natural disease history and therapeutic endpoints. Response rates to a 48-wk combined peginterferon/ribavirin treatment range to 40%-69% for HCV 4, 55%-60% for HCV 5 and 60%-90% for HCV 6. Response-guided schedules are recommended to optimize the outcomes of peginterferon/ribavirin treatment in HCV 4 and, in form of preliminary data, for HCV 6, but no data are yet available to support such an individualization of therapy for HCV 5. Recently, the direct-acting antivirals (DAAs) with pan-genotypic activities simeprevir, sofosbuvir and daclatasvir have been recommended in triple regimens with peginterferon/ribavirin for the treatment of HCV genotypes 4 to 6 infections. In the future, DAA-based interferon-free therapies are awaited to drastically improve treatment outcomes in HCV. However, efforts to improve treatment outcomes with peginterferon/ribavirin should continue, as the HCV 4-6 infected population is mainly based in resource-limited settings with restricted access to the costly DAAs. PMID:25789294

  10. A re-evaluation of the origin of hepatitis C virus genotype 2 in West Africa

    PubMed Central

    Forbi, Joseph C.; Sue, Amanda; Layden, Jennifer E.; Switzer, William M.; Opare-Sem, Ohene K.; Phillips, Richard O.; Khudyakov, Yury E.

    2015-01-01

    Hepatitis C virus (HCV) is classified into seven genotypes based on genetic diversity, and most genotypes have been found in Africa. Infections with HCV genotype 2 (HCV2) are most prevalent in West Africa and it was suggested that HCV2 originated in West Africa. To better understand the evolutionary epidemiology of HCV2 in Africa, we examined new NS5B sequences of HCV2 strains obtained from Côte d'Ivoire, Ghana and Nigeria sequenced at the Centers for Disease Control and Prevention with those available from West, North and Central Africa. Bayesian phylogeographic analysis using a discrete trait model showed that Ghana was the most likely geographical region for the origin of HCV2. Spread of HCV2 from Ghana did not appear to be through diffusion to adjacent countries along the coast. Rather, it was transmitted from Ghana to many distant countries in Africa, suggesting that certain routes of geographical dissemination were historically more efficient than mere proximity and that the HCV2 epidemic history in West Africa is extremely complex. PMID:25888623

  11. Characterization of rubella virus genotypes among pregnant women in northern Vietnam, 2011-2013.

    PubMed

    Van Le, Son; Le, Duc Hoang; Hoang, Huong Thi; Hoang, Ha; Nguyen, Nam Trung; Chu, Ha Hoang

    2015-02-01

    Rubella virus (RV) infection is an unresolved clinical complication that affects children in developing countries including Vietnam. RV infection during the first trimester of pregnancy causes severe birth defects known as congenital rubella syndrome. This study reports on the genomic characterization of RV strains circulating in northern Vietnam during 2011-2013. RV-IgM positive amniotic fluid specimens were collected from 38 women from northern Vietnam who presented with clinical rubella at the National Hospital of Obstetrics and Gynecology in Hanoi, Vietnam. The RV genes were determined by nested PCR with primers amplifying the 739-nucleotide coding region of the E1 gene. The sequences from the amplified DNA fragments were phylogenetically analyzed and compared to reference RV strains. Seventeen out of 38 samples are positive for RV detecting. All new RV isolates are clustered to genotype 2B. Eighteen amino acid mutations were found in the T and B cell epitopes. These results suggest that genotype 2B RV strains frequently circulate in northern Vietnam. These data describe the RV genotype in Vietnam with the aim of improving maternal and child health in this country. PMID:25111367

  12. Co-circulation of two genotypes of dengue virus serotype 3 in Guangzhou, China, 2009

    PubMed Central

    2012-01-01

    Dengue is emerging as the most important mosquito borne viral disease in the world. In mainland China, sporadic and large outbreaks of dengue illness caused by the four serotypes of dengue virus (DENV-1 to DENV-4) have been well documented. Guangdong province is the major affected area in China, and DENV-1 has dominantly circulated in Guangdong for a long time. In this study, a family cluster of DENV-3 infection in Guangzhou was described. Three cases were diagnosed as dengue fever based on clinical manifestation, serological and RT-PCR assays. Two DENV-3 strains were isolated in C6/36 cells and the complete genome sequences were determined. Phylogenetic analysis revealed that the new DENV-3 isolates from the family cluster were grouped within genotype III. Considering the fact that several DENV-3 strains within genotype V were also identified in Guangzhou in 2009, at least two genotypes of DENV-3 co-circulated in Guangzhou. Careful investigation and virological analysis should be warranted in the future. PMID:22721418

  13. Characterization of seven genotypes (A to E, G and H) of hepatitis B virus recovered from Japanese patients infected with human immunodeficiency virus type 1.

    PubMed

    Shibayama, Takao; Masuda, Gohta; Ajisawa, Atsushi; Hiruma, Kiyoshi; Tsuda, Fumio; Nishizawa, Tsutomu; Takahashi, Masaharu; Okamoto, Hiroaki

    2005-05-01

    To investigate the prevalence of hepatitis B virus (HBV) genotypes and characteristics of HBV isolates among Japanese patients infected with human immunodeficiency virus type 1 (HIV), serum samples collected between September 1990 and March 2002 from 471 HIV-infected patients (age, 38.8 +/- 11.4 [mean +/- standard deviation] years; male, 90%) were tested for hepatitis B surface antigen (HBsAg) and HBV DNA. Positivity for HBsAg and HBV DNA was seen in 42 patients (8.9%), 41 of whom had contracted HIV infection through sexual activity and 1 had hemophilia. Genotypes of HBV were determined by comparative and phylogenetic analyses of the S gene sequence (396 nucleotides [nt]). The distribution of HBV genotypes among the 42 HBV-viremic patients was: A (50%), B (5%), C (24%), D (5%), E (2%), H (10%), A plus D (2%), A plus G (2%). The hemophilia patient had HBV genotype D. Genotypes E, G, and H which had not been reported in Japan, were found in one patient each who had traveled to Zambia, the US, and South America, respectively. Genotypes A and D, which are rare in Japan, were found in patients who had no history of traveling abroad. The entire genome of the HB-JI411 (genotype E [3,212 nt]), HB-JI444G (genotype G [3,248 nt]), and HB-JI260 (genotype H [3,218 nt]) isolates had the highest identity of 98.3%, 99.9%, and 98.5%, respectively, with reported HBV isolates of the same genotype. Most Japanese patients coinfected with HIV and HBV had HBV genotypes that are found rarely or had not been reported in Japan. PMID:15779062

  14. High Genetic Diversity of Newcastle Disease Virus in Poultry in West and Central Africa: Cocirculation of Genotype XIV and Newly Defined Genotypes XVII and XVIII

    PubMed Central

    Snoeck, Chantal J.; Owoade, Ademola A.; Couacy-Hymann, Emmanuel; Alkali, Bello R.; Okwen, Mbah P.; Adeyanju, Adeniyi T.; Komoyo, Giscard F.; Nakouné, Emmanuel; Le Faou, Alain

    2013-01-01

    Despite rampant Newcastle disease virus (NDV) outbreaks in Africa for decades, the information about the genetic characteristics of the virulent strains circulating in West and Central Africa is still scarce. In this study, 96 complete NDV fusion gene sequences were obtained from poultry sampled in Cameroon, Central African Republic, Côte d'Ivoire, and Nigeria between 2006 and 2011. Based on rational criteria recently proposed for the classification of NDV strains into classes, genotypes, and subgenotypes, we revisited the classification of virulent strains, in particular those from West and Central Africa, leading to their grouping into genotype XIV and newly defined genotypes XVII and XVIII, each with two subgenotypes. Phylogenetic analyses revealed that several (sub)genotypes are found in almost every country. In Cameroon, most strains were related to vaccine strains, but a single genotype XVII strain was also found. Only three highly similar genotype XVII strains were detected in Central African Republic. Subgenotypes XVIIa, XVIIIa, and XVIIIb cocirculated in Côte d'Ivoire, while subgenotypes XIVa, XIVb, XVIIa, XVIIb, and XVIIIb were found in Nigeria. While these genotypes are so far geographically restricted, local and international trade of domestic and exotic birds may lead to their spread beyond West and Central Africa. A high genetic diversity, mutations in important neutralizing epitopes paired with suboptimal vaccination, various levels of clinical responses of poultry and wild birds to virulent strains, strains with new cleavage sites, and other genetic modifications found in these genotypes tend to undermine and complicate NDV management in Africa. PMID:23658271

  15. Genotyping of the fish rhabdovirus, viral haemorrhagic septicaemia virus, by restriction fragment length polymorphisms

    USGS Publications Warehouse

    Einer-Jensen, Katja; Winton, James R.; Lorenzen, Niels

    2005-01-01

    The aim of this study was to develop a standardized molecular assay that used limited resources and equipment for routine genotyping of isolates of the fish rhabdovirus, viral haemorrhagic septicaemia virus (VHSV). Computer generated restriction maps, based on 62 unique full-length (1524 nt) sequences of the VHSV glycoprotein (G) gene, were used to predict restriction fragment length polymorphism (RFLP) patterns that were subsequently grouped and compared with a phylogenetic analysis of the G-gene sequences of the same set of isolates. Digestion of PCR amplicons from the full-lengthG-gene by a set of three restriction enzymes was predicted to accurately enable the assignment of the VHSV isolates into the four major genotypes discovered to date. Further sub-typing of the isolates into the recently described sub-lineages of genotype I was possible by applying three additional enzymes. Experimental evaluation of the method consisted of three steps: (i) RT-PCR amplification of the G-gene of VHSV isolates using purified viral RNA as template, (ii) digestion of the PCR products with a panel of restriction endonucleases and (iii) interpretation of the resulting RFLP profiles. The RFLP analysis was shown to approximate the level of genetic discrimination obtained by other, more labour-intensive, molecular techniques such as the ribonuclease protection assay or sequence analysis. In addition, 37 previously uncharacterised isolates from diverse sources were assigned to specific genotypes. While the assay was able to distinguish between marine and continental isolates of VHSV, the differences did not correlate with the pathogenicity of the isolates.

  16. Molecular characterization, distribution, and dynamics of hepatitis C virus genotypes in blood donors in Colombia.

    PubMed

    Mora, Mónica Viviana Alvarado; Romano, Camila Malta; Gomes-Gouvêa, Michele Soares; Gutiérrez, Maria Fernanda; Carrilho, Flair José; Pinho, João Renato Rebello

    2010-11-01

    Hepatitis C virus (HCV) is a frequent cause of acute and chronic hepatitis and a leading cause for cirrhosis of the liver and hepatocellular carcinoma. HCV is classified in six major genotypes and more than 70 subtypes. In Colombian blood banks, serum samples were tested for anti-HCV antibodies using a third-generation ELISA. The aim of this study was to characterize the viral sequences in plasma of 184 volunteer blood donors who attended the "Banco Nacional de Sangre de la Cruz Roja Colombiana," Bogotá, Colombia. Three different HCV genomic regions were amplified by nested PCR. The first of these was a segment of 180 bp of the 5'UTR region to confirm the previous diagnosis by ELISA. From those that were positive to the 5'UTR region, two further segments were amplified for genotyping and subtyping by phylogenetic analysis: a segment of 380 bp from the NS5B region; and a segment of 391 bp from the E1 region. The distribution of HCV subtypes was: 1b (82.8%), 1a (5.7%), 2a (5.7%), 2b (2.8%), and 3a (2.8%). By applying Bayesian Markov chain Monte Carlo simulation, it was estimated that HCV-1b was introduced into Bogotá around 1950. Also, this subtype spread at an exponential rate between about 1970 to about 1990, after which transmission of HCV was reduced by anti-HCV testing of this population. Among Colombian blood donors, HCV genotype 1b is the most frequent genotype, especially in large urban conglomerates such as Bogotá, as is the case in other South American countries. PMID:20872715

  17. Hepatitis B Virus Genotype D Isolates Circulating in Chapecó, Southern Brazil, Originate from Italy.

    PubMed

    Gusatti, Carolina Souza; Costi, Cintia; Halon, Maria Laura; Grandi, Tarciana; Medeiros, Arlete Ferrari Rech; Silva, Cláudia Maria Dornelles; Gomes, Selma Andrade; Silva, Marcia Susana Nunes; Niel, Christian; Rossetti, Maria Lucia Rosa

    2015-01-01

    Hepatitis B virus genotype A1 (HBV/A1), of African origin, is the most prevalent genotype in Brazil, while HBV/F predominates in the other South American countries. However, HBV/D is the most common in the three states of southern Brazil, where 'islands' of elevated prevalence, as Chapecó and other cities, have been described. In this study, 202 HBV chronic carriers attending in 2013 the viral hepatitis ambulatory of Chapecó, were investigated. In comparison with previous studies performed in the same ambulatory, a rapid aging of the HBV infected population was observed (mean age of the newly diagnosed patients increasing from 29.9 ± 10.3 years in 1996 to 44.4 ± 13.3 years in 2013), probably due to a singular vaccination schedule at Chapecó that included not only children but also adolescents. Phylogenetic and BLAST analyses (S region) classified 91 HBV isolates into genotypes A (n = 3) and D (n = 88). The majority of HBV/D isolates were closely related to D3 sequences. To understand the reasons for the absence or near absence of genotypes A and F, and how HBV/D was introduced in the south of Brazil, HBV/D infected patients were inquired about their genealogical and geographical origins. Forty-three (52%) patients have their four grandparents of Italian origin, vs. seven (8%) who have their four grandparents of Brazilian origin. At all, 65 out of 83 (78%) patients had at least one grandparent originating from Italy. Taking into consideration the fact that Italy is one of the few countries where subgenotype D3 is predominant, the results strongly suggested that HBV/D was introduced in Brazil through Italian immigration which culminated between 1870 and 1920. PMID:26275046

  18. Genotype Considerations for Virus-Like Particle-Based Bivalent Norovirus Vaccine Composition

    PubMed Central

    Malm, Maria; Tamminen, Kirsi; Lappalainen, Suvi; Uusi-Kerttula, Hanni; Vesikari, Timo

    2015-01-01

    Norovirus (NoV) genogroup I (GI) and GII are responsible for most human infections with NoV. Because of the high genetic variability of NoV, natural infection does not induce sufficient protective immunity to different genotypes or to variants of the same genotype and there is little or no cross-protection against different genogroups. NoV-derived virus-like particles (VLPs) are promising vaccine candidates that induce high levels of NoV-specific humoral and cellular immune responses. It is believed that a bivalent NoV vaccine consisting of a representative VLP from GI and GII is a minimum requirement for an effective vaccine. Here, we compared the abilities of monovalent immunizations with NoV GI.1-2001, GI.3-2002, GII.4-1999, and GII.4-2010 New Orleans VLPs to induce NoV type-specific and cross-reactive immune responses and protective blocking antibody responses in BALB/c mice. All of the VLPs induced comparable levels of type-specific serum IgG antibodies, as well as blocking antibodies to the VLPs used for immunization. However, the abilities of different VLP genotypes to induce cross-reactive IgG and cross-blocking antibodies varied remarkably. Our results confirm previous findings of a lack of cross-protective immune responses between GI and GII NoVs. These data support the rationale for including NoV GI.3 and GII.4-1999 VLPs in the bivalent vaccine formulation, which could be sufficient to induce protective immune responses across NoV genotypes in the two common genogroups in humans. PMID:25903355

  19. Genotype 1 hepatitis C virus envelope features that determine antiviral response assessed through optimal covariance networks.

    PubMed

    Murray, John M; Moenne-Loccoz, Rémy; Velay, Aurélie; Habersetzer, François; Doffoël, Michel; Gut, Jean-Pierre; Fofana, Isabel; Zeisel, Mirjam B; Stoll-Keller, Françoise; Baumert, Thomas F; Schvoerer, Evelyne

    2013-01-01

    The poor response to the combined antiviral therapy of pegylated alfa-interferon and ribavarin for hepatitis C virus (HCV) infection may be linked to mutations in the viral envelope gene E1E2 (env), which can result in escape from the immune response and higher efficacy of viral entry. Mutations that result in failure of therapy most likely require compensatory mutations to achieve sufficient change in envelope structure and function. Compensatory mutations were investigated by determining positions in the E1E2 gene where amino acids (aa) covaried across groups of individuals. We assessed networks of covarying positions in E1E2 sequences that differentiated sustained virological response (SVR) from non-response (NR) in 43 genotype 1a (17 SVR), and 49 genotype 1b (25 SVR) chronically HCV-infected individuals. Binary integer programming over covariance networks was used to extract aa combinations that differed between response groups. Genotype 1a E1E2 sequences exhibited higher degrees of covariance and clustered into 3 main groups while 1b sequences exhibited no clustering. Between 5 and 9 aa pairs were required to separate SVR from NR in each genotype. aa in hypervariable region 1 were 6 times more likely than chance to occur in the optimal networks. The pair 531-626 (EI) appeared frequently in the optimal networks and was present in 6 of 9 NR in one of the 1a clusters. The most frequent pairs representing SVR were 431-481 (EE), 500-522 (QA) in 1a, and 407-434 (AQ) in 1b. Optimal networks based on covarying aa pairs in HCV envelope can indicate features that are associated with failure or success to antiviral therapy. PMID:23840641

  20. Hepatitis B Virus Genotype D Isolates Circulating in Chapecó, Southern Brazil, Originate from Italy

    PubMed Central

    Gusatti, Carolina Souza; Costi, Cintia; Halon, Maria Laura; Grandi, Tarciana; Medeiros, Arlete Ferrari Rech; Silva, Cláudia Maria Dornelles; Gomes, Selma Andrade; Silva, Marcia Susana Nunes; Niel, Christian; Rossetti, Maria Lucia Rosa

    2015-01-01

    Hepatitis B virus genotype A1 (HBV/A1), of African origin, is the most prevalent genotype in Brazil, while HBV/F predominates in the other South American countries. However, HBV/D is the most common in the three states of southern Brazil, where ‘islands’ of elevated prevalence, as Chapecó and other cities, have been described. In this study, 202 HBV chronic carriers attending in 2013 the viral hepatitis ambulatory of Chapecó, were investigated. In comparison with previous studies performed in the same ambulatory, a rapid aging of the HBV infected population was observed (mean age of the newly diagnosed patients increasing from 29.9 ± 10.3 years in 1996 to 44.4 ± 13.3 years in 2013), probably due to a singular vaccination schedule at Chapecó that included not only children but also adolescents. Phylogenetic and BLAST analyses (S region) classified 91 HBV isolates into genotypes A (n = 3) and D (n = 88). The majority of HBV/D isolates were closely related to D3 sequences. To understand the reasons for the absence or near absence of genotypes A and F, and how HBV/D was introduced in the south of Brazil, HBV/D infected patients were inquired about their genealogical and geographical origins. Forty-three (52%) patients have their four grandparents of Italian origin, vs. seven (8%) who have their four grandparents of Brazilian origin. At all, 65 out of 83 (78%) patients had at least one grandparent originating from Italy. Taking into consideration the fact that Italy is one of the few countries where subgenotype D3 is predominant, the results strongly suggested that HBV/D was introduced in Brazil through Italian immigration which culminated between 1870 and 1920. PMID:26275046

  1. Analysis of the Molecular Evolution of Hepatitis B Virus Genotypes in Symptomatic Acute Infections in Argentina

    PubMed Central

    Rodrigo, María Belén; Mojsiejczuk, Laura Noelia; Torres, Carolina; Sevic, Ina; González López Ledesma, María Mora; Perez, Paula Soledad; Bouzas, María Belén; Galdame, Omar; Marciano, Sebastián; Fainboim, Hugo; Flichman, Diego Martín; Campos, Rodolfo Héctor

    2016-01-01

    Hepatitis B virus (HBV) is a globally distributed human pathogen that leads to both self-limited and chronic infections. At least eight genotypes (A-H) with distinct geographical allocations and phylodynamic behaviors have been described. They differ substantially in many virological and probably some clinical parameters. The aim of this study was to analyze full-length HBV genome sequences from individuals with symptomatic acute HBV infections using phylogenetic and coalescent methods. The phylogenetic analysis resulted in the following subgenotype distribution: F1b (52.7%), A2 (18.2%), F4 (18.2%) and A1, B2, D3 and F2a 1.8% each. These results contrast with those previously reported from chronic infections, where subgenotypes F1b, F4, A2 and genotype D were evenly distributed. This differential distribution might be related to recent internal migrations and/or intrinsic biological features of each viral genotype that could impact on the probability of transmission. The coalescence analysis showed that after a diversification process started in the 80s, the current sequences of subgenotype F1b were grouped in at least four highly supported lineages, whereas subgenotype F4 revealed a more limited diversification pattern with most lineages without offspring in the present. In addition, the genetic characterization of the studied sequences showed that only two of them presented mutations of clinical relevance at S codifyng region and none at the polymerase catalytic domains. Finally, since the acute infections could be an expression of the genotypes currently being transmitted to new hosts, the predominance of subgenotype F1b might have epidemiological, as well as, clinical relevance due to its potential adverse disease outcome among the chronic cases. PMID:27433800

  2. Development of an improved genotyping assay for the detection of hepatitis C virus genotypes and subtypes in Pakistan.

    PubMed

    Idrees, Muhammad

    2008-06-01

    A new genotyping system was established for the specific detection of HCV genotypes 1a, 1b, 1c, 2a, 2b, 2c, 3a, 3b, 3c, 4a-h, 5a and 6a during the course of this study. The system is based on entire core region and a part of 5' noncoding region (5'NCR) with genotype-specific primers. Genotype-specific primers were designed on the basis of 114 HCV isolates. Serum samples with known genotypes were used as positive controls to validate the assay developed and to generate PCR band patterns. Band patterns generated from the clinical serum samples from HCV patients were compared to the patterns produced from these control samples. In addition, the type-specific bands were sequenced from the test patients and control clinical samples to validate further the test results. To determine sensitivity and specificity of the assay, a total 260 samples were analyzed simultaneously by this HCV genotyping method and that developed by Ohno and Murex HCV Serotyping 1-6 Assay. The system showed 79.2% concordance with Ohno's system and 65.38% with serotyping system. Samples with discordant results were sequenced and their genotypes were determined by molecular evolutionary analysis. The data indicate that the method described in this study may offer better sensitivity and specificity for the detection directly of HCV genotypes present at low levels in HCV patient samples. PMID:18423633

  3. Pathologic characterization of genotypes XIV and XVII Newcastle disease viruses and efficacy of classical vaccination on specific pathogen-free birds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To characterize the clinico-pathological characteristics of recently-described genotypes of Newcastle disease virus (NDV), one representative strain of genotype XIV and two of genotype XVII, all isolated from West Africa, were used to infect four-week-old, specific pathogen free (SPF) chickens. The ...

  4. Complete genome sequence of two genotype III Japanese encephalitis virus isolates from West Bengal, India

    PubMed Central

    Taraphdar, Debjani; Chatterjee, Shyamalendu

    2015-01-01

    Background & objectives: Japanese encephalitis (JE), caused by a mosquito-borne virus JE virus (JEV), is a serious health problem in West Bengal, India. In this study, we report the complete genome sequence of two JEV isolates from West Bengal. The amino acid and nucleotide sequence homology was compared with other Indian strains. Methods: Two JEV isolates (IND-WB-JE1 and IND-WB-JE2) obtained in 2008 and 2010, respectively, from two districts of the State of West Bengal, respectively were analyzed for genetic variations by sequencing the 10934 bp whole genome of the virus. Of these two districts, one was covered under JE vaccination programme in 2007. Results: Phylogenetic analysis showed that both the isolates belonged to the genotype III. A total of 16 mutations were identified in the two isolates studied with respect to Vellore P20778 strain. One unique mutation A3215S was only found in IND-WB-JE2 isolate, but not in the isolate IND-WB-JE1. These two isolates showed maximum homology with P20778 strain of India. Interpretation & conclusions: This study reports on complete gene based phylogenetic analysis of JEV isolates from the State of West Bengal. It was evident from the results that JEV was still under circulation in both vaccine covered and not covered districts of West Bengal. PMID:26261169

  5. Cell culture replication of a genotype 1b hepatitis C virus isolate cloned from a patient who underwent liver transplantation.

    PubMed

    Koutsoudakis, George; Perez-del-Pulgar, Sofia; Coto-Llerena, Mairene; Gonzalez, Patricia; Dragun, Jakub; Mensa, Laura; Crespo, Gonzalo; Navasa, Miguel; Forns, Xavier

    2011-01-01

    The introduction of the genotype 2a isolate JFH1 was a major breakthrough in the field of hepatitis C virus (HCV), allowing researchers to study the complete life cycle of the virus in cell culture. However, fully competent culture systems encompassing the most therapeutically relevant HCV genotypes are still lacking, especially for the highly drug-resistant genotype 1b. For most isolated HCV clones, efficient replication in cultured hepatoma cells requires the introduction of replication-enhancing mutations. However, such mutations may interfere with viral assembly, as occurs in the case of the genotype 1b isolate Con1. In this study, we show that a clinical serum carrying a genotype 1b virus with an exceptionally high viral load was able to infect Huh7.5 cells. Similar to previous reports, inoculation of Huh7.5 cells by natural virus is very inefficient compared to infection by cell culture HCV. A consensus sequence of a new genotype 1b HCV isolate was cloned from the clinical serum (designated Barcelona HCV1), and then subjected to replication studies. This virus replicated poorly in a transient fashion in Huh7.5 cells after electroporation with in vitro transcribed RNA. Nonetheless, approximately 3 weeks post electroporation and thereafter, core protein-positive cells were detected by immunofluorescence. Surprisingly, small amounts of core protein were also measurable in the supernatant of electroporated cells, suggesting that HCV particles might be assembled and released. Our findings not only enhance the current method of cloning in vitro HCV replication-competent isolates, but also offer valuable insights for the realization of fully competent culture systems for HCV. PMID:21887279

  6. Cell Culture Replication of a Genotype 1b Hepatitis C Virus Isolate Cloned from a Patient Who Underwent Liver Transplantation

    PubMed Central

    Koutsoudakis, George; Perez-del-Pulgar, Sofia; Coto-Llerena, Mairene; Gonzalez, Patricia; Dragun, Jakub; Mensa, Laura; Crespo, Gonzalo; Navasa, Miguel; Forns, Xavier

    2011-01-01

    The introduction of the genotype 2a isolate JFH1 was a major breakthrough in the field of hepatitis C virus (HCV), allowing researchers to study the complete life cycle of the virus in cell culture. However, fully competent culture systems encompassing the most therapeutically relevant HCV genotypes are still lacking, especially for the highly drug-resistant genotype 1b. For most isolated HCV clones, efficient replication in cultured hepatoma cells requires the introduction of replication-enhancing mutations. However, such mutations may interfere with viral assembly, as occurs in the case of the genotype 1b isolate Con1. In this study, we show that a clinical serum carrying a genotype 1b virus with an exceptionally high viral load was able to infect Huh7.5 cells. Similar to previous reports, inoculation of Huh7.5 cells by natural virus is very inefficient compared to infection by cell culture HCV. A consensus sequence of a new genotype 1b HCV isolate was cloned from the clinical serum (designated Barcelona HCV1), and then subjected to replication studies. This virus replicated poorly in a transient fashion in Huh7.5 cells after electroporation with in vitro transcribed RNA. Nonetheless, approximately 3 weeks post electroporation and thereafter, core protein-positive cells were detected by immunofluorescence. Surprisingly, small amounts of core protein were also measurable in the supernatant of electroporated cells, suggesting that HCV particles might be assembled and released. Our findings not only enhance the current method of cloning in vitro HCV replication-competent isolates, but also offer valuable insights for the realization of fully competent culture systems for HCV. PMID:21887279

  7. Molecular variants of human papilloma virus 16 E2, E4, E5, E6 and E7 genes associated with cervical neoplasia in Romanian patients.

    PubMed

    Plesa, Adriana; Anton, Gabriela; Iancu, Iulia V; Diaconu, Carmen C; Huica, Irina; Stanescu, Anca D; Socolov, Demetra; Nistor, Elena; Popa, Elena; Stoian, Mihai; Botezatu, Anca

    2014-12-01

    The aim of this study was to identify and associate the sequence variations of human Papillomavirus 16 (HPV16) genes from women who live in two different areas of Romania and associate them with malignant progression. One hundred twenty-four HPV16-positive cervical isolates were collected, and the E2, E4, E5, E6 and E7 viral genes were sequenced. Two new missense mutations in the E6 gene (C279G and A305C) were found (together or alone, in association with other mutations) in 44 of 124 cases. The most frequently simultaneously mutated genes were E4/E2 hinge, E5 and E6 (p = 0.0004) in squamous cell carcinoma (SCC) samples. Also, for SCC patients, the best-correlated mutation patterns were obtained for E4/E2 hinge-E5 (r = 0.7984; p < 0.0001). No sample was found to have all of the investigated viral genes concurrently mutated. Phylogenetic analysis was performed to characterize the viral variants. Similar results were found for SCC and cervical intraepithelial neoplasia III (CINIII) cases. After all of the target gene sequences were assembled, all patients were found to be infected with viruses of the HPV16- European-German (EG) lineage, and two clusters were identified, the first (55/96 variants) from Moldavia and the second (41/96 variants) from Bucharest. The distinct cluster derived from EG in Moldavia could partially explain the increased frequency of SCC in this area. This study has generated a comprehensive set of sequence variation data on HPV16 circulating in Romania to join the existing data and highlight the important role of HPV16 variants during cervical carcinogenesis. PMID:25143263

  8. Development of RT-qPCR assays for the specific identification of two major genotypes of avian infectious bronchitis virus.

    PubMed

    Marandino, Ana; Tomás, Gonzalo; Hernández, Martín; Panzera, Yanina; Craig, María Isabel; Vagnozzi, Ariel; Vera, Federico; Techera, Claudia; Grecco, Sofía; Banda, Alejandro; Hernández, Diego; Pérez, Ruben

    2016-09-01

    Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus (27.6kb) that causes one of the most persistent respiratory disease in poultry. The virus is classified in genotypes with different epidemiological relevance and clinical implications. The present study reports the development and validation of specific RT-qPCR assays for the detection of two major IBV genotypes: South America I (SAI) and Asia/South America II (A/SAII). The SAI genotype is an exclusive and widespread South American lineage while the A/SAII genotype is distributed in Asia, Europe and South America. Both identification assays employ TaqMan probes that hybridize with unique sequences in the spike glycoprotein gene. The assays successfully detected all the assessed strains belonging to both genotypes, showing high specificity and absence of cross-reactivity. Using serial dilutions of in vitro-transcribed RNA we obtained acceptable determination coefficients, PCR efficiencies and relatively small intra- and inter-assay variability. The assays demonstrated a wide dynamic range between 10(1)-10(7) and 10(2)-10(7) RNA copies/reaction for SAI and A/SAII strains, respectively. The possibility to characterize a large number of samples in a rapid, sensitive and reproducible way makes these techniques suitable tools for routine testing, IBV control, and epidemiological research in poultry. PMID:27181213

  9. Genotypes and phylogeographical relationships of infectious hematopoietic necrosis virus in California, USA

    USGS Publications Warehouse

    Kelley, G.O.; Bendorf, C.M.; Yun, S.C.; Kurath, G.; Hedrick, R.P.

    2007-01-01

    Infectious hematopoietic necrosis virus (IHNV) contains 3 major genogroups in North America with discreet geographic ranges designated as upper (U), middle (M), and lower (L). A comprehensive genotyping of 237 IHNV isolates from hatchery and wild salmonids in California revealed 25 different sequence types (a to y) all in the L genogroup; specifically, the genogroup contained 14 sequence types that were unique to individual isolates as well as 11 sequence types representing 2 or more identical isolates. The most evident trend was the phylogenetic and geographical division of the L genogroup into 2 distinct subgroups designated as LI and LII. Isolates within Subgroup LI were primarily found within waterways linked to southern Oregon and northern California coastal rivers. Isolates in Subgroup LII were concentrated within inland valley watersheds that included the Sacramento River, San Joaquin River, and their tributaries. The temporal and spatial patterns of virus occurrence suggested that infections among adult Chinook salmon in the hatchery or that spawn in the river are a major source of virus potentially infecting other migrating or resident salmonids in California. Serum neutralization results of the California isolates of IHNV corroborated a temporal trend of sequence divergence; specifically, 2 progressive shifts in which more recent virus isolates represent new serotypes. A comparison of the estimates of divergence rates for Subgroup LI (1 ?? ICT5 mutations per nucleotide site per year) indicated stasis similar to that observed in the U genogroup, while the Subgroup LII rate (1 ?? 10 3 mutations per nucleotide site per year) suggested a more active evolution similar to that of the M genogroup. ?? Inter-Research 2007.

  10. Chronically infected wild boar can transmit genotype 3 hepatitis E virus to domestic pigs.

    PubMed

    Schlosser, Josephine; Vina-Rodriguez, Ariel; Fast, Christine; Groschup, Martin H; Eiden, Martin

    2015-10-22

    Hepatitis E virus (HEV) causes acute hepatitis E in humans in developing countries, but sporadic and autochthonous cases do also occur in industrialized nations. In Europe, food-borne zoonotic transmission of genotype 3 (gt3) has been associated with the consumption of raw and undercooked products from domestic pig and wild boar. As shown recently, naturally acquired HEV gt3 replicates efficiently in experimentally infected wild boar and is transmissible from a wild boar to domestic pigs. Generally, following an acute infection swine suffer from a transient febrile illness and viremia in connection with fecal virus shedding. However, little is known about sub-acute or chronic HEV infections in swine, and how and where HEV survives the immune response. In this paper, we describe the incidental finding of a chronic HEVgt3 infection in two naturally infected European wild boar which were raised and housed at FLI over years. The wild boar displayed fecal HEV RNA excretion and viremia over nearly the whole observation period of more than five months. The animal had mounted a substantial antibody response, yet without initial clearance of the virus by the immune system. Further analysis indicated a subclinical course of HEV with no evidence of chronic hepatitis. Additionally, we could demonstrate that this chronic wild boar infection was still transmissible to domestic pigs, which were housed together with this animal. Sentinel pigs developed fecal virus shedding accompanied by seroconversion. Wild boar should therefore be considered as an important reservoir for transmission of HEV gt3 in Europe. PMID:26344041

  11. Complete genome sequence of a genotype XVII Newcastle disease virus, isolated from an apparently healthy domestic duck in Nigeria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The first complete genome sequence of a strain of Newcastle disease virus (NDV) of genotype XVII is described here. A velogenic strain (duck/Nigeria/903/KUDU-113/1992) was isolated from an apparently healthy free-roaming domestic duck sampled in Kuru, Nigeria, in 1992. Phylogenetic analysis of the f...

  12. Molecular Characterization of two Potato Virus S Isolates from Late Blight Resistant Genotypes of Potato (Solanum tuberosum)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Potato virus S (PVS) has a widespread distribution in the U.S. However, only two complete nucleotide sequences have been published. A recent survey of potato fields in the state of Washington confirms that PVS is widely prevalent. Late blight resistant (LBR) potato cultivars and genotypes were sho...

  13. Characterization and Sequencing of a Genotype VIId Newcastle Disease Virus Isolated from Laying Ducks in Jiangsu, China

    PubMed Central

    Liu, Mei; Shen, Xinyue; Cheng, Xu; Li, Jianmei

    2015-01-01

    We report here the complete genome sequence and biological characterization of a virulent Newcastle disease virus (NDV) strain, NDV/duck/Jiangsu/JSD0812/2008, isolated from laying ducks in Jiangsu Province, China. The genome is 15,192 nucleotides in length and is classified in subgenotype VIId of genotype VII, class II. PMID:26634760

  14. Complete Genome Sequence of Genotype Ib Newcastle Disease Virus Isolated from a Mallard (Anas platyrhynchos) in Russia

    PubMed Central

    Sobolev, Ivan A.; Glushchenko, Alexandra V.; Shestopalov, Alexander M.

    2015-01-01

    We report here the complete genome sequence of a Newcastle disease virus isolate, NDV/Yakutiya/mallard/852/2011, isolated from a mallard in Russia. On the basis of phylogenetic analysis, this strain was clustered into class II genotype Ib. PMID:26634762

  15. Characterization and Sequencing of a Genotype VIId Newcastle Disease Virus Isolated from Laying Ducks in Jiangsu, China.

    PubMed

    Liu, Mei; Shen, Xinyue; Cheng, Xu; Li, Jianmei; Dai, Yabin

    2015-01-01

    We report here the complete genome sequence and biological characterization of a virulent Newcastle disease virus (NDV) strain, NDV/duck/Jiangsu/JSD0812/2008, isolated from laying ducks in Jiangsu Province, China. The genome is 15,192 nucleotides in length and is classified in subgenotype VIId of genotype VII, class II. PMID:26634760

  16. Characterization and Sequencing of a Genotype XII Newcastle Disease Virus Isolated from a Peacock (Pavo cristatus) in Peru

    PubMed Central

    Izquierdo-Lara, Ray; Tataje-Lavanda, Luis; Figueroa, Aling; Segovia, Karen; Gonzalez, Rosa; Cribillero, Giovana; Montalvan, Angela; Fernández-Díaz, Manolo; Icochea, Eliana

    2015-01-01

    Here, we report the first complete sequence and biological characterization of a Newcastle disease virus (NDV) isolated from a peacock in South America (NDV/peacock/Peru/2011). This isolate, classified as genotype XII in class II, highlights the need for increased surveillance of noncommercial avian species. PMID:26227592

  17. Characterization and Sequencing of a Genotype XII Newcastle Disease Virus Isolated from a Peacock (Pavo cristatus) in Peru.

    PubMed

    Chumbe, Ana; Izquierdo-Lara, Ray; Tataje-Lavanda, Luis; Figueroa, Aling; Segovia, Karen; Gonzalez, Rosa; Cribillero, Giovana; Montalvan, Angela; Fernández-Díaz, Manolo; Icochea, Eliana

    2015-01-01

    Here, we report the first complete sequence and biological characterization of a Newcastle disease virus (NDV) isolated from a peacock in South America (NDV/peacock/Peru/2011). This isolate, classified as genotype XII in class II, highlights the need for increased surveillance of noncommercial avian species. PMID:26227592

  18. Environment and host genotype determine the outcome of a plant-virus interaction: from antagonism to mutualism.

    PubMed

    Hily, Jean-Michel; Poulicard, Nils; Mora, Miguel-Ángel; Pagán, Israel; García-Arenal, Fernando

    2016-01-01

    It has been hypothesized that plant-virus interactions vary between antagonism and conditional mutualism according to environmental conditions. This hypothesis is based on scant experimental evidence, and to test it we examined the effect of abiotic factors on the Arabidopsis thaliana-Cucumber mosaic virus (CMV) interaction. Four Arabidopsis genotypes clustering into two allometric groups were grown under six environments defined by three temperature and two light-intensity conditions. Plants were either CMV-infected or mock-inoculated, and the effects of environment and infection on temporal and resource allocation life-history traits were quantified. Life-history traits significantly differed between allometric groups over all environments, with group 1 plants tolerating abiotic stress better than those of group 2. The effect of CMV infection on host fitness (virulence) differed between genotypes, being lower in group 1 genotypes. Tolerance to abiotic stress and to infection was similarly achieved through life-history trait responses, which resulted in resource reallocation from growth to reproduction. Effects of infection varied according to plant genotype and environment from detrimental to beneficial for host fitness. These results are highly relevant and demonstrate that plant viruses can be pleiotropic parasites along the antagonism-mutualism continuum, which should be considered in analyses of the evolution of plant-virus interactions. PMID:26365599

  19. Hepatitis B virus genotypes and G1896A precore mutation in 486 Spanish patients with acute and chronic HBV infection.

    PubMed

    Rodriguez-Frias, F; Jardi, R; Buti, M; Schaper, M; Hermosilla, E; Valdes, A; Allende, H; Martell, M; Esteban, R; Guardia, J

    2006-05-01

    This study aims to determine the prevalence of hepatitis B virus (HBV) genotypes (A-F) and their association with the G1896A precore mutation in 486 patients positive for HBV surface antigen. Genotypes were determined by RFLP and precore mutation by real-time PCR. Genotypes D (48.1%) and A (39.5%) were the most common, followed by F (4.1%) and B, C and E (<1%). The A to D ratio (A:D) was 1.4 in HBeAg+ chronic hepatitis B (CHB), 0.6 in HBeAg- CHB and 1.4 in HBeAg- inactive carriers. Distribution of these genotypes was different between HBeAg+ CHB and HBeAg- CHB (P = 0.02), and between HBeAg- CHB and HBeAg- inactive carriers (P = 0.009). Genotype A was the most prevalent in HBeAg+ CHB with elevated alanine aminotransferase (ALT) (68.6%) and genotype D in HBeAg+ CHB with fluctuating ALT (60.7%). There was a difference in genotype prevalence between chronic and acute infection (P = 0.03). The precore mutant correlated with high levels of HBV-DNA in genotype d HBeAg- CHB. Genotype D is not as highly prevalent in Spanish patients as would be expected in a Mediterranean area. The unequal prevalence of genotypes between acute and chronic infection suggests that genotype A is associated with a higher tendency to cause chronic infection. PMID:16637866

  20. Virology. Mutation rate and genotype variation of Ebola virus from Mali case sequences.

    PubMed

    Hoenen, T; Safronetz, D; Groseth, A; Wollenberg, K R; Koita, O A; Diarra, B; Fall, I S; Haidara, F C; Diallo, F; Sanogo, M; Sarro, Y S; Kone, A; Togo, A C G; Traore, A; Kodio, M; Dosseh, A; Rosenke, K; de Wit, E; Feldmann, F; Ebihara, H; Munster, V J; Zoon, K C; Feldmann, H; Sow, S

    2015-04-01

    The occurrence of Ebola virus (EBOV) in West Africa during 2013-2015 is unprecedented. Early reports suggested that in this outbreak EBOV is mutating twice as fast as previously observed, which indicates the potential for changes in transmissibility and virulence and could render current molecular diagnostics and countermeasures ineffective. We have determined additional full-length sequences from two clusters of imported EBOV infections into Mali, and we show that the nucleotide substitution rate (9.6 × 10(-4) substitutions per site per year) is consistent with rates observed in Central African outbreaks. In addition, overall variation among all genotypes observed remains low. Thus, our data indicate that EBOV is not undergoing rapid evolution in humans during the current outbreak. This finding has important implications for outbreak response and public health decisions and should alleviate several previously raised concerns. PMID:25814067

  1. Serological evidence of type 2 (North American genotype) porcine reproductive and respiratory syndrome virus in Nepal.

    PubMed

    Sharma, Barun Kumar; Manandhar, Salina; Devleesschauwer, Brecht

    2016-03-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) has spread throughout Asia, causing significant losses to commercial farmers and smallholders. However, little is known about PRRS in Nepal, a South Asian country with a gradually increasing pig industry. In 2011, a pilot project was initiated to identify the status of PRRSV in pigs of the Kathmandu Valley of Nepal. Out of 98 serum samples, 31 (32 %; 95 % CI 23-42 %) were found positive by ELISA. All positive samples belonged to the type 2 (North American) genotype. Molecular evaluation by real-time PCR however did not yield positive results. At the herd level, seropositivity was associated with a history of abortion and premature birth. Veterinarians, farmers and government should be aware of this threat to the Nepalese pig industry and initiate an appropriate response. PMID:26712360

  2. Characterization of partial NS5B region among hepatitis C virus genotype 6 subtypes isolated from Thai blood donors.

    PubMed

    Chaiwong, Suriya; Sistayanarain, Anchalee

    2016-10-01

    The hepatitis C virus (HCV) is an important cause of liver dysfunction which continues to spread in Thailand, particularly as genotype 6. The NS5B gene fragment is particularly variable and thus provides a valuable tracker for its spread. Therefore, the purpose of this study was to characterize the HCV genotype 6 based on partial NS5B region using Thai blood donor samples. Twenty-nine samples were genotyped as HCV 6 by nested PCR, nucleotide sequencing and amino acid sequence analysis. Amplified products were identified as HCV genotypes 6f, 6c, 6n, and 6i. There were amino acid variations of 4-18 residues in subtypes 6f, 6c, and 6n whereas subtype 6i was conserved when compared with their referent strains. In subtypes 6f, 6c, 6n, and 6i, the amino acid mutations at positions 244, 309, and 310 which are associated with HCV resistance were present. In summary, the sequences and phylogenetic analysis of NS5B of HCV used in our study yielded the genotypes 6f, 6c, 6n, and 6i. This finding indicates diversity of amino acids in NS5B of HCV. Characterizing the partial NS5B region among hepatitis C virus genotype 6 subtypes may predict efficacious anti-HCV therapy. J. Med. Virol. 88:1785-1790, 2016. © 2016 Wiley Periodicals, Inc. PMID:27018495

  3. Genotyping of infectious laryngotracheitis virus using allelic variations from multiple genomic regions.

    PubMed

    Choi, Eun-Jung; La, Tae-Min; Choi, In-Soo; Song, Chang-Seon; Park, Seung-Yong; Lee, Joong-Bok; Lee, Sang-Won

    2016-08-01

    Live attenuated vaccines are extensively used worldwide to control the outbreak of infectious laryngotracheitis. Virulent field strains showing close genetic relationship with the infectious laryngotracheitis virus (ILTV) vaccines of chicken embryo origin have been detected in the poultry industry. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, a reliable molecular epidemiological method, of multiple genomic regions was performed. The PCR-RFLP is a time-consuming method that requires considerable amount of intact viral genomic DNA to amplify genomic regions greater than 4 kb. In this study, six variable genomic regions were selected and amplified for sequencing. The multi-allelic PCR-sequence genotyping showed better discrimination power than that of previous PCR-sequencing schemes using single or two target regions. The allelic variation patterns yielded 16 strains of ILTV classified into 14 different genotypes. Three Korean field strains, 550/05/Ko, 0010/05/Ko and 40032/08/Ko, were found to have the same genotype as the commercial vaccine strain, Laryngo Vac (Zoetis, Florham Park, NJ, USA). Three other Korean field strains, 40798/10/Ko, 12/07/Ko, and 30678/14/Ko, showed recombined allelic patterns. The multi-allelic PCR-sequencing method was proved to be an efficient and practical procedure to classify the different strains of ILTV. The method could serve as an alternate diagnostic and differentiating tool for the classification of ILTV, and contribute to understanding of the epidemiology of the disease at a global level. PMID:26956802

  4. Hepatitis C virus prevalence and genotype distribution in Pakistan: Comprehensive review of recent data

    PubMed Central

    Umer, Muhammad; Iqbal, Mazhar

    2016-01-01

    Hepatitis C virus (HCV) is endemic in Pakistan and its burden is expected to increase in coming decades owing mainly to widespread use of unsafe medical procedures. The prevalence of HCV in Pakistan has previously been reviewed. However, the literature search conducted here revealed that at least 86 relevant studies have been produced since the publication of these systematic reviews. A revised updated analysis was therefore needed in order to integrate the fresh data. A systematic review of data published between 2010 and 2015 showed that HCV seroprevalence among the general adult Pakistani population is 6.8%, while active HCV infection was found in approximately 6% of the population. Studies included in this review have also shown extremely high HCV prevalence in rural and underdeveloped peri-urban areas (up to 25%), highlighting the need for an increased focus on this previously neglected socioeconomic stratum of the population. While a 2.45% seroprevalence among blood donors demands immediate measures to curtail the risk of transfusion transmitted HCV, a very high prevalence in patients attending hospitals with various non-liver disease related complaints (up to 30%) suggests a rise in the incidence of nosocomial HCV spread. HCV genotype 3a continues to be the most prevalent subtype infecting people in Pakistan (61.3%). However, recent years have witnessed an increase in the frequency of subtype 2a in certain geographical sub-regions within Pakistan. In Khyber Pakhtunkhwa and Sindh provinces, 2a was the second most prevalent genotype (17.3% and 11.3% respectively). While the changing frequency distribution of various genotypes demands an increased emphasis on research for novel therapeutic regimens, evidence of high nosocomial transmission calls for immediate measures aimed at ensuring safe medical practices. PMID:26819533

  5. Pan-genotypic Hepatitis C Virus Inhibition by Natural Products Derived from the Wild Egyptian Artichoke

    PubMed Central

    Elsebai, Mahmoud Fahmi; Koutsoudakis, George; Saludes, Verónica; Pérez-Vilaró, Gemma; Turpeinen, Ari; Mattila, Sampo; Pirttilä, Anna Maria; Fontaine-Vive, Fabien; Mehiri, Mohamed; Meyerhans, Andreas

    2015-01-01

    ABSTRACT Hepatitis C virus (HCV) infection is the leading cause of chronic liver diseases. Water extracts of the leaves of the wild Egyptian artichoke (WEA) [Cynara cardunculus L. var. sylvestris (Lam.) Fiori] have been used for centuries in the Sinai Peninsula to treat hepatitis symptoms. Here we isolated and characterized six compounds from the water extracts of WEA and evaluated their HCV inhibition capacities in vitro. Importantly, two of these compounds, grosheimol and cynaropicrin, inhibited HCV with half-maximal effective concentrations (EC50s) in the low micromolar range. They inhibited HCV entry into target cells and were active against both cell-free infection as well as cell-cell transmission. Furthermore, the antiviral activity of both compounds was pan-genotypic as HCV genotypes 1a, 1b, 2b, 3a, 4a, 5a, 6a, and 7a were inhibited. Thus, grosheimol and cynaropicrin are promising candidates for the development of new pan-genotypic entry inhibitors of HCV infection. IMPORTANCE Because there is no preventive HCV vaccine available today, the discovery of novel anti-HCV cell entry inhibitors could help develop preventive measures against infection. The present study describes two compounds isolated from the wild Egyptian artichoke (WEA) with respect to their structural elucidation, absolute configuration, and quantitative determination. Importantly, both compounds inhibited HCV infection in vitro. The first compound was an unknown molecule, and it was designated “grosheimol,” while the second compound is the known molecule cynaropicrin. Both compounds belong to the group of sesquiterpene lactones. The mode of action of these compounds occurred during the early steps of the HCV life cycle, including cell-free and cell-cell infection inhibition. These natural compounds present promising candidates for further development into anti-HCV therapeutics. PMID:26656684

  6. Rapid genotyping of beak and feather disease virus using high-resolution DNA melt curve analysis.

    PubMed

    Sarker, Subir; Ghorashi, Seyed A; Forwood, Jade K; Raidal, Shane R

    2014-11-01

    Beak and feather disease virus (BFDV) is a significant pathogen both for wild and captive psittacine birds globally. Genotypic differentiation of BFDV isolates is crucial to establish effective control strategies for the conservation of endangered species and epidemiological investigations of disease outbreaks. The technique developed in this study is a simple, rapid and inexpensive genotyping method for BFDV using PCR and subsequent high-resolution melt (HRM) curve analysis. This was achieved using PCR amplification of the conserved Rep gene in the presence of a fluorescent DNA intercalating dye (SYTO9). HRM curve analysis of the resultant amplicon could readily differentiate between reference strain (92-SR14) and 18 other BFDV isolates used in this study. Analysis of the nucleotide sequences of the amplicon from each isolate revealed that each melt curve profile was related to a unique DNA sequence. The potential of the PCR-HRM curve analysis to differentiate inter-host genetic variation among critically endangered orange-bellied parrots, lorikeets and cockatoos was also evaluated. Phylogenetic tree topology based on partial Rep gene sequences used in this study showed that BFDV Rep gene sequence patterns were correlated with the results of HRM curve analysis. The results presented in this study indicate that this technique could be used in both clinical research and differentiation of BFDV isolates in a fraction of time without further nucleotide sequencing and provides a novel approach for the genetic screening of BFDV in clinical virology laboratories. PMID:25102431

  7. NK cell immunophenotypic and genotypic analysis of infants with severe respiratory syncytial virus infection.

    PubMed

    Noyola, Daniel E; Juárez-Vega, Guillermo; Monjarás-Ávila, César; Escalante-Padrón, Francisco; Rangel-Ramírez, Verónica; Cadena-Mota, Sandra; Monsiváis-Urenda, Adriana; García-Sepúlveda, Christian A; González-Amaro, Roberto

    2015-07-01

    Respiratory syncytial virus (RSV) is the leading cause of severe lower respiratory tract infection in infants. Reduced numbers of NK cells have been reported in infants with severe RSV infection; however, the precise role of NK cells during acute RSV infection is unclear. In this study the NK and T cell phenotypes, LILRB1 gene polymorphisms and KIR genotypes of infants hospitalized with RSV infection were analyzed. Compared to controls, infants with acute RSV infection showed a higher proportion of LILRB1+ T cells; in addition, a subgroup of infants with RSV infection showed an increase in LILRB1+ NK cells. No differences in NKG2C, NKG2A, or CD161 expression between RSV infected infants and controls were observed. LILRB1 genotype distribution of the rs3760860 A>G, and rs3760861 A>G single nucleotide polymorphisms differed between infants with RSV infection and healthy donors, whereas no differences in any of the KIR genes were observed. Our results suggest that LILRB1 participates in the pathogenesis of RSV infection. Further studies are needed to define the role of LILRB1+ NK in response to RSV and to confirm an association between LILRB1 polymorphisms and the risk of severe RSV infection. PMID:25988502

  8. Biological and phylogenetic characterization of a genotype VII Newcastle disease virus from Venezuela: efficacy of field vaccination.

    PubMed

    Perozo, Francisco; Marcano, Rosmar; Afonso, Claudio L

    2012-04-01

    Here we report the biological and molecular characterization of a virulent genotype VII Newcastle disease virus (NDV) circulating in Venezuela and the assessment of the vaccination efficacy under field conditions compared to controlled rearing conditions. Biological pathotyping showed a mean embryo dead time of 50 h and an intracerebral pathogenicity index of 1.86. Sequence-based phylogenetic analysis demonstrated that the virus belongs to genotype VII in class II (a genotype often found in Asia and Africa), representing the first report of the presence of this genotype in the continent of South America. A vaccine-challenge trial in commercial broilers reared in fields or in a experimental setting included dual (live/killed) priming of 1-day-old chicks plus two live NDV and infectious bursal disease virus (IBDV) field vaccinations at days 7 and 17, followed by a very stringent genotype VII NDV challenge at day 28. Serology for NDV and IBDV, bursal integrity, and protection against NDV lethal challenge were assessed. At 28 days, field vaccinates showed significantly lower NDV (1,356 versus 2,384) and higher IBD (7,295 versus 1,489) enzyme-linked immunosorbent assay (ELISA) antibody titers than the experimentally reared birds. A lower bursal size and bursa-body weight ratio (P < 0.05) and higher bursa lesion score were also detected in the field set. Only 57.1% of field vaccinates survived the lethal challenge, differing (P < 0.05) from 90.5% survival in the experimental farm. Overall, results confirmed the presence of the genotype VII viruses in South America and suggest that field-associated factors such as immunosuppression compromise the efficacy of the vaccination protocols implemented. PMID:22238433

  9. Distribution and Predominance of Genotype 3 in Hepatitis C Virus Carriers in the Province of Kahramanmaras, Turkey

    PubMed Central

    Caliskan, Ahmet; Kirisci, Ozlem; Ozkaya, Esra; Ozden, Sevinc; Tumer, Seray; Caglar, Serkan; Guler, Selma Ates; Senol, Hande

    2015-01-01

    Background: The hepatitis C virus (HCV) has six major genotypes and more than 100 subtypes, and the determination of the responsible genotype, collection of epidemiological data, tailoring antiviral therapy, and prediction of prognosis have an important place in disease management. Objectives: The aim of the present study was to determine the distribution of HCV genotypes across geographic regions and compare these data with those obtained from other geographic locations. Patients and Methods: The HCV genotypes were identified in HCV RNA positive blood samples, obtained from different centers. The HCV genotype was determined using molecular methods [Real-Time Polymerase Chain Reaction (RT-PCR)] in 313 patients, who were found to be positive for HCV RNA. The presence of HCV RNA was investigated using the RT-PCR method in serum samples delivered to the Microbiology Laboratory at Kahramanmaras Necip Fazıl City Hospital, Kahramanmaras, Turkey, from the centers located in Kahramanmaras City center and peripheral districts of the province, between March 2010 and August 2014. The HCV genotype analysis was performed in HCV RNA positive samples, using RT-PCR reagents kit. Urine samples from the patients were tested for amphetamine with an Amphetamines II (AMPS2) kit, cocaine was tested with a Cocaine II (COC2) kit, opiates were tested with an Opiates II (OPI2) kit, and cannabinoids were tested with a Cannabinoids II (THC2) kit in Roche/Hitachi Cobas c501 device. Results: The blood samples collected from 313 patients were included in the study. Of these patients, 212 (67.7%) were male and 101 (32.3%) were female. The mean age of the patients was 41.29 ± 20.32 years. In terms of HCV genotype distribution, 162 patients (51.7%) had genotype 1, 144 patients (46%) had genotype 3, four patients (1.3%) had genotype 2, and three patients (1%) had genotype 4. The results of urine drug tests were available in only 65 patients (20.2%). Of these, 61 (93.8%) patients had HCV genotype 3

  10. Genomic characterization of emergent pseudorabies virus in China reveals marked sequence divergence: Evidence for the existence of two major genotypes.

    PubMed

    Ye, Chao; Zhang, Qing-Zhan; Tian, Zhi-Jun; Zheng, Hao; Zhao, Kuan; Liu, Fei; Guo, Jin-Chao; Tong, Wu; Jiang, Cheng-Gang; Wang, Shu-Jie; Shi, Mang; Chang, Xiao-Bo; Jiang, Yi-Feng; Peng, Jin-Mei; Zhou, Yan-Jun; Tang, Yan-Dong; Sun, Ming-Xia; Cai, Xue-Hui; An, Tong-Qing; Tong, Guang-Zhi

    2015-09-01

    Recently pseudorabies outbreaks have occurred in many vaccinated farms in China. To identify genetic characteristics of pseudorabies virus (PRV) strains, we obtained the genomic sequences of PRV strains HeN1 and JS, which were compared to 4 PRV genomes and 729 partial gene sequences. PRV strains isolated in China showed marked sequence divergence compared to European and American strains. Phylogenetic analysis revealed that for the first time PRV can be divided into 2 distinct clusters, with Chinese strains being genotype II and PRVs isolated from other countries being genotype I. Restriction fragment length polymorphism analysis confirmed differences between HeN1 and Bartha strains, as did the presence of unique insertion/deletion polymorphisms and microsatellites. This divergence between the two genotypes may have been generated from long-term, independent evolution, which could also explain the low efficacy of the Bartha vaccine in protecting pigs infected with genotype II PRV. PMID:25965793

  11. Genotypes of rubella virus and the epidemiology of rubella infections in the Democratic Republic of the Congo, 2004-2013.

    PubMed

    Pukuta, Elizabeth; Waku-Kouomou, Diane; Abernathy, Emily; Illunga, Benoit Kebela; Obama, Ricardo; Mondonge, Vital; Dahl, Benjamin A; Maresha, Balcha G; Icenogle, Joseph; Muyembe, Jean-Jacques

    2016-10-01

    Rubella is a viral infection that may cause fetal death or congenital defects, known as congenital rubella syndrome (CRS), during early pregnancy. The World Health Organization (WHO) recommends that countries assess the burden of rubella and CRS, including the determination of genotypes of circulating viruses. The goal of this study was to identify the genotypes of rubella viruses in the Democratic Republic of the Congo (DRC). Serum or throat swab samples were collected through the measles surveillance system. Sera that tested negative for measles IgM antibody were tested for rubella IgM antibody. Serum collected within 4 days of rash onset and throat swabs were screened by real-time RT-PCR for rubella virus RNA. For positive samples, an amplicon of the E1 glycoprotein gene was amplified by RT-PCR and sequenced. 11733 sera were tested for rubella IgM and 2816 (24%) were positive; 145 (5%) were tested for the presence of rubella RNA by real-time RT-PCR and 10 (7%) were positive. Seventeen throat swabs were analyzed by RT-PCR and three were positive. Sequences were obtained from eight of the positive samples. Phylogenetic analysis showed that the DRC rubella viruses belonged to genotypes 1B, 1E, 1G, and 2B. This report provides the first information on the genotypes of rubella virus circulating in the DRC. These data contribute to a better understanding of rubella burden and the dynamics of rubella virus circulation in Africa. Efforts to establish rubella surveillance in the DRC are needed to support rubella elimination in Africa. J. Med. Virol. 88:1677-1684, 2016. © 2016 Wiley Periodicals, Inc. PMID:27479298

  12. Genotyping by multiplex polymerase chain reaction for detection of endemic hepatitis B virus transmission.

    PubMed Central

    Repp, R; Rhiel, S; Heermann, K H; Schaefer, S; Keller, C; Ndumbe, P; Lampert, F; Gerlich, W H

    1993-01-01

    A nested polymerase chain reaction (PCR) protocol was developed for rapid genotyping of hepatitis B virus (HBV). During the first PCR round, a universal HBV primer pair was used to amplify the entire pre-S region of the HBV genome. Within the pre-S region, many nucleotide exchanges are observed. These are partly correlated to the serological hepatitis B surface antigen subtypes. Five additional subtype-specific primers were selected from that region which, together with two universal non-group-specific primers, generated specific combinations of two to four DNA fragments of defined sizes. By this approach, 55 hepatitis B surface antigen-positive patients from a pediatric oncology unit in Germany were analyzed. Fifty-four patients who had been infected within 2 years had an identical pattern in the multiplex PCR, suggesting a common source of infection and person-to-person transmission within the unit. One child who was infected 5 years later had a different PCR pattern and, therefore, must have been infected from a different source. Furthermore, 109 serum samples taken from pregnant Cameroonian women and 25 serum samples from their babies taken 6 months after birth were analyzed. In one case, mother-to-infant transmission of the virus was demonstrated. Apart from its role in epidemiological studies on HBV, multiplex PCR may also be a useful tool for rapid genetic analysis in other fields if there is a moderate degree of sequence variation which enables the design of specific primers. Images PMID:8501209

  13. Diagnosis and genotyping of African swine fever viruses from 2015 outbreaks in Zambia.

    PubMed

    Thoromo, Jonas; Simulundu, Edgar; Chambaro, Herman M; Mataa, Liywalii; Lubaba, Caesar H; Pandey, Girja S; Takada, Ayato; Misinzo, Gerald; Mweene, Aaron S

    2016-01-01

    In early 2015, a highly fatal haemorrhagic disease of domestic pigs resembling African swine fever (ASF) occurred in North Western, Copperbelt, and Lusaka provinces of Zambia. Molecular diagnosis by polymerase chain reaction targeting specific amplification of p72 (B646L) gene of ASF virus (ASFV) was conducted. Fourteen out of 16 domestic pigs from the affected provinces were found to be positive for ASFV. Phylogenetic analyses based on part of the p72 and the complete p54 (E183L) genes revealed that all the ASFVs detected belonged to genotypes I and Id, respectively. Additionally, epidemiological data suggest that the same ASFV spread from Lusaka to other provinces possibly through uncontrolled and/or illegal pig movements. Although the origin of the ASFV that caused outbreaks in domestic pigs in Zambia could not be ascertained, it appears likely that the virus may have emerged from within the country or region, probably from a sylvatic cycle. It is recommended that surveillance of ASF, strict biosecurity, and quarantine measures be imposed in order to prevent further spread and emergence of new ASF outbreaks in Zambia. PMID:27247062

  14. FCGR2A and FCGR3A Genotypes in Human Immunodeficiency Virus Mother-to-Child Transmission.

    PubMed

    Milligan, Caitlin; Richardson, Barbra A; John-Stewart, Grace; Nduati, Ruth; Overbaugh, Julie

    2015-12-01

    Background.  Fc-mediated effector functions have been suggested to influence human immunodeficiency virus (HIV) acquisition and disease progression. Analyzing the role of host Fc gamma receptor (FcγR) polymorphisms on HIV outcome in mother-to-child transmission (MTCT) will increase our understanding of how host genetics may alter immune responses in prevention, therapy, and disease. This study analyzed the impact of FCGR2A and FCGR3A genotypes on MTCT in a cohort in which Fc-mediated antibody functions are predictive of infant HIV outcome. Methods.  Human immunodeficiency virus-positive mothers and their infants from a historical MTCT cohort were genotyped for FCGR2A and FCGR3A. We assessed the impact of these genotypes on transmission and acquisition of HIV and disease progression using χ(2) tests, survival analyses, and logistic regression. Results.  Among 379 mother-infant pairs, infant FCGR2A and FCGR3A genotypes were not associated with infant HIV infection or disease progression. Maternal FCGR2A was not associated with transmission, but there was a trend between maternal FCGR3A genotype and transmission (P = .07). When dichotomizing mothers into FCGR3A homozygotes and heterozygotes, heterozygotes had a 64.5% higher risk of transmission compared with homozygotes (P = .02). This risk was most evident in the early breastfeeding window, but a trend was only observed when restricting analyses to breastfeeding mothers (hazards ratio, 1.64; P = .064). Conclusions.  Infant FCGR2A and FCGR3A genotypes were not associated with HIV infection or disease progression, and, thus, host FcγR genotype may not significantly impact vaccination or therapeutic regimens that depend on Fc-mediated antibody functions. Maternal FCGR3A genotype may influence early breastfeeding transmission risk, but more studies should be conducted to clarify this association and its mechanism. PMID:26613093

  15. Genotypes and viral load of hepatitis C virus among persons attending a voluntary counseling and testing center in Ethiopia.

    PubMed

    Abreha, Tesfay; Woldeamanuel, Yimtubezinash; Pietsch, Corinna; Maier, Melanie; Asrat, Daniel; Abebe, Almaz; Hailegiorgis, Bereket; Aseffa, Abraham; Liebert, Uwe Gerd

    2011-05-01

    The prevalence of different genotypes of hepatitis C virus (HCV) in Ethiopia is not known. HCV genotypes influence the response to therapy with alpha-interferon alone or in combination with ribavirin. A cross sectional study was conducted on attendees of voluntary counseling and testing center. Serum samples from 1,954 (734 HIV positive and 1,220 HIV negative) individuals were screened for HCV antibody. Active HCV infection was confirmed by quantitative PCR in 18 of the 71 samples with anti-HCV antibodies. The HCV viral load ranged from 39,650 to 9,878,341 IU/ml (median 1,589,631 IU/ml) with no significant difference [χ(2)(17) = 18.00, P = 0.389] between persons positive or negative for HIV. The viral load of HCV was, however, higher in older study subjects (r = 0.80, P = 0.000). HCV genotypes were determined using the VERSANT HCV Genotype Assay (LiPA) and sequence analysis of the NS5b region of the HCV genome. Diverse HCV genotypes were found including genotypes 1, 2, 4, and 5. There was no difference in the distribution regarding the HIV status. As in other parts of the world, genotyping of HCV must be considered whenever HCV is incriminated as a cause of hepatitis. PMID:21351106

  16. Method: a single nucleotide polymorphism genotyping method for Wheat streak mosaic virus

    PubMed Central

    2012-01-01

    Background The September 11, 2001 attacks on the World Trade Center and the Pentagon increased the concern about the potential for terrorist attacks on many vulnerable sectors of the US, including agriculture. The concentrated nature of crops, easily obtainable biological agents, and highly detrimental impacts make agroterrorism a potential threat. Although procedures for an effective criminal investigation and attribution following such an attack are available, important enhancements are still needed, one of which is the capability for fine discrimination among pathogen strains. The purpose of this study was to develop a molecular typing assay for use in a forensic investigation, using Wheat streak mosaic virus (WSMV) as a model plant virus. Method This genotyping technique utilizes single base primer extension to generate a genetic fingerprint. Fifteen single nucleotide polymorphisms (SNPs) within the coat protein and helper component-protease genes were selected as the genetic markers for this assay. Assay optimization and sensitivity testing was conducted using synthetic targets. WSMV strains and field isolates were collected from regions around the world and used to evaluate the assay for discrimination. The assay specificity was tested against a panel of near-neighbors consisting of genetic and environmental near-neighbors. Result Each WSMV strain or field isolate tested produced a unique SNP fingerprint, with the exception of three isolates collected within the same geographic location that produced indistinguishable fingerprints. The results were consistent among replicates, demonstrating the reproducibility of the assay. No SNP fingerprints were generated from organisms included in the near-neighbor panel, suggesting the assay is specific for WSMV. Using synthetic targets, a complete profile could be generated from as low as 7.15 fmoles of cDNA. Conclusion The molecular typing method presented is one tool that could be incorporated into the forensic

  17. Ledipasvir + sofosbuvir (Harvoni). A therapeutic advance in genotype 1 hepatitis C virus infection, despite uncertainties.

    PubMed

    2015-12-01

    Treatment for chronic hepatitis C depends on the hepatitis C virus (HCV) genotype and the patient's clinical characteristics. A fixed-dose combination of ledipasvir + sofosbuvir has been authorised in the European Union for adults with HCV genotype 1 (HCV-1), HCV-3 or HCV-4 infection. Ledipasvir targets the HCV protein NS5A, while sofosbuvir inhibits the HCV RNA polymerase NS5B. The ledipasvir+ sofosbuvircombination has not been compared directly with other antiviral drugs. No information is available on its ability to prevent hepatic complications, even in patients with cirrhosis. In four trials including over 1800 treatment-naive patients infected with HCV-1, a 12-week course of ledipasvir + sofosbuviryielded a sustained virological response in nearly every case. This is better than that reported with peginterferon alfa-based protocols. In four trials including more than 900 HCV-1-infected patients in whom treatments including peginterferon alfa had failed, a 24-week course of ledipasvir+ sofosbuvir yielded a sustained virological response in nearly every case, which is far better than reported with peginterferon alfa + ribavirin + protease inhibitor combinations, based on indirect comparison. In these trials, a 24-week course of the ledipasvir + sofosbuvir combination was effective in almost all patients with compensated cirrhosis. The same treatment also showed major efficacy in a non-comparative trial in 337 HCV-1-infected patients with decompensated cirrhosis or who had undergone liver transplantation. In mid-2015, very few data are available on the ledipasvir + sofosbuvir combination in HCV-1-infected patients in whom sofosbuvir combination therapy has failed, or in patients with HCV-3 or HCV-4 infection. Comparative data on the adverse effects of the ledipasvir + sofosbuvir combination are mainly based on a double-blind, placebo-controlled trial in 155 patients. Overall, serious adverse effects were infrequent in this and other trials. The main adverse

  18. Effects of chicken anaemia virus and infectious bursal disease virus-induced immunodeficiency on infectious bronchitis virus replication and genotypic drift.

    PubMed

    Gallardo, Rodrigo A; van Santen, Vicky L; Toro, Haroldo

    2012-10-01

    We followed changes in a portion of the S1 gene sequence of the dominant populations of an infectious bronchitis virus (IBV) Arkansas (Ark) vaccine strain during serial passage in chickens infected with the immunosuppressive chicken anaemia virus (CAV) and/or infectious bursal disease virus (IBDV) as well as in immunocompetent chickens. The IBV-Ark vaccine was applied ocularly and tears were collected from infected chickens for subsequent ocular inoculation in later passages. The experiment was performed twice. In both experiments the dominant S1 genotype of the vaccine strain was rapidly and negatively selected in all chicken groups (CAV, IBDV, CAV+IBDV and immunocompetent). Based on the S1 genotype, the same IBV subpopulations previously reported in immunocompetent chickens and named component (C) 1 to C5 emerged both in immunocompetent and immunodeficient chickens. During the first passage different subpopulations emerged, followed by the establishment of one or two predominant populations after further passages. Only when the subpopulation designated C2 became established in either CAV-infected or IBDV-infected chickens was IBV maintained for more than four passages. These results indicate that selection does not cease in immunodeficient chickens and that phenotype C2 may show a distinct adaptation to this environment. Subpopulations C1 or C4 initially became established in immunocompetent birds but became extinct after only a few succeeding passages. A similar result was observed in chickens co-infected with CAV+IBDV. These results suggest that the generation of genetic diversity in IBV is constrained. This finding constitutes further evidence for phenotypic drift occurring mainly as a result of selection. PMID:22897690

  19. Molecular characterization of hepatitis B virus and a 9-year clinical profile in a patient infected with genotype I.

    PubMed

    Osiowy, Carla; Kaita, Kelly; Solar, Kaarina; Mendoza, Kenneth

    2010-05-01

    An unusual hepatitis B virus (HBV) variant, assigned provisionally to genotype I, was recently reported, characterized by an anomalous genotyping pattern and putative recombination; however, the natural history of this unusual strain is unknown. This study analyzed longitudinal sera collected over a 9-year period from a patient infected with this variant to investigate the clinical profile and intrahost viral evolution over time. The patient, who had immigrated to Canada in 1998 from Vietnam, was treated with lamivudine in 2000. Approximately 4-5 years following the withdrawal of lamivudine therapy, a genomic "shift" occurred coincident with ALT flares and increasing HBV viral load, resulting in numerous stable nucleotide substitutions within the core coding region, suggesting altered immune control that may provide a selective advantage to the virus. Analysis of quasispecies diversity over time demonstrated further this shift, with two sequence clusters associated with time points either prior to or following relapse observed, including increased diversity among quasispecies prior to relapse. In keeping with the complex nature of genotype I strains, majority population genomes had a mean genetic distance from genotype C of 7.6 +/- 0.1%, although large genomic segments lacked significant homology with any HBV genotype. Further study is needed to understand the evolutionary origin and natural history of infection with this unique HBV variant. PMID:20419807

  20. Correlation between Genetic Variations and Serum Level of Interleukin 28B with Virus Genotypes and Disease Progression in Chronic Hepatitis C Virus Infection

    PubMed Central

    Al-Qahtani, Ahmed; Al-Anazi, Mashael; Abdo, Ayman A.; Sanai, Faisal M.; Al-Hamoudi, Waleed; Alswat, Khalid A.; Al-Ashgar, Hamad I.; Khan, Mohammed Q.; Khalaf, Nisreen; Al-Ahdal, Mohammed N.

    2015-01-01

    Recent studies have demonstrated that polymorphisms near the interleukin-28B (IL-28B) gene could predict the response to Peg-IFN-a/RBV combination therapy in HCV-infected patients. The aim of the study was to correlate the serum level of IL28B in HCV-infected patients with virus genotype/subgenotype and disease progression. IL28B serum level was detected and variations at five single nucleotide polymorphisms (SNPs) in IL28B gene region were genotyped and analyzed. The variation of IL28B genetic polymorphisms was found to be strongly associated with HCV infection when healthy control group was compared to HCV-infected patients with all P values <0.0001. Functional analysis revealed that subjects carrying rs8099917-GG genotype had higher serum level of IL28B than those with GT or TT genotypes (P = 0.04). Also, patients who were presented with cirrhosis (Cirr) only or with cirrhosis plus hepatocellular carcinoma (Cirr+HCC) had higher levels of serum IL28B when compared to chronic HCV-infected patients (P = 0.005 and 0.003, resp.). No significant association was found when serum levels of IL28B were compared to virus genotypes/subgenotypes. This study indicates that variation at SNP rs8099917 could predict the serum levels of IL28B in HCV-infected patients. Furthermore, IL28B serum level may serve as a useful marker for the development of HCV-associated sequelae. PMID:25811035

  1. Roles of human apolipoprotein E in the infectivity and replication of hepatitis C virus genotype 2a.

    PubMed

    Jung, Bo-Kyoung; Kim, Hye-Ran; Park, Gyu-Nam; Luo, Guangxiang; Chang, Kyung-Soo

    2016-06-01

    Hepatitis C virus (HCV) infection is associated with lipoproteins, and apolipoprotein E (apoE) plays an essential role in infectious HCV particles. Although the role of apoE in HCV infection is well known, its role in the replication of HCV remains unclear. The aims of this study were to determine the role of apoE in the RNA replication of major HCV genotypes 1b and 2a, and to determine whether this role is HCVgenotype-dependent using HCV genotype 1b replicon cells and HCV genotype 2a producing (HP) cells. HCV infection was blocked in Huh7.5 cells treated with low-density lipoproteins, very low-density lipoproteins, or apoE3. An apoE3-specific monoclonal antibody also efficiently neutralized HCV infectivity, and HCV infection was dramatically suppressed by the knockdown of apoE expression with an apoE-specific small interfering RNA, suggesting a requirement for apoE in infectious HCV particles. HCV RNA replication was not affected in HP cells treated with each apoE isoform or transfected with apoE-specific siRNAs. However, the knockdown of apoE expression suppressed RNA replication of HCV genotype 1b. The siRNA-mediated knockdown of apoE, apoA1, and apoB expression also suppressed the RNA replication of HCV genotype 1b, but not that of HCV genotype 2a. Taken together, these findings indicate that apoE plays an important role in HCV genotype 2a infection and in HCV genotype 1b RNA replication, but not in the replication of HCV genotype 2a. These results provide important information for the future development of HCV-genotypespecific anti-HCV agents. PMID:27225463

  2. Antigenic Variation of East/Central/South African and Asian Chikungunya Virus Genotypes in Neutralization by Immune Sera

    PubMed Central

    Chua, Chong-Long; Sam, I-Ching; Merits, Andres; Chan, Yoke-Fun

    2016-01-01

    Background Chikungunya virus (CHIKV) is a re-emerging mosquito-borne virus which causes epidemics of fever, severe joint pain and rash. Between 2005 and 2010, the East/Central/South African (ECSA) genotype was responsible for global explosive outbreaks across India, the Indian Ocean and Southeast Asia. From late 2013, Asian genotype CHIKV has caused outbreaks in the Americas. The characteristics of cross-antibody efficacy and epitopes are poorly understood. Methodology/Principal Findings We characterized human immune sera collected during two independent outbreaks in Malaysia of the Asian genotype in 2006 and the ECSA genotype in 2008–2010. Neutralizing capacity was analyzed against representative clinical isolates as well as viruses rescued from infectious clones of ECSA and Asian CHIKV. Using whole virus antigen and recombinant E1 and E2 envelope glycoproteins, we further investigated antibody binding sites, epitopes, and antibody titers. Both ECSA and Asian sera demonstrated stronger neutralizing capacity against the ECSA genotype, which corresponded to strong epitope-antibody interaction. ECSA serum targeted conformational epitope sites in the E1-E2 glycoprotein, and E1-E211K, E2-I2T, E2-H5N, E2-G118S and E2-S194G are key amino acids that enhance cross-neutralizing efficacy. As for Asian serum, the antibodies targeting E2 glycoprotein correlated with neutralizing efficacy, and I2T, H5N, G118S and S194G altered and improved the neutralization profile. Rabbit polyclonal antibody against the N-terminal linear neutralizing epitope from the ECSA sequence has reduced binding capacity and neutralization efficacy against Asian CHIKV. These findings imply that the choice of vaccine strain may impact cross-protection against different genotypes. Conclusion/Significance Immune serum from humans infected with CHIKV of either ECSA or Asian genotypes showed differences in binding and neutralization characteristics. These findings have implications for the continued

  3. Characterisation of hepatitis C virus genotype among blood donors at the regional blood transfusion centre of Ouagadougou, Burkina Faso

    PubMed Central

    Zeba, Moctar Tokèda Abdoul; Sanou, Mahamoudou; Bisseye, Cyrille; Kiba, Alice; Nagalo, Bolni Marius; Djigma, Florencia Wendkuuni; Compaoré, Tegwindé Rebecca; Nebié, Yacouba Koumpingnin; Kienou, Kisito; Sagna, Tani; Pietra, Virginio; Moret, Rémy; Simporé, Jacques

    2014-01-01

    Background Hepatitis C virus (HCV) is responsible for about 900 deaths every year in Burkina Faso. In this country, serological screening for hepatitis B and C viruses is only carried out systematically among blood donors. The aim of this study was to determine the prevalence and genotypes of HCV among blood donors using reverse transcription polymerase chain reaction (PCR) and real-time PCR, respectively. Materials and methods Serum samples were screened for antibodies to HCV using an enzyme-linked immunosorbent assay (ARCHITECT-i1000SR-ABBOTT). All the reactive samples for HCV antibodies were re-tested using a second enzyme-linked immunosorbent assay (Bio-Rad, Marnes la Coquette, France) for confirmation. RNA was detected in all the reactive samples for antibodies to HCV. HCV RNA positive samples were genotyped using the HCV Real-TM Genotype kit (Sacace Biotechnologies, Italy). Results Among 2,200 blood donors, the prevalences of antibodies to HCV and viral RNA were 4.4% (95% confidence interval=3.5–5.3) and 1.5% (95% confidence interval=1.0–2.0), respectively. Among HCV RNA carriers, genotyping showed that HCV genotypes 2 and 3 were the most prevalent as they were detected in 18 (56.3%) and 5 (15.6%) individuals, respectively. HCV genotypes 1a and 4 were the least frequent among the blood donors. HCV mixed genotypes 2/3 and 2/4 were also detected among the blood donors. Conclusion The prevalence of HCV found in this study is lower than previously reported prevalences. Large-scale studies are needed to obtain a better picture of the molecular epidemiology of HCV in Burkina Faso. PMID:24599906

  4. Evaluation of a novel serotyping system for hepatitis C virus: strong correlation with standard genotyping methodologies.

    PubMed

    Dixit, V; Quan, S; Martin, P; Larson, D; Brezina, M; DiNello, R; Sra, K; Lau, J Y; Chien, D; Kolberg, J

    1995-11-01

    Direct sequencing and analysis of viral genomes are definitive methods for identifying various hepatitis C virus (HCV) genotypes. However, HCV genome sequencing methods are cumbersome and unsuitable for analyzing large numbers of clinical samples. We have developed a convenient, reliable, and reproducible RIBA strip immunoblot assay system for determining HCV serotype. Briefly, the assay consists of an immunoblot strip on which there are five lanes of immobilized serotype-specific HCV peptides from the nonstructural (NS-4) and core regions of the genomes of HCV types 1,2, and 3. HCV serotype is deduced by determining the greatest intensity of reactivity to the NS-4 serotype-specific HCV peptide band in relation to the intensity of the human immunoglobulin G internal control bands on each strip. HCV core peptide reactivity is used only in the absence of NS-4 reactivity. We used this assay to successfully serotype a high percentage of sera from well-documented HCV-infected patients. Our serotyping results correlated 99% with the findings from the standard restriction fragment length polymorphism genotyping methods. Less than 5% of the serum samples were untypeable. For a selected group of alpha interferon-treated patients we observed that the nonresponders (76.2%) and a majority of the responders who relapsed (72.2%) had type 2 HCV infection. A small population (n= 8) of complete responders was split 3:4:1 as type 1, type 2, and type 3, respectively. Our data indicate that this new serotyping assay has the potential to be a highly specific and reliable method for typing of HCV infection in patients. PMID:8576357

  5. Restricted Enzooticity of Hepatitis E Virus Genotypes 1 to 4 in the United States ▿

    PubMed Central

    Dong, Chen; Meng, Jihong; Dai, Xing; Liang, Jiu-Hong; Feagins, Alicia R.; Meng, Xiang-Jin; Belfiore, Natalia M.; Bradford, Carol; Corn, Joseph L.; Cray, Carolyn; Glass, Gregory E.; Gordon, Melvin L.; Hesse, Richard A.; Montgomery, Donald L.; Nicholson, William L.; Pilny, Anthony A.; Ramamoorthy, Sheela; Shaver, Douglas D.; Drobeniuc, Jan; Purdy, Michael A.; Fields, Howard A.; Kamili, Saleem; Teo, Chong-Gee

    2011-01-01

    Hepatitis E is recognized as a zoonosis, and swine are known reservoirs, but how broadly enzootic its causative agent, hepatitis E virus (HEV), is remains controversial. To determine the prevalence of HEV infection in animals, a serological assay with capability to detect anti-HEV-antibody across a wide variety of animal species was devised. Recombinant antigens comprising truncated capsid proteins generated from HEV-subgenomic constructs that represent all four viral genotypes were used to capture anti-HEV in the test sample and as an analyte reporter. To facilitate development and validation of the assay, serum samples were assembled from blood donors (n = 372), acute hepatitis E patients (n = 94), five laboratory animals (rhesus monkey, pig, New Zealand rabbit, Wistar rat, and BALB/c mouse) immunized with HEV antigens, and four pigs experimentally infected with HEV. The assay was then applied to 4,936 sera collected from 35 genera of animals that were wild, feral, domesticated, or otherwise held captive in the United States. Test positivity was determined in 457 samples (9.3%). These originated from: bison (3/65, 4.6%), cattle (174/1,156, 15%), dogs (2/212, 0.9%), Norway rats (2/318, 0.6%), farmed swine (267/648, 41.2%), and feral swine (9/306, 2.9%). Only the porcine samples yielded the highest reactivities. HEV RNA was amplified from one farmed pig and two feral pigs and characterized by nucleotide sequencing to belong to genotype 3. HEV infected farmed swine primarily, and the role of other animals as reservoirs of its zoonotic spread appears to be limited. PMID:21998412

  6. Restricted enzooticity of hepatitis E virus genotypes 1 to 4 in the United States.

    PubMed

    Dong, Chen; Meng, Jihong; Dai, Xing; Liang, Jiu-Hong; Feagins, Alicia R; Meng, Xiang-Jin; Belfiore, Natalia M; Bradford, Carol; Corn, Joseph L; Cray, Carolyn; Glass, Gregory E; Gordon, Melvin L; Hesse, Richard A; Montgomery, Donald L; Nicholson, William L; Pilny, Anthony A; Ramamoorthy, Sheela; Shaver, Douglas D; Drobeniuc, Jan; Purdy, Michael A; Fields, Howard A; Kamili, Saleem; Teo, Chong-Gee

    2011-12-01

    Hepatitis E is recognized as a zoonosis, and swine are known reservoirs, but how broadly enzootic its causative agent, hepatitis E virus (HEV), is remains controversial. To determine the prevalence of HEV infection in animals, a serological assay with capability to detect anti-HEV-antibody across a wide variety of animal species was devised. Recombinant antigens comprising truncated capsid proteins generated from HEV-subgenomic constructs that represent all four viral genotypes were used to capture anti-HEV in the test sample and as an analyte reporter. To facilitate development and validation of the assay, serum samples were assembled from blood donors (n = 372), acute hepatitis E patients (n = 94), five laboratory animals (rhesus monkey, pig, New Zealand rabbit, Wistar rat, and BALB/c mouse) immunized with HEV antigens, and four pigs experimentally infected with HEV. The assay was then applied to 4,936 sera collected from 35 genera of animals that were wild, feral, domesticated, or otherwise held captive in the United States. Test positivity was determined in 457 samples (9.3%). These originated from: bison (3/65, 4.6%), cattle (174/1,156, 15%), dogs (2/212, 0.9%), Norway rats (2/318, 0.6%), farmed swine (267/648, 41.2%), and feral swine (9/306, 2.9%). Only the porcine samples yielded the highest reactivities. HEV RNA was amplified from one farmed pig and two feral pigs and characterized by nucleotide sequencing to belong to genotype 3. HEV infected farmed swine primarily, and the role of other animals as reservoirs of its zoonotic spread appears to be limited. PMID:21998412

  7. High prevalence of occult hepatitis B virus genotype H infection among children with clinical hepatitis in west Mexico

    PubMed Central

    Escobedo-Melendez, Griselda; Panduro, Arturo; Fierro, Nora A; Roman, Sonia

    2014-01-01

    Studies on the prevalence of infection with hepatitis B virus (HBV) among children are scarce in Latin American countries, especially in Mexico. This study was aimed to investigate the prevalence of HBV infection, occult hepatitis B infection (OBI) and HBV genotypes among children with clinical hepatitis. In total, 215 children with clinical hepatitis were evaluated for HBV infection. HBV serological markers and HBV DNA were analysed. OBI diagnosis and HBV genotyping was performed. HBV infection was found in 11.2% of children with clinical hepatitis. Among these HBV DNA positive-infected children, OBI was identified in 87.5% (n = 21/24) of the cases and 12.5% (n = 3/24) were positive for both HBV DNA and hepatitis B surface antigen. OBI was more frequent among children who had not been vaccinated against hepatitis B (p < 0.05) than in those who had been vaccinated. HBV genotype H was prevalent in 71% of the children followed by genotype G (8%) and genotype A (4%). In conclusion, OBI is common among Mexican children with clinical hepatitis and is associated with HBV genotype H. The results show the importance of the molecular diagnosis of HBV infection in Mexican paediatric patients with clinical hepatitis and emphasise the necessity of reinforcing hepatitis B vaccination in children. PMID:25099333

  8. Palindromic-nucleotide substitutions (PNS) of hepatitis C virus genotypes 1 and 5a from South Africa.

    PubMed

    Prabdial-Sing, N; Giangaspero, M; Puren, A J; Mahlangu, J; Barrow, P; Bowyer, S M

    2011-08-01

    The HCV stem-loop subdomains III-a, -b and -c have been shown to reflect the characteristics of the virus and identify isolates by genus, genotype and subtype. The aim of this study was to investigate the genotype-specific PNS within the 5'UTR of prevalent HCV genotypes (1 and 5a) found in South Africa. The genotype 5a (N = 35) and genotype 1 sequences (N=20) were from patients presenting with liver disease or haemophilia, respectively. PNS HCV typing characteristics, defined previously, were observed. The PNS method differentiated subtypes 1a and 1c from subtype 1b by the base change at nucleotide position 243. A lack of structural data from the variable loci V1 of the 5'UTR did not allow us to further differentiate the subtypes of 1. A nucleotide change from a thymine (T) to a cytosine (C) at position 183 was found among genotype 5a sequences. This mutation changed the stable U-AA bond to a Y AA bulge at base-pair position 32. There was an insertion of a single adenine (A) at position 207. At present PNS analysis is labour intensive but, with development of further software to aid the computer analysis, it has the potential to provide a rapid, reliable alternative to phylogenetic analysis. PMID:21600241

  9. Similar hepatitis C virus RNA kinetics in HIV/hepatitis C virus monoinfected genotype 2 or 3 matched controls during hepatitis C virus combination therapy.

    PubMed

    Karlström, Olle; Sönnerborg, Anders; Weiland, Ola

    2008-04-23

    We prospectively studied early hepatitis C virus kinetics and sustained virological response rates in HIV/HCV coinfected (n = 13) and HCV monoinfected matched controls (n = 26) with HCV genotype 2/3 treated with pegylated interferon (peg-IFN) alpha-2a 135 microg/week plus ribavirin 11 mg/kg daily during 24 weeks. No significant difference in HCV-RNA decay was seen at any time point during the initial 12 weeks of therapy. Sustained virological response was achieved in 9/13 (69%) versus 20/26 (77%) patients (intent-to-treat), respectively. The lower-than-standard peg-IFN dose offered high compliance and reasonable sustained virological response rates. PMID:18427210

  10. Whole-Genome Sequencing of Measles Virus Genotypes H1 and D8 During Outbreaks of Infection Following the 2010 Olympic Winter Games Reveals Viral Transmission Routes.

    PubMed

    Gardy, Jennifer L; Naus, Monika; Amlani, Ashraf; Chung, Walter; Kim, Hochan; Tan, Malcolm; Severini, Alberto; Krajden, Mel; Puddicombe, David; Sahni, Vanita; Hayden, Althea S; Gustafson, Reka; Henry, Bonnie; Tang, Patrick

    2015-11-15

    We used whole-genome sequencing to investigate a dual-genotype outbreak of measles occurring after the XXI Olympic Winter Games in Vancouver, Canada. By sequencing 27 complete genomes from H1 and D8 genotype measles viruses isolated from outbreak cases, we estimated the virus mutation rate, determined that person-to-person transmission is typically associated with 0 mutations between isolates, and established that a single introduction of H1 virus led to the expansion of the outbreak beyond Vancouver. This is the largest measles genomics project to date, revealing novel aspects of measles virus genetics and providing new insights into transmission of this reemerging viral pathogen. PMID:26153409

  11. Esophageal papilloma: Flexible endoscopic ablation by radiofrequency

    PubMed Central

    del Genio, Gianmattia; del Genio, Federica; Schettino, Pietro; Limongelli, Paolo; Tolone, Salvatore; Brusciano, Luigi; Avellino, Manuela; Vitiello, Chiara; Docimo, Giovanni; Pezzullo, Angelo; Docimo, Ludovico

    2015-01-01

    Squamous papilloma of the esophagus is a rare benign lesion of the esophagus. Radiofrequency ablation is an established endoscopic technique for the eradication of Barrett esophagus. No cases of endoscopic ablation of esophageal papilloma by radiofrequency ablation (RFA) have been reported. We report a case of esophageal papilloma successfully treated with a single session of radiofrequency ablation. Endoscopic ablation of the lesion was achieved by radiofrequency using a new catheter inserted through the working channel of endoscope. The esophageal ablated tissue was removed by a specifically designed cup. Complete ablation was confirmed at 3 mo by endoscopy with biopsies. This case supports feasibility and safety of as a new potential indication for BarrxTM RFA in patients with esophageal papilloma. PMID:25789102

  12. Determining hepatitis C virus genotype distribution among high-risk groups in Iran using real-time PCR

    PubMed Central

    Jamalidoust, Marzieh; Namayandeh, Mandana; Asaei, Sadaf; Aliabadi, Nasrin; Ziyaeyan, Mazyar

    2014-01-01

    AIM: To assess hepatitis C virus (HCV) genotype patterns among high-risk Iranian groups, using real-time RT-PCR. METHODS: In this study, we evaluated the distribution of different HCV genotypes among injection drug users and other high-risk groups over a 4-year period (from 2009 to 2012) using real-time polymerase chain reaction (PCR). Sera from 888 HCV-infected patients residing in southern and southwest Iran were genotyped using real-time PCR with common primers and specific probes. These patients were grouped into distinct exposure categories. Illicit drug users constituted the primary group and were further evaluated for HCV genotype distribution and parameters such as age range. RESULTS: Of the examined HCV-infected patients, 62% were substance abusers, although the route of transmission could not be determined in approximately 30% of these patients. HCV genotyping revealed that Gt1 was the most prevalent genotype among the drug users as well as among patients with thalassemia, hemophilia, solid organ recipients and those on hemodialysis. Mixed infections were only seen in addict groups, where Gt2 genotype was also found. The highest frequencies in HCV-positive addict patients were observed in the 31-40 age group. Our research also showed that the addiction age has increased, whereas the addiction rate has dropped in this region. Most illicit drug users had more than one risk factor such as tattoo and/or a history of imprisonment. CONCLUSION: This study revealed that the most common HCV-infection route and HCV-genotype in southern and southwest Iran was illicit drug abuse and Gt1, respectively. PMID:24914351

  13. Measles viruses of genotype H1 evade recognition by vaccine-induced neutralizing antibodies targeting the linear haemagglutinin noose epitope.

    PubMed

    Finsterbusch, Tim; Wolbert, Anne; Deitemeier, Ingrid; Meyer, Kerstin; Mosquera, Maria Mar; Mankertz, Annette; Santibanez, Sabine

    2009-11-01

    The linear haemagglutinin noose epitope (HNE; aa 379-410) is a protective B-cell epitope and considered to be highly conserved in both the vaccine and the wild-type measles virus (MeV) haemagglutinin (H) proteins. Vaccine virus-derived monoclonal antibodies (mAbs) BH6 and BH216, which target the HNE, neutralized MeVs of genotypes B3, C2, D4, D5, D6, D7 and D8, and the vaccine strain Edmonston Zagreb. In the case of genotype H1, only strain Berlin.DEU/44.01 was neutralized by these mAbs, whereas strains Shenyang.CHN/22.99 and Sofia.BGR/19.05 were not. The H gene sequences of these two strains showed an exchange of proline 397 (P397) to leucine (L397). Mutated H proteins, with P397 exchanged to L and vice versa, were compared with original H proteins by indirect fluorescence assay. H proteins exhibiting P397 but not those with L397 were recognized by BH6 and BH216. This indicates that L397 leads to the loss of the neutralizing HNE. In contrast, human sera obtained from vaccinees (n=10) did not discriminate between genotype H1 variants P397 and L397. This concurs with the epidemiological observation that the live-attenuated vaccine protects against both H1 variants. Furthermore, we demonstrated that MeVs of genotype H1 also lack the neutralizing epitopes defined by the vaccine virus-induced mAbs BH15, BH125 and BH47. The loss of several neutralizing epitopes, as shown for H1 viruses currently circulating endemically in Asia, implies that epitope monitoring should be considered to be included in measles surveillance. PMID:19625457

  14. Identification and genome characterization of genotype B and genotype C bovine parainfluenza type 3 viruses isolated in the United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Bovine parainfluenza 3 viruses (BPI3V) are respiratory pathogens of cattle that cause disease singly but are often associated with bovine respiratory disease complex (BRDC) in conjunction with other viral and bacterial agents. Bovine vaccines currently contain BPI3V to provide protection...

  15. The pan-genotype specificity of the hepatitis C virus anti-core monoclonal antibody C7-50 is contingent on the quasispecies profile of a population.

    PubMed

    Palmer, Brendan A; Menton, John; Levis, John; Kenny-Walsh, Elizabeth; Crosbie, Orla; Fanning, Liam J

    2012-11-01

    The inter/intra-genotype quasispecies makeup of hepatitis C virus (HCV) has retarded the development of antibodies capable of pan-genotype reactivity. Mutations, even in conserved domains, are tolerated to a degree. In this report, we characterise the pan-genotype specificity of the commercially available monoclonal anti-HCV core antibody C7-50. We demonstrate the antibody's ability to detect HCV core protein following infection of Huh7 cells with serum-derived HCV of genotypes 2-5 and that a single-site polymorphism in a genotype 3a core amino acid sequence is sufficient to disrupt antibody recognition of the epitope. This same polymorphism is a feature of genotype 3 viruses. PMID:22828781

  16. Low Protective Efficacy of the Current Japanese Encephalitis Vaccine against the Emerging Genotype 5 Japanese Encephalitis Virus

    PubMed Central

    Gao, Xiaoyan; Li, Minghua; Cui, Shiheng; Li, Xiaolong; Cao, Yuxi; Lei, Wenwen; Lu, Zhi; He, Ying; Wang, Huanyu; Yan, Jinghua; Gao, George Fu; Liang, Guodong

    2016-01-01

    Background The current Japanese encephalitis (JE) vaccine derived from G3 JE virus (JEV) can induce protective immunity against G1–G4 JEV genotypes. However, protective efficacy against the emerging G5 genotype has not been reported. Methods/Principal Findings Using in vitro and in vivo tests, biological phenotype and cross-immunoreactions were compared between G3 JEV and G5 JEV (wild strains). The PRNT90 method was used to detect neutralizing antibodies against different genotypes of JEV in JE vaccine-immunized subjects and JE patients. In JE vaccine-immunized mice, the lethal challenge protection rates against G3 and G5 JEV wild strains were 100% and 50%, respectively. The seroconversion rates (SCRs) of virus antibodies against G3 and G5 JEV among vaccinated healthy subjects were 100% and 35%, respectively. All clinically identified JE patients showed high levels of G3 JEV neutralizing antibodies (≥1:10–1280) with positive serum geometric mean titers (GMTs) of 43.2, while for G5 JEV, neutralizing antibody conversion rates were only 64% with positive serum GMTs of 11.14. Moreover, the positive rate of JEV neutralizing antibodies against G5 JEV in pediatric patients was lower than in adults. Conclusions/Significance Low levels of neutralizing/protective antibodies induced by the current JE vaccine, based on the G3 genotype, were observed against the emerging G5 JEV genotype. Our results demonstrate the need for more detailed studies to reevaluate whether or not the apparent emergence of G5 JEV can be attributed to failure of the current vaccine to induce appropriate immune protectivity against this genotype of JEV. PMID:27139722

  17. Mapping the distribution of maize streak virus genotypes across the forest and transition zones of Ghana.

    PubMed

    Oppong, Allen; Offei, Samuel K; Ofori, Kwadwo; Adu-Dapaah, Hans; Lamptey, Joseph N L; Kurenbach, Brigitta; Walters, Matthew; Shepherd, Dionne N; Martin, Darren P; Varsani, Arvind

    2015-02-01

    Throughout sub-Saharan Africa, maize streak virus strain A (MSV-A), the causal agent of maize streak disease (MSD), is an important biological constraint on maize production. In November/December 2010, an MSD survey was carried out in the forest and transition zones of Ghana in order to obtain MSV-A virulence sources for the development of MSD-resistant maize genotypes with agronomic properties suitable for these regions. In 79 well-distributed maize fields, the mean MSD incidence was 18.544 % and the symptom severity score was 2.956 (1 = no symptoms and 5 = extremely severe). We detected no correlation between these two variables. Phylogenetic analysis of cloned MSV-A isolates that were fully sequenced from samples collected in 51 of these fields, together with those sampled from various other parts of Africa, indicated that all of the Ghanaian isolates occurred within a broader cluster of West African isolates, all belonging to the highly virulent MSV-A1 subtype. Besides being the first report of a systematic MSV survey in Ghana, this study is the first to characterize the full-genome sequences of Ghanaian MSV isolates. The 51 genome sequences determined here will additionally be a valuable resource for the rational selection of representative MSV-A variant panels for MSD resistance screening. PMID:25344899

  18. Highly divergent dengue virus type 1 genotype sets a new distance record

    PubMed Central

    Pyke, Alyssa T.; Moore, Peter R.; Taylor, Carmel T.; Hall-Mendelin, Sonja; Cameron, Jane N.; Hewitson, Glen R.; Pukallus, Dennis S.; Huang, Bixing; Warrilow, David; van den Hurk, Andrew F.

    2016-01-01

    Dengue viruses (DENVs) are the leading cause of mosquito-borne viral disease of humans. They exist in both endemic and sylvatic ecotypes. In 2014, a viremic patient who had recently visited the rainforests of Brunei returned to Australia displaying symptoms consistent with DENV infection. A unique DENV strain was subsequently isolated from the patient, which we propose belongs to a new genotype within DENV serotype 1 (DENV-1). Bayesian evolutionary phylogenetic analysis suggests that the putative sylvatic DENV-1 Brunei 2014 (Brun2014) is the most divergent DENV-1 yet recorded and increases the time to the most recent common ancestor (MRCA) for DENV-1 from ≈120 years to ≈315 years. DENV-1 classification of the Brun2014 strain was further supported by monoclonal antibody serotyping data. Phenotypic characterization demonstrated that Brun2014 replication rates in mosquito cells and infection rates in Aedes aegypti mosquitoes were not significantly different from an epidemic DENV-1 strain. Given its ability to cause human illness and infect Ae. aegypti, potential urban spillover and clinical disease from further Brun2014 transmission cannot be discounted. PMID:26924208

  19. Interferon treatment for chronic hepatitis C infection in hemophiliacs--influence of virus load, genotype, and liver pathology on response.

    PubMed

    Hanley, J P; Jarvis, L M; Andrew, J; Dennis, R; Hayes, P C; Piris, J; Lee, R; Simmonds, P; Ludlam, C A

    1996-03-01

    In this study, we assessed the effectiveness of interferon treatment in 31 hemophiliacs with chronic hepatitis C virus (HCV) infection. Interferon alfa-2a (3 MU three times weekly) was administered for 6 months. Response was assessed by both serial alanine transaminase (ALT) and HCV RNA levels measured by a sensitive semiquantitative polymerase chain reaction (PCR) method. HCV genotype was determined by restriction fragment length polymorphism (RFLP), and evidence of changing genotypes during interferon therapy was sought. Severity of liver disease was assessed by both noninvasive and invasive methods, including laparoscopic liver inspection and biopsy. Sustained normalization of ALT levels occurred in eight patients (28%), and seven (24%) became nonviremic as assessed by PCR (<80 HCV/mL). Responders universally cleared HCV RNA within 2 months of starting interferon. Genotype 3a was associated with a favorable response to interferon. No evidence was found for a change in circulating genotype in patients who failed to respond to interferon or who relapsed. This study confirms that response rates to interferon are low in hemophiliacs as compared with other groups with chronic HCV infection. We have also demonstrated that virus load measurement over the first 8 to 12 weeks of treatment is an extremely useful method to identify responders at an early stage. PMID:8634415

  20. Recurrence of hepatitis C virus genotype-4 infection following orthotopic liver transplantation: Natural history and predictors of outcome

    PubMed Central

    Mudawi, Hatim; Helmy, Ahmed; Kamel, Yasser; Al Saghier, Mohammed; Al Sofayan, Mohammed; Al Sebayel, Mohammed; Khalaf, Hatem; Al Bahili, Hamad; Al Shiek, Yasser; Alawi, Khalil; AlJedai, Ahmed; Mohamed, Hazem; Al Hamoudi, Waleed; Abdo, Ayman

    2009-01-01

    BACKGROUND AND OBJECTIVES: There are few reports on hepatitis C virus genotype 4 (HCV-4) recurrences after orthotopic liver transplantation (OLT). Therefore, we undertook a study to determine the epidemiological, clinical and virological characteristics of patients with biopsy-proven recurrent HCV infection and analyzed the factors that influence recurrent disease severity. We also compared disease recurrence and outcomes between HCV-4 and other genotypes. PATIENTS AND METHODS: All patients who underwent OLT (locally or abroad) for HCV related hepatic cirrhosis from 1991 to 2006 and had recurrent HCV infection were identified. Clinical, laboratory and pathological data before and after OLT were collected and analyzed. RESULTS: Of 116 patients who underwent OLT for hepatitis C, 46 (39.7%) patients satisfied the criteria of recurrent hepatitis C. Twenty-nine (63%) patients were infected with HCV genotype 4. Mean (SD) for age was 54.9 (10.9) years. Nineteen of the HCV genotype 4 patients (65.5%) were males, 21 (72.4%) received deceased donor grafts, and 7 (24.1%) developed ≥1 acute rejection episodes. Pathologically, 7 (24.1%) and 4 (13.8%) patients had inflammation grade 3-4 and fibrosis stage 3-4, respectively. Follow-up biopsy in 9 (31%) HCV genotype 4 patients showed stable, worse and improved fibrosis stage in 5, 2 and 2 patients, respectively. Of the 7 patients in the recurrent HCV group who died, 6 were infected with genotype 4 and 4 of them died of HCV-related disease. CONCLUSION: This analysis suggests that HCV recurrence following OLT in HCV-4 patients is not significantly different from its recurrence for other genotypes. PMID:19318754

  1. Characterization of Samples Identified as Hepatitis C Virus Genotype 1 without Subtype by Abbott RealTime HCV Genotype II Assay Using the New Abbott HCV Genotype Plus RUO Test

    PubMed Central

    Mokhtari, Camelia; Ebel, Anne; Reinhardt, Birgit; Merlin, Sandra; Proust, Stéphanie

    2015-01-01

    Hepatitis C virus (HCV) genotyping continues to be relevant for therapeutic strategies. Some samples are reported as genotype 1 (gt 1) without subtype by the Abbott RealTime HCV Genotype II (GT II) test. To characterize such samples further, the Abbott HCV Genotype Plus RUO (Plus) assay, which targets the core region for gt 1a, gt 1b, and gt 6 detection, was evaluated as a reflex test in reference to NS5B or 5′-untranslated region (UTR)/core region sequencing. Of 3,626 routine samples, results of gt 1 without subtype were received for 171 samples (4.7%), accounting for 11.5% of gt 1 specimens. The Plus assay and sequencing were applied to 98 of those samples. NS5B or 5′-UTR/core region sequencing was successful for 91/98 specimens (92.9%). Plus assay and sequencing results were concordant for 87.9% of specimens (80/91 samples). Sequencing confirmed Plus assay results for 82.6%, 85.7%, 100%, and 89.3% of gt 1a, gt 1b, gt 6, and non-gt 1a/1b/6 results, respectively. Notably, 12 gt 6 samples that had been identified previously as gt 1 without subtype were assigned correctly here; for 25/28 samples reported as “not detected” by the Plus assay, sequencing identified the samples as gt 1 with subtypes other than 1a/1b. The genetic variability of HCV continues to present challenges for the current genotyping platforms regardless of the applied methodology. Samples identified by the GT II assay as gt 1 without subtype can be further resolved and reliably characterized by the new Plus assay. PMID:26582834

  2. Effect of natural exposure to vaccine-derived North American genotype PRRS virus on the serological response in naïve pigs.

    PubMed

    Lillie, K; Igelbrink, R; Hoferer, M; Fiebig, K; Nathues, H; Greiser-Wilke, I; Grosse Beilage, E

    2008-01-01

    Diagnosis of porcine reproductive and respiratory syndrome virus (PRRSV) is often performed by serological testing, but ELISA does not differentiate between infections with wild-type or vaccine virus. Two attenuated live vaccines [European (EU) or North American (NA) genotype] are used. In addition to wild-type isolates, vaccine or vaccine-derived viruses occur frequently. This is often not considered when the ELISA results are used to differentiate between epizootic and enzootic infections. In this study, an infection with the NA genotype vaccine-derived virus was detected in two herds previously PRRSV negative and ELISA results [sample to positive (s/p) ratios] were analysed. The virus was identified by RT-PCR and nucleotide sequences of ORF5 had 97% (herd A) and 99% (herd B) identity with the genome of a ML PRRSV vaccine belonging to the NA genotype. Pigs of different age became positive with an average s/p ratio of 2.24 (A) and 1.18 (B). The data clearly demonstrate that spontaneous infection with a vaccine-derived virus of the NA genotype induces ELISA s/p ratios similar to those induced by vaccination or by infection with wild-type virus. We conclude that for a correct interpretation of serological results the circulation of vaccine or vaccine-derived virus isolates has to be excluded by RT-PCR, even if vaccination is not ongoing. PMID:18397502

  3. In vitro replication competence of a hepatitis B genotype D/A recombinant virus: dissimilar biological behaviour regarding its parental genotypes.

    PubMed

    Trinks, Julieta; Sugiyama, Masaya; Tanaka, Yasuhito; Kurbanov, Fuat; Benetucci, Jorge; Giménez, Edgardo; Weissenbacher, Mercedes C; Mizokami, Masashi; Oubiña, José R

    2013-12-01

    Hepatitis B virus (HBV) DNA recombinants contribute to ~30% of the overall full-length sequences already deposited in GenBank. However, their biological behaviour has not been analysed so far. In this study, the in vitro replication kinetics of the first D/A recombinant from the American continent differed from its parental genotypes, exhibiting higher extracellular levels of HBV DNA and hepatitis B e antigen. Southern blots of intracellular core-associated HBV DNA were in agreement with such results. Because this recombinant was obtained from an Argentinian injecting drug user belonging to a vulnerable community, these results are of singular relevance for regional public health. Further in vivo studies are urgently needed to determine the pathogenicity of these replicative competent clones. PMID:24026673

  4. Comparative sensitivity of commercial tests for hepatitis E genotype 3 virus antibody detection.

    PubMed

    Avellon, Ana; Morago, Lucia; Garcia-Galera del Carmen, Maria; Munoz, Milagros; Echevarría, Jose-Manuel

    2015-11-01

    Hepatitis E virus (HEV) acute infection is often diagnosed only by anti-HEV IgM ELISA methods, whose sensitivity varies, according to different reports. Reports assessing the specificity of commercial assays for anti-HEV IgG testing are scarce, and estimates of sensitivity and specificity are both controversial. The aim of this work is to assess the sensitivity of different commercial techniques for HEV genotype 3 antibody (anti-HEV) IgM and IgG detection in entirely specific sample panels including both high and low antibody concentrations. The anti-HEV IgM and IgG ELISA methods compared were: DSI, Mikrogen, Wantai, Euroimmun, MP, and Dia.pro. The rapid test All Diag was also included in the anti-HEV IgM comparison. Our results show that low anti-HEV IgM concentrations were better detected by DSI, Mikrogen, and All Diag, these tests being the most sensitive in our study. Euroimmun, MP and Dia.pro gave concordant results, showing lower sensitivity than the others. Regarding anti-HEV IgG our results revealed similar anti-HEV IgG sensitivity. Furthermore, there was a striking overall lack of concordance among the results. We present a thorough review of previous comparative reports, with particular reference to the anti-HEV IgG comparison, since published results differ from ours. This discrepancy may be related to the improved versions of the tests for MP and Dia.pro that we employed. PMID:25959136

  5. Genotype Distribution and Molecular Epidemiology of Hepatitis C Virus in Hubei, Central China

    PubMed Central

    Peng, Jing; Lu, Yanjun; Liu, Weiyong; Zhu, Yaowu; Yan, Xiaoling; Xu, Jingxin; Wang, Xiong; Wang, Yue; Liu, Wei; Sun, Ziyong

    2015-01-01

    Background Little is known about the molecular epidemiology of hepatitis C virus (HCV) infection in Central China. Methodology/Principal Findings A total of 570 patients from Hubei Province in central China were enrolled. These patients were tested positive for HCV antibody prior to blood transfusion. Among them, 177 were characterized by partial NS5B and/or Core-E1 sequences and classified into five subtypes: 1b, 83.0% (147/177); 2a, 13.0% (23/177); 3b, 2.3% (4/177); 6a, 1.1% (2/177); 3a, 0.6% (1/177). Analysis of genotype-associated risk factors revealed that paid blood donation and transfusion before 1997 were strongly associated with subtypes 1b and 2a, while some subtype 2a cases were also found in individuals with high risk sexual behaviors; subtypes 3b, 6a, and 3a were detected only in intravenous drug users. Phylogeographic analyses based on the coalescent datasets demonstrated that 1b, 2a, 3b, and 6a were locally epidemic in Hubei Province. Among them, subtype 1b Hubei strains may have served as the origins of this subtype in China, and 2a and 3b Hubei strains may have descended from the northwest and southwest of China, respectively, while 6a Hubei strains may have been imported from the central south and southwest. Conclusion/Significance The results suggest that the migration patterns of HCV in Hubei are complex and variable among different subtypes. Implementation of mandatory HCV screening before donation has significantly decreased the incidence of transfusion-associated HCV infection since 1997. More attention should be paid to intravenous drug use and unsafe sexual contact, which may have become new risk factors for HCV infection in Hubei Province. PMID:26325070

  6. Detection of hepatitis A virus genotype IB variants in clams from Maputo Bay, Mozambique.

    PubMed

    Nenonen, Nancy P; Hernroth, Bodil; Chauque, Arlindo A; Hannoun, Charles; Bergström, Tomas

    2006-07-01

    Clams provide an important source of food and income for the population of Maputo, Mozambique, where conditions of poor water supply and inadequate sanitation favor endemic infection with hepatitis A virus (HAV). To determine the role of bivalves in an endemic area, clams gathered from Maputo Bay were bought from market and examined for HAV. Four batches, total 150 clams, were sampled over the year. RNA extracted from individual digestive glands was assayed by nested RT-PCR and sequencing of HAV 5' noncoding region (5' NCR). Specific HAV signals were detected in one batch, 23 of 34 clams (67%) testing positive. Phylogenetic analyses of VP3/VP1, VP1/P2A, and 5' NCR determined clustering of clam strains as genotype I, subtype B. In addition to identifying HAV IB strains with predicted conserved amino acid sequence, IB variants exhibiting novel amino acid substitutions at the VP1/P2A junction were detected. HAV strains from clams showed 93%-99% homology with wild-type IB strains from South African outbreaks and from a panel of HAV IgM positive Swedish patients. DNA from enteric human adenovirus 40/41 was found in a limited number of clams from two batches, 6/34 (17%) and 4/35 (11%). Detection of HAV subgenotype IB in bivalves provided indirect evidence of the strains circulating in a densely populated coastal region where HAV is presumed to be hyperendemic. The results suggest that clams may be an important source of HAV in Maputo region, and indicate the need for further molecular study of strains circulating in the indigenous population. PMID:16721847

  7. Efficacy and safety of daclatasvir and asunaprevir for hepatitis C virus genotype 1b infection

    PubMed Central

    Nam, Hee Chul; Lee, Hae Lim; Yang, Hyun; Song, Myeong Jun

    2016-01-01

    Background/Aims: The treatment strategy for hepatitis C virus (HCV) has been changing rapidly since the introduction of direct-acting antivirals such as daclatasvir (DCV) and asunaprevir (ASV). We evaluated the efficacy and safety of DCV and ASV for HCV in real-life practice. Methods: Patients were treated with 60 mg of DCV once daily plus 200 mg of ASV twice daily for 24 weeks, and followed for 12 weeks. The primary endpoint was a sustained virological response at 12 weeks after treatment (SVR12) and safety. Results: This retrospective study included eight patients with chronic HCV genotype 1b infection. All of the enrolled patients were diagnosed with liver cirrhosis, and their mean age was 65.75 years. One patient was a nonresponder and two patients relapsed with previous pegylated interferon (PegIFN) and ribavirin (RBV) treatment. None of the patient showed NS5A mutation. An SVR12 was achieved in 88% of cases by the DCV and ASV combination therapy. The serum transaminase level and the aspartate-aminotransferase-to-platelet ratio were improved after the treatment. DCV and ASV were well tolerated in most of the patients, with treatment discontinuation due to adverse events (elevated liver enzyme and decompensation) occurring in two patients. Conclusion: In this study, combination of DCV and ASV treatment achieved a high sustained virological response with few adverse events even in those with cirrhosis, advanced age, and nonresponse/relapse to previous interferon-based therapy. Close monitoring of safety issues may be necessary when treating chronic HCV patients receiving DCV and ASV, especially in older patient and those with cirrhosis. PMID:27377910

  8. Response Prediction and Treatment Tailoring for Chronic Hepatitis C Virus Genotype 1 Infection▿

    PubMed Central

    Lindh, Magnus; Alestig, Erik; Arnholm, Birgitta; Eilard, Anders; Hellstrand, Kristoffer; Lagging, Martin; Wahlberg, Thomas; Wejstål, Rune; Westin, Johan; Norkrans, Gunnar

    2007-01-01

    We monitored early viral response during the treatment of hepatitis C virus (HCV) infection with the aim of identifying predictors of treatment outcome. We studied 53 patients with genotype 1 infection who received 180 μg/week pegylated interferon alfa-2a and 1,000 or 1,200 mg/day ribavirin depending on body weight and serially assessed HCV RNA in serum, using the Cobas TaqMan assay. Thirty-one patients (58%) achieved sustained viral response (SVR). SVR was obtained in 100% (10/10) of patients with pretreatment viremia concentrations below 400,000 IU/ml, in 100% (14/14) of patients with more than 1.5 log reduction of HCV RNA after 4 days of treatment, and in 95% (22/23) of patients with a rate of decline in viremia higher than 0.70 log units/week during the second phase. Non-SVR was seen in all patients with a second-phase decline rate lower than 0.35 log units/week. Patients with slopes between 0.50 and 0.80 log units/week achieved SVR (4/4) unless the treatment dose was modified (3/3). We conclude that the second-phase slope appears to be an accurate and useful predictor of treatment response. On the basis of these findings, we propose a model of tailored treatment which takes into account the second-phase slope and the amount of HCV RNA after 21 days of treatment. PMID:17581934

  9. Phylogeography and evolutionary history of hepatitis B virus genotype F in Brazil

    PubMed Central

    2013-01-01

    Background Hepatitis B virus (HBV) genotype F (HBV/F) is considered to be indigenous to the Americas, but its emergence and spread in the continent remain unknown. Previously, only two HBV/F complete genome sequences from Brazil were available, limiting the contribution of Brazilian isolates to the phylogenetic studies of HBV/F. The present study was carried out to assess the proportion and geographic distributions of HBV/F subgenotypes in Brazil, to determine the full-length genomic sequences of HBV/F isolates from different Brazilian geographic regions, and to investigate the detailed evolutionary history and phylogeography of HBV/F in Brazil. Methods Complete HBV/F genomes isolated from 12 Brazilian patients, representing the HBV/F subgenotypes circulating in Brazil, were sequenced and analyzed together with sequences retrieved from GenBank, using the Bayesian coalescent and phylogeographic framework. Results Phylogenetic analysis using all Brazilian HBV/F S-gene sequences available in GenBank showed that HBV/F2a is found at higher frequencies countrywide and corresponds to all sequences isolated in the Brazilian Amazon Basin. In addition, the evolutionary analysis using complete genome sequences estimated an older median ancestral age for the Brazilian HBV/F2a compared to the Brazilian HBV/F1b and HBV/F4 subgenotypes, suggesting that HBV/F2a represents the original native HBV of Brazil. The phylogeographic patterns suggested a north-to-south flow of HBV/F2a from Venezuela to Brazil, whereas HBV/F1b and HBV/F4 strains appeared to have spread from Argentina to Brazil. Conclusions This study suggests a plausible route of introduction of HBV/F subgenotypes in Brazil and demonstrates the usefulness of recently developed computational tools for investigating the evolutionary history of HBV. PMID:23855930

  10. Complete sequencing of a gibbon hepatitis B virus genome reveals a unique genotype distantly related to the chimpanzee hepatitis B virus.

    PubMed

    Norder, H; Ebert, J W; Fields, H A; Mushahwar, I K; Magnius, L O

    1996-04-01

    We have sequenced the complete genome of a hepatitis B virus (HBV) strain that was transmitted from a gibbon with chronic hepatitis B to a chimpanzee that subsequently developed acute hepatitis B. The genome was 3,182 nucleotides long and had a genetic organization identical to and including the characteristics of other mammalian hepadnaviruses. Thus, the regulatory elements, the direct repeats, and the four open reading frames (ORFs) of this virus were all maintained, although there were amino acid substitutions affecting all the ORFs. Within the S gene encoding for the hepatitis B surface antigen (HBsAg), the subtype could be deduced as ayw3 in accordance with previous serological results. There were 25 amino acid substitutions affecting the P gene, 12 of which were within the spacer region. This region, which was the most divergent part of the genome compared to other HBV strains, also encodes for the pre-S proteins. A comparison with sequences of other hepadnaviruses revealed that the genome of gibbon HBV was unique as compared to previously described HBV genotypes. It was most similar to the chimpanzee HBV strain with which it shared 90.3% nucleic acid homology at the level of the complete genome and 96.3% homology at the level of the S-gene region corresponding to HBsAg, although being a distinct genotype as compared to the latter virus. Analyses performed using five different algorithms for phylogenetic tree construction showed more than 99% bootstrap support for the gibbon and the chimpanzee HBV to be grouped within the human HBV strains and that they represented later offshoots than the HBV strains of genotype F. However, in most of the dendrograms both the gibbon and the chimpanzee strains represented early lineages, indicating that these viruses are indigenous to their respective hosts and not recent acquisitions from man. PMID:8615024

  11. Genotype-specific mutations in the polymerase gene of hepatitis B virus potentially associated with resistance to oral antiviral therapy.

    PubMed

    Mirandola, Silvia; Sebastiani, Giada; Rossi, Cristina; Velo, Emanuela; Erne, Elke Maria; Vario, Alessandro; Tempesta, Diego; Romualdi, Chiara; Campagnolo, Davide; Alberti, Alfredo

    2012-12-01

    The evolution of hepatitis B virus (HBV) and the role of different variants during antiviral therapy may be influenced by HBV genotype. We have therefore analysed substitutions potentially related to nucleos(t)ide analogues (NAs) resistance at 42 positions within RT-region in a cohort of patients with chronic hepatitis B in relation to HBV-genotype. RT mutations analysis was performed by direct sequencing in 200 NAs-naïve patients and in 64 LAM or LAM+ADV experienced patients with NAs resistance, infected mainly by HBV-genotypes D and A. 27 polymorphic-sites were identified among the 42 positions analysed and 64 novel mutations were detected in 23 positions. Genotype-D displayed the highest mutation frequency (6.4%) among all HBV-genotypes analysed. Single or multiple mutations were detected in 80% of naïve patients. Overall, the most frequent single mutations were at residues rt54, rt53 and rt91 which may associate with significantly lower HBV-DNA levels (p=0.001). Comparison with sequencing data of patients failing LMV or LAM+ADV therapy revealed an higher frequency of novel genotype-specific mutations if compared with naïve patients: 3 mutations under LAM monotherapy in HBV-D (rtS85F; rtL91I; rtC256G) and 3 mutations under ADV therapy in HBV-A (rtI53V; rtW153R; rtF221Y). In HBV-D treated patients the dominant resistance mutation was rtL80V (31.4%) and rtM204I (60%) in LAM+ADV group while LAM-treated patients showed a preference of rtM204V (51.9%). Interestingly, none of HBV-A patients had mutation rtM204I under ADV add-on treatment but all of them had the "V" AA substitution. These results suggested that in patients with CHB, HBV-genotype might be relevant in the evolution and development of drug resistance showing also different mutation patterns in the YMDD motif between HBV genotype D and A. PMID:23026293

  12. Characterisation of genotype VII Newcastle disease virus (NDV) isolated from NDV vaccinated chickens, and the efficacy of LaSota and recombinant genotype VII vaccines against challenge with velogenic NDV

    PubMed Central

    Roohani, Kiarash; Yeap, Swee Keong; Ideris, Aini; Bejo, Mohd Hair; Omar, Abdul Rahman

    2015-01-01

    A Newcastle disease virus (NDV) isolate designated IBS002 was isolated from a commercial broiler farm in Malaysia. The virus was characterised as a virulent strain based on the multiple basic amino acid motif of the fusion (F) cleavage site 112RRRKGF117 and length of the C-terminus extension of the hemagglutinin-neuraminidase (HN) gene. Furthermore, IBS002 was classified as a velogenic NDV with mean death time (MDT) of 51.2 h and intracerebral pathogenicity index (ICPI) of 1.76. A genetic distance analysis based on the full-length F and HN genes showed that both velogenic viruses used in this study, genotype VII NDV isolate IBS002 and genotype VIII NDV isolate AF2240-I, had high genetic variations with genotype II LaSota vaccine. In this study, the protection efficacy of the recombinant genotype VII NDV inactivated vaccine was also evaluated when added to an existing commercial vaccination program against challenge with velogenic NDV IBS002 and NDV AF2240-I in commercial broilers. The results indicated that both LaSota and recombinant genotype VII vaccines offered full protection against challenge with AF2240-I. However, the LaSota vaccine only conferred partial protection against IBS002. In addition, significantly reduced viral shedding was observed in the recombinant genotype VII-vaccinated chickens compared to LaSota-vaccinated chickens. PMID:25643805

  13. The Cost-Effectiveness of Sofosbuvir-Based Regimens for Treatment of Hepatitis C Virus Genotype 2 or 3 Infection

    PubMed Central

    Linas, Benjamin P.; Barter, Devra M.; Morgan, Jake R.; Pho, Mai T.; Leff, Jared A.; Schackman, Bruce R.; Horsburgh, C. Robert; Assoumou, Sabrina A.; Salomon, Joshua A.; Weinstein, Milton C.; Freedberg, Kenneth A.; Kim, Arthur Y.

    2015-01-01

    Background Chronic infection with hepatitis C virus (HCV) genotype 2 or 3 can be treated with sofosbuvir without interferon. Because sofosbuvir is costly, its benefits should be compared with the additional resources used. Objective To estimate the cost-effectiveness of sofosbuvir-based treatments for HCV genotype 2 or 3 infection in the United States. Design Monte Carlo simulation, including deterministic and probabilistic sensitivity analyses. Data Sources Randomized trials, observational cohorts, and national health care spending surveys. Target Population 8 patient types defined by HCV genotype (2 vs. 3), treatment history (naive vs. experienced), and cirrhosis status (noncirrhotic vs. cirrhotic). Time Horizon Lifetime. Perspective Payer. Intervention Sofosbuvir-based therapies, pegylated interferon–ribavirin, and no therapy. Outcome Measures Discounted quality-adjusted life-years (QALYs), costs, and incremental cost-effectiveness ratios (ICERs). Results of Base-Case Analysis The ICER of sofosbuvir-based treatment was less than $100 000 per QALY in cirrhotic patients (genotype 2 or 3 and treatment-naive or treatment-experienced) and in treatment-experienced noncirrhotic patients but was greater than $200 000 per QALY in treatment-naive noncirrhotic patients. Results of Sensitivity Analysis The ICER of sofosbuvir-based therapy for treatment-naive noncirrhotic patients with genotype 2 or 3 infection was less than $100 000 per QALY when the cost of sofosbuvir was reduced by approximately 40% and 60%, respectively. In probabilistic sensitivity analyses, cost-effectiveness conclusions were robust to uncertainty in treatment efficacy. Limitation The analysis did not consider possible benefits of preventing HCV transmission. Conclusion Sofosbuvir provides good value for money for treatment-experienced patients with HCV genotype 2 or 3 infection and those with cirrhosis. At their current cost, sofosbuvir-based regimens for treatment-naive noncirrhotic patients exceed

  14. Inactivated porcine reproductive and respiratory syndrome virus vaccine adjuvanted with Montanide™ Gel 01 ST elicits virus-specific cross-protective inter-genotypic response in piglets.

    PubMed

    Tabynov, Kairat; Sansyzbay, Abylay; Tulemissova, Zhanara; Tabynov, Kaissar; Dhakal, Santosh; Samoltyrova, Aigul; Renukaradhya, Gourapura J; Mambetaliyev, Muratbay

    2016-08-30

    The efficacy of a novel BEI-inactivated porcine reproductive and respiratory syndrome virus (PRRSV) candidate vaccine in pigs, developed at RIBSP Republic of Kazakhstan and delivered with an adjuvant Montanide™ Gel 01 ST (D/KV/ADJ) was compared with a commercial killed PRRSV vaccine (NVDC-JXA1, C/KV/ADJ) used widely in swine herds of the Republic of Kazakhstan. Clinical parameters (body temperature and respiratory disease scores), virological and immunological profiles [ELISA and virus neutralizing (VN) antibody titers], macroscopic lung lesions and viral load in the lungs (quantitative real-time PCR and cell culture assay) were assessed in vaccinated and both genotype 1 and 2 PRRSV challenged pigs. Our results showed that the commercial vaccine failed to protect pigs adequately against the clinical disease, viremia and lung lesions caused by the challenged field isolates, Kazakh strains of PRRSV type 1 and type 2 genotypes. In contrast, clinical protection, absence of viremia and lung lesions in D/KV/ADJ vaccinated pigs was associated with generation of VN antibodies in both homologous vaccine strain LKZ/2010 (PRRSV type 2) and a heterogeneous type 1 PRRSV strain (CM/08) challenged pigs. Thus, our data indicated the induction of cross-protective VN antibodies by D/KV/ADJ vaccine, and importantly demonstrated that an inactivated PRRSV vaccine could also induce cross-protective response across the viral genotype. PMID:27527768

  15. Responder Interferon λ Genotypes Are Associated With Higher Risk of Liver Fibrosis in HIV–Hepatitis C Virus Coinfection

    PubMed Central

    Moqueet, Nasheed; Cooper, Curtis; Gill, John; Hull, Mark; Platt, Robert W.; Klein, Marina B.

    2016-01-01

    Background. Liver fibrosis progresses faster in individuals coinfected with human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Interferon λ3 (IFN-λ3) has both antiviral and proinflammatory properties. Genotypes at IFNL single-nucleotide proteins (SNPs; rs12979860CC and rs8099917TT) are linked to higher HCV clearance, potentially via rs8103142. We examined the relationship between IFN-λ genotypes and significant liver fibrosis in HIV-HCV coinfection. Methods. From the prospective Canadian Co-infection Cohort (n = 1423), HCV RNA–positive participants in whom IFN-λ genotypes were detected and who were free of fibrosis, end-stage liver disease, and chronic hepatitis B at baseline (n = 485) were included. Time to significant fibrosis (defined as an aspartate transaminase level to platelet count ratio index [APRI] of ≥1.5) by IFN-λ genotypes was analyzed using Cox proportional hazards, with adjustment for age, sex, ethnicity, alcohol use, CD4+ T-cell count, HCV genotype, γ-glutamyl transferase level, and baseline APRI. Haplotype analysis was performed, with adjustment for ethnicity. Results. A total of 125 participants developed fibrosis over 1595 person-years (7.84 cases/100 person-years; 95% confidence interval [CI], 6.58–9.34 cases/100 person-years). Each genotype was associated with an increased fibrosis risk, with adjusted hazard ratios of 1.37 (95% CI, .94–2.02) for rs12979860CC, 1.34 (95% CI, .91–1.97) for rs8103142TT, and 1.79 (95% CI, 1.24–2.57) for rs8099917TT. Haplotype TCT was also linked with a higher risk (hazard ratio, 1.14 [95% CI, .73–1.77]). Conclusions. IFN-λ SNPs rs12979860, rs8099917, and rs81013142 were individually linked to higher rates of fibrosis in individuals with HIV-HCV coinfection. IFN-λ genotypes may be useful to target HCV treatments to people who are at higher risk of liver disease. PMID:26984148

  16. Phylogeography and epidemic history of hepatitis C virus genotype 4 in Africa

    PubMed Central

    Iles, James C.; Raghwani, Jayna; Harrison, G.L. Abby; Pepin, Jacques; Djoko, Cyrille F.; Tamoufe, Ubald; LeBreton, Matthew; Schneider, Bradley S.; Fair, Joseph N.; Tshala, Felix M.; Kayembe, Patrick K.; Muyembe, Jean Jacques; Edidi-Basepeo, Samuel; Wolfe, Nathan D.; Simmonds, Peter; Klenerman, Paul; Pybus, Oliver G.

    2014-01-01

    HCV genotype 4 is prevalent in many African countries, yet little is known about the genotype׳s epidemic history on the continent. We present a comprehensive study of the molecular epidemiology of genotype 4. To address the deficit of data from the Democratic Republic of the Congo (DRC) we PCR amplified 60 new HCV isolates from the DRC, resulting in 33 core- and 48 NS5B-region sequences. Our data, together with genotype 4 database sequences, were analysed using Bayesian phylogenetic approaches. We find three well-supported intra-genotypic lineages and estimate that the genotype 4 common ancestor existed around 1733 (1650–1805). We show that genotype 4 originated in central Africa and that multiple lineages have been exported to north Africa since ~1850, including subtype 4a which dominates the epidemic in Egypt. We speculate on the causes of the historical intra-continental spread of genotype 4, including population movements during World War 2. PMID:25105489

  17. Protective Effect of Human Leukocyte Antigen B27 in Hepatitis C Virus Infection Requires the Presence of a Genotype-Specific Immunodominant CD8+ T-Cell Epitope

    PubMed Central

    Kersting, Nadine; Fitzmaurice, Karen; Oniangue-Ndza, Cesar; Kemper, Michael N.; Humphreys, Isla; McKiernan, Susan; Kelleher, Dermot; Lohmann, Volker; Bowness, Paul; Huzly, Daniela; Rosen, Hugo R.; Kim, Arthur Y.; Lauer, Georg M.; Allen, Todd M.; Barnes, Eleanor; Roggendorf, Michael; Blum, Hubert E.; Thimme, Robert

    2015-01-01

    Human leukocyte antigen B27 (HLA-B27) is associated with protection in human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infection. This protective role is linked to single immunodominant HLA-B27-restricted CD8+ T-cell epitopes in both infections. In order to define the relative contribution of a specific HLA-B27-restricted epitope to the natural course of HCV infection, we compared the biological impact of the highly conserved HCV genotype 1 epitope, for which the protective role has been described, with the corresponding region in genotype 3 that differs in its sequence by three amino acid residues. The genotype 3a peptide was not recognized by CD8+ T cells specific for the genotype 1 peptide. Furthermore, patients with acute or chronic infection with HCV genotype 3a did not mount T-cell responses to this epitope region, and their autologous viral sequences showed no evidence of T-cell pressure. Finally, we found a significantly higher frequency of HLA-B27 positivity in patients with chronic HCV genotype 3a infection compared to genotype 1 infection, indicating that there is no protection by HLA-B27 in HCV genotype 3 infection. Conclusion Our data indicate that the protective effect of HLA-B27 is limited to HCV genotype 1 infection and does not expand to other genotypes such as genotype 3a. This can most likely be explained by intergenotype sequence diversity leading to the loss of the immunodominant HLA-B27 epitope in viral strains other than genotype 1. Our results underline the central role of a single HLA-B27-restricted epitope-specific CD8+ T-cell response in mediating protection in HCV genotype 1 infection. PMID:20034048

  18. Pathogenic and Genotypic Characterization of a Japanese Encephalitis Virus Isolate Associated with Reproductive Failure in an Indian Pig Herd

    PubMed Central

    Desingu, P. A.; Ray, Pradeep K.; Patel, B. H. M.; Singh, R.; Singh, R. K.; Saikumar, G

    2016-01-01

    Background India is endemic to Japanese encephalitis virus (JEV) and recurrent outbreaks occur mainly in rice growing areas. Pigs are considered to be the amplifying host for JEV and infection in gestating pigs results in reproductive failure. Most studies conducted on JEV infection in Indian pigs have been serological surveys and very little is known about JEV genotypes circulating in pigs. So the potential risk posed by pigs in JEV transmission and the genetic relationship between viruses circulating in pigs, mosquitoes and humans is poorly understood. Methodology/Principal Findings This study was conducted in pigs with a history of reproductive failure characterized by stillborn piglets with neuropathological lesions. Japanese encephalitis (JE) suspected brain specimens inoculated intracerebrally into mice and Vero cells resulted in successful isolation of JEV/SW/IVRI/395A/2014. Clinicopathological observations in infected mice, demonstration of JEV antigen in brain, and analysis of the envelope protein identified the swine isolate as being neurovirulent. Phylogenetic analysis based on prM and E gene sequences showed that it belonged to genotype III. This swine isolate was closely related to JEV associated with the 2005 outbreak in India and JaoArS982 from Japan. Phylogenetic analysis of JEV strains collected between 1956 and 2014 in India categorized the GIII viruses into different clades blurring their spatial distribution, which has been discernible in the previous century. Conclusions/Significance Isolation of JEV from stillborn piglets and its close genetic relationship with viruses detected at least three decades ago in humans and mosquitoes in Japan suggests that the virus may have been circulating among Indian pigs for several decades. The close similarity between the present swine isolate and those detected in humans affected in the 2005 outbreak in Uttar Pradesh, India, suggests the need for more intensive surveillance of pigs and implementation of

  19. Susceptibility of goldsinny wrasse, Ctenolabrus rupestris L. (Labridae), to viral haemorrhagic septicaemia virus (VHSV) genotype III: Experimental challenge and pathology.

    PubMed

    Matejusova, I; Noguera, P A; Hall, M; McBeath, A J A; Urquhart, K; Simons, J; Fordyce, M J; Lester, K; Ho, Y-M; Murray, W; Bruno, D W

    2016-04-15

    Cleaner fish, such as wrasse, are being increasingly used to combat the sea lice infestation of Atlantic salmon (Salmo salar L.) in many European countries. To determine susceptibility of the goldsinny wrasse (Ctenolabrus rupestris L.) and pathogenesis of the viral haemorrhagic septicaemia virus (VHSV) genotype III isolate 12-654, previously associated with VHSV infection in the Shetland Islands in 2012, fish were experimentally challenged by intraperitoneal injection (IP), bath immersion and cohabitation routes. Cumulative proportion of moribund wrasse reached 17% following the virus immersion challenge while by the IP-route moribunds exceeded 50% within 14days post-challenge. Typical signs of VHS as reported in rainbow trout (Oncorhynchus mykiss), were not observed in moribund goldsinny wrasse. The most pronounced histopathological changes, consistent regardless of the route of infection, were observed within the heart and included atrium myofibril degeneration, focal infiltration and multifocal necrosis, with prominent swelling of the endocardium and occasional detachment. Pathological changes in the atrium were associated with presence of the viral antigen as confirmed by a positive immunohistochemical staining. Virus clearance and heart tissue recovery were noted although further experiments are required to confirm these observations. The results of a cohabitation experiment confirmed that goldsinny wrasse shed viable virus and therefore represent a risk of virus transmission to other VHSV susceptible species. Similarities between the pathology in goldsinny wrasse induced through the controlled experimental challenges and that of wrasse spp. from an infection occurrence in Shetland are discussed. PMID:27016771

  20. Complete genome sequence analysis identifies a new genotype of brassica yellows virus that infects cabbage and radish in China.

    PubMed

    Zhang, Xiao-Yan; Xiang, Hai-Ying; Zhou, Cui-Ji; Li, Da-Wei; Yu, Jia-Lin; Han, Cheng-Gui

    2014-08-01

    For brassica yellows virus (BrYV), proposed to be a member of a new polerovirus species, two clearly distinct genotypes (BrYV-A and BrYV-B) have been described. In this study, the complete nucleotide sequences of two BrYV isolates from radish and Chinese cabbage were determined. Sequence analysis suggested that these isolates represent a new genotype, referred to here as BrYV-C. The full-length sequences of the two BrYV-C isolates shared 93.4-94.8 % identity with BrYV-A and BrYV-B. Further phylogenetic analysis showed that the BrYV-C isolates formed a subgroup that was distinct from the BrYV-A and BrYV-B isolates based on all of the proteins except P5. PMID:24599564

  1. Patho-epidemiological study on Genotype-XIII Newcastle disease virus infection in commercial vaccinated layer farms

    PubMed Central

    Khorajiya, J. H.; Pandey, Sunanda; Ghodasara, Priya D.; Joshi, B. P.; Prajapati, K. S.; Ghodasara, D. J.; Mathakiya, R. A.

    2015-01-01

    Aim: The present research work was carried out to study the patho-epidemiological aspects of Genotype-XIII Newcastle disease virus (NDV) infection in commercial layer in and around Anand, Gujarat. As the outbreaks have reported in vaccinated flocks, it was felt necessary to study the disease with respect to its changing pathogenicity and relevant aspects. Materials and Methods: The study comprised of patho-epidemiology of Newcastle disease (ND) by information collected from different layer farms suffering from the disease in relation to incidence pattern and mortality, duration of mortality, susceptible age, and loss due to production performance. Clinical signs were recorded based on observations. During post-mortem, gross lesions were also recorded. For histopathological examination visceral organs according to lesions were collected in 10% formalin and processed slide stained by hematoxylin and eosin for microscopic examination. Cultivation of virus was done in embryonated specific pathogen-free (SPF) eggs of 9-11 days and isolation of virus was done for haemagglutination (HA) and haemagglutination inhibition (HI) test and to identify pathotype of virus by intracerebral pathogenicity index (ICPI) test to determine the virulence of virus. The Genotype-XIII NDV was confirmed by F gene sequence and whole genome sequence. Results: During the study mortality due to ND was recorded in 13 layer flocks in spite of routine vaccination, which usually contain Genotype-II strain of virus. The mortality was observed as high as above 50% with an average of 21.21%. The susceptible age for disease was found to be 6-14 weeks. The duration of mortality observed was 23 days. The disease resulted in a significant reduction in body weight, feed intake and drop in egg production. Majority of the outbreaks appeared during extremely hot months of April to June. Greenish diarrhoea was frequently seen in birds that survived early in infection. Mortality continued for 2-3 weeks and

  2. Hepatic steatosis in hepatitis C virus genotype 3 infection: does it correlate with body mass index, fibrosis, and HCV risk factors?

    PubMed

    Sharma, Pratima; Balan, Vijayan; Hernandez, Jose; Rosati, Marianne; Williams, James; Rodriguez-Luna, Hector; Schwartz, Joan; Harrison, Edwyn; Anderson, Monte; Byrne, Thomas; Vargas, Hugo E; Douglas, David D; Rakela, Jorge

    2004-01-01

    Hepatic steatosis is a recognized feature of hepatitis C viral infection, particularly in genotype 3. The demographics and the associations contributing to moderate to severe steatosis in genotype 3 are not very well studied. The aim of this study is to determine the demographics and association of steatosis with fibrosis, obesity, diabetes, lipid levels, and risk factors among patients with hepatitis C virus (HCV) genotype 3. Two hundred ninety-three consecutive HCV patients (genotype 1, n = 218; genotype 2, n = 43; genotype 3, n = 32) at our institution were studied retrospectively. Demographic information such as height, weight, genotype, risk factors, serum cholesterol and triglyceride, and liver biopsy was collected. Steatosis was graded using the Brunt classification. HCV genotype 3-infected patients were younger (P < 0.04) and had lower serum cholesterol levels (P < 0.02) compared to nongenotype 3 patients. Moderate to severe steatosis was more prevalent in HCV genotype 3 patients (P < 0.001) with intravenous drug abuse as a risk factor (P = 0.04). Genotype 3 was the independent predictor of steatosis in all patients. There was no statistical association between grade of steatosis and body mass index, fibrosis, necroinflammation, or hyperlipidemia when only HCV genotype 3 patients were included in the multivariate logistic model. Hepatic steatosis is a feature of genotype 3. Patients with HCV genotype 3 are younger and have lower serum cholesterol levels. Genotype 3 is the independent predictor for steatosis in HCV patients. HCV genotype 3 patients with moderate to severe steatosis are more likely to have intravenous drug use as a risk factor. PMID:14992430

  3. Use of immuno-dominant epitope derived from genotype 4 as a diagnostic reagent for detecting the antibodies against Hepatitis E Virus

    PubMed Central

    2013-01-01

    Background Despite the genotype 4 has become the dominant cause of hepatitis E disease in China, none antigen derived from genotype 4 of hepatitis E virus (HEV) was used in current commercial anti-HEV immunoassay, and the serological reactivity of antigen derive from genotype 4 is not well-charactered. Methods We expressed and purified the 4 main immuno-dominant epitopes derived from genotype 1 and 4 including ORF2 (410-621aa) of genotype 4, ORF3 (47-114aa) of genotype 4, ORF2 (396-606aa) of genotype 1 and ORF3 (56-123aa) of genotype 4. Results The ORF2 of genotype 4 displayed good diagnostics performance according to ROC analysis using in-house panel, and the immunoassays based the ORF2 of genotype 4 was then developed to detect the anti-HEV IgG antibodies and evaluated further in 530 anti-HEV IgG positive specimens and 380 negative specimens. The sensitivity and the specificity is 98.1% (520/530) and 94.7% (360/380) for immunoassay based on ORF2 of genotype 4, 96.6% (512/530) and 92.6% (352/380) for commercial immunoassay based on genotype 1. It is noted that all of the positive samples will be detected by combing two assays together. The anti-HEV immunoassays based on genotype 4 are in accordance with Chinese anti-HEV national standard,and show an good agreement of 95.8% with commercial assay (kappa=0.913, P=0.014). Conclusions The immunoassay based on ORF2G4 displays good performance, and combining assay based on genotype 1 together with genotype 4 will benefit the HEV diagnosis in large scale samples. PMID:23618011

  4. Emergence of dengue virus 4 genotype II in Guangzhou, China, 2010: Survey and molecular epidemiology of one community outbreak

    PubMed Central

    2012-01-01

    Background The re-emergence of dengue virus 4 (DENV-4) has become a public health concern in South America, Southeast Asia and South Asia. However, it has not been known to have caused a local outbreak in China for the past 20 years. The purpose of this study was to elucidate the epidemiology of one local community outbreak caused by DENV-4 in Guangzhou city, China, in 2010; and to determine the molecular characteristics of the genotype II virus involved. Case presentations During September and October of 2010, one imported case, a Guangzhou resident who travelled back from Thailand, resulted in 18 secondary autochthonous cases in Guangzhou City, with an incidence rate of 5.53 per 10,000 residents. In indigenous cases, 14 serum samples tested positive for IgM against DENV and 7 for IgG from a total of 15 submitted serum samples, accompanied by 5 DENV-4 isolates. With identical envelope gene nucleotide sequences, the two isolates (D10168-GZ from the imported index case and Guangzhou 10660 from the first isolate in the autochthonous cases) were grouped into DENV-4 genotype II after comparison to 32 previous DENV-4 isolates from GenBank that originated from different areas. Conclusions Based on epidemiological and phylogenetic analyses, the outbreak, which was absent for 20 years after the DENV-4 genotype I outbreak in 1990, was confirmed as DENV-4 genotype II and initially traced to the imported index case, a Guangzhou resident who travelled back from Thailand. PMID:22497881

  5. Hepatitis E Virus in Cambodia: Prevalence among the General Population and Complete Genome Sequence of Genotype 4

    PubMed Central

    Yamada, Hiroko; Takahashi, Kazuaki; Lim, Olline; Svay, Somana; Chuon, Channarena; Hok, Sirany; Do, Son Huy; Fujimoto, Mayumi; Akita, Tomoyuki; Goto, Noboru; Katayama, Keiko; Arai, Masahiro; Tanaka, Junko

    2015-01-01

    Hepatitis E virus (HEV) is a growing public health problem in many countries. In this study, we investigated HEV seroprevalence among the general population in the Siem Reap province, Cambodia, and performed HEV genetic analysis with the aim to develop an HEV prevention strategy. This seroepidemiological cross-sectional study conducted from 2010 to 2014 included 868 participants from four different locations in Siem Reap province, Cambodia. They answered questionnaires and provided blood samples for the analysis of hepatitis virus infections. Among the participants (360 men and 508 women; age range, 7–90 years), the prevalence of anti-HEV IgG was 18.4% (95% confidence interval: 15.9–21.0); HEV RNA was detected in two participants (0.23%) and was classified as genotype 3 and 4. Full-length genome of the genotype 4 isolate, CVS-Sie10, was sequenced; it contained 7,222 nucleotides and three ORFs and demonstrated high sequence identity with the swine China isolates swGX40 (95.57%), SS19 (94.37%), and swDQ (91.94%). Multivariate logistic regression analysis revealed that men, elderly people, and house workers were risk groups significantly associated with the positivity for anti-HEV IgG. This is the first report on the detection of HEV genotype 4 in humans in Cambodia and on the complete genome sequence of HEV genotype 4 from this country. Our study demonstrates that new HEV infection cases occur frequently among the general population in Cambodia, and effective preventive measures are required. PMID:26317620

  6. Hepatitis E Virus in Cambodia: Prevalence among the General Population and Complete Genome Sequence of Genotype 4.

    PubMed

    Yamada, Hiroko; Takahashi, Kazuaki; Lim, Olline; Svay, Somana; Chuon, Channarena; Hok, Sirany; Do, Son Huy; Fujimoto, Mayumi; Akita, Tomoyuki; Goto, Noboru; Katayama, Keiko; Arai, Masahiro; Tanaka, Junko

    2015-01-01

    Hepatitis E virus (HEV) is a growing public health problem in many countries. In this study, we investigated HEV seroprevalence among the general population in the Siem Reap province, Cambodia, and performed HEV genetic analysis with the aim to develop an HEV prevention strategy. This seroepidemiological cross-sectional study conducted from 2010 to 2014 included 868 participants from four different locations in Siem Reap province, Cambodia. They answered questionnaires and provided blood samples for the analysis of hepatitis virus infections. Among the participants (360 men and 508 women; age range, 7-90 years), the prevalence of anti-HEV IgG was 18.4% (95% confidence interval: 15.9-21.0); HEV RNA was detected in two participants (0.23%) and was classified as genotype 3 and 4. Full-length genome of the genotype 4 isolate, CVS-Sie10, was sequenced; it contained 7,222 nucleotides and three ORFs and demonstrated high sequence identity with the swine China isolates swGX40 (95.57%), SS19 (94.37%), and swDQ (91.94%). Multivariate logistic regression analysis revealed that men, elderly people, and house workers were risk groups significantly associated with the positivity for anti-HEV IgG. This is the first report on the detection of HEV genotype 4 in humans in Cambodia and on the complete genome sequence of HEV genotype 4 from this country. Our study demonstrates that new HEV infection cases occur frequently among the general population in Cambodia, and effective preventive measures are required. PMID:26317620

  7. Non-travel related Hepatitis E virus genotype 3 infections in the Netherlands; A case series 2004 – 2006

    PubMed Central

    Borgen, Katrine; Herremans, Tineke; Duizer, Erwin; Vennema, Harry; Rutjes, Saskia; Bosman, Arnold; de Roda Husman, Ana Maria; Koopmans, Marion

    2008-01-01

    Background Human hepatitis E virus (HEV) infections are considered an emerging disease in industrialized countries. In the Netherlands, Hepatitis E virus (HEV) infections have been associated with travel to high-endemic countries. Non-travel related HEV of genotype 3 has been diagnosed occasionally since 2000. A high homology of HEV from humans and pigs suggests zoonotic transmission but direct molecular and epidemiological links have yet to be established. We conducted a descriptive case series to generate hypotheses about possible risk factors for non-travel related HEV infections and to map the genetic diversity of HEV. Methods A case was defined as a person with HEV infection laboratory confirmed (positive HEV RT-PCR and/or HEV IgM) after 1 January 2004, without travel to a high-endemic country three months prior to onset of illness. For virus identification 148 bp of ORF2 was sequenced and compared with HEV from humans and pigs. We interviewed cases face to face using a structured questionnaire and collected information on clinical and medical history, food preferences, animal and water contact. Results We interviewed 19 cases; 17 were male, median age 50 years (25–84 y), 12 lived in the North-East of the Netherlands and 11 had preexisting disease. Most common symptoms were dark urine (n = 16) and icterus (n = 15). Sixteen ate pork ≥ once/week and six owned dogs. Two cases had received blood transfusions in the incubation period. Seventeen cases were viremic (genotype 3 HEV), two had identical HEV sequences but no identified relation. For one case, HEV with identical sequence was identified from serum and surface water nearby his home. Conclusion The results show that the modes of transmission of genotype-3 HEV infections in the Netherlands remains to be resolved and that host susceptibility may play an important role in development of disease. PMID:18462508

  8. Neurovirulence comparison of chikungunya virus isolates of the Asian and East/Central/South African genotypes from Malaysia.

    PubMed

    Chiam, Chun Wei; Chan, Yoke Fun; Ong, Kien Chai; Wong, Kum Thong; Sam, I-Ching

    2015-11-01

    Chikungunya virus (CHIKV), an alphavirus of the family Togaviridae, causes fever, polyarthritis and rash. There are three genotypes: West African, Asian and East/Central/South African (ECSA). The latter two genotypes have caused global outbreaks in recent years. Recent ECSA CHIKV outbreaks have been associated with severe neurological disease, but it is not known if different CHIKV genotypes are associated with different neurovirulence. In this study, the neurovirulence of Asian (MY/06/37348) and ECSA (MY/08/065) strains of CHIKV isolated in Malaysia were compared. Intracerebral inoculation of either virus into suckling mice was followed by virus titration, histopathology and gene expression analysis of the harvested brains. Both strains of CHIKV replicated similarly, yet mice infected with MY/06/37348 showed higher mortality. Histopathology findings showed that both CHIKV strains spread within the brain (where CHIKV antigen was localized to astrocytes and neurons) and beyond to skeletal muscle. In MY/06/37348-infected mice, apoptosis, which is associated with neurovirulence in alphaviruses, was observed earlier in brains. Comparison of gene expression showed that a pro-apoptotic gene (eIF2αK2) was upregulated at higher levels in MY/06/37348-infected mice, while genes involved in anti-apoptosis (BIRC3), antiviral responses and central nervous system protection (including CD40, IL-10RA, MyD88 and PYCARD) were upregulated more highly in MY/08/065-infected mice. In conclusion, the higher mortality observed following MY/06/37348 infection in mice is due not to higher viral replication in the brain, but to differentially expressed genes involved in host immune responses. These findings may help to identify therapeutic strategies and biomarkers for neurological CHIKV infections. PMID:26276497

  9. Ledipasvir-Sofosbuvir: A Once-Daily Oral Treatment Option for Chronic Hepatitis C Virus Genotype 1 Infection.

    PubMed

    Jensen, Christopher M; Holle, Lisa M

    2016-05-01

    Chronic hepatitis C virus (HCV) genotype 1 historically has been the most difficult to treat HCV genotype, and patients infected with this genotype had been previously treated with interferon-based therapy. In recent years, however, treatment options for chronic HCV infection have rapidly changed to an all-oral regimen. Ledipasvir-sofosbuvir is an oral fixed-dose (ledipasvir 90 mg-sofosbuvir 400 mg) combination of two direct-acting antiviral drugs. Four phase 3 clinical trials (ION-1-4) evaluated ledipasvir-sofosbuvir with and without ribavirin in patients with HCV genotype 1. High rates of sustained virologic response (SVR) occurred with ledipasvir-sofosbuvir alone in treatment-naïve and treatment-experienced patients without cirrhosis as well as in treatment-naïve patients with cirrhosis when administered for 12 weeks. In treatment-experienced patients with cirrhosis, 24 weeks of ledipasvir-sofosbuvir was also highly effective. Furthermore, treatment-naïve patients without cirrhosis (particularly those with HCV RNA serum concentrations < 6 million IU/ml) can achieve a similar SVR with only 8 weeks of therapy. Similarly, in patients coinfected with human immunodeficiency virus and HCV genotype 1 who were treated with ledipasvir-sofosbuvir for 12 weeks, a high SVR was observed in those with and without cirrhosis as well as treatment-naïve and treatment-experienced patients. Ledipasvir-sofosbuvir is well tolerated, with fatigue, headache, nausea, diarrhea, and insomnia being the most common adverse effects, which are typically mild to moderate in nature. This combination antiviral can be taken with or without food. Key factors to consider when prescribing ledipasvir-sofosbuvir are drug interactions including those mediated by the P-glycoprotein transporter and increased pH, cost of the drug or insurance coverage, comorbid conditions, and patient and provider preferences. Postmarketing experience and ongoing clinical trials will further define the safety and role

  10. Detection and genetic characterization of hepatitis E virus (HEV) genotype 3 subtype c in wild boars in Italy.

    PubMed

    Di Profio, Federica; Melegari, Irene; Sarchese, Vittorio; Robetto, Serena; Marruchella, Giuseppe; Bona, Maria Cristina; Orusa, Riccardo; Martella, Vito; Marsilio, Fulvio; Di Martino, Barbara

    2016-10-01

    Hepatitis E virus (HEV) was detected in stools collected from wild boars in Italy, with an overall prevalence of 1.5 % (3/196). The sequence of a ~3.0-kb portion at the 3' end of the genome of one such strain, HEV/WB/P6-15/ITA, was determined. In the full-length ORF2, which encodes the capsid protein, the virus was genetically closest to wild boar and human HEV strains currently classified as genotype 3 subtype c. Interestingly, the 3' end of ORF2 of the WB/P6-15/ITA matched the 340-nucleotide (nt) sequence (94.0 % nt identity) of the human strain PeGe, identified in 2015 from a patient with acute hepatitis E in Genoa, Italy, suggesting that similar HEV strains are circulating in the same geographical setting in humans and animals. PMID:27393602

  11. Hemoglobin Decrease with Iron Deficiency Induced by Daclatasvir plus Asunaprevir Combination Therapy for Chronic Hepatitis C Virus Genotype 1b

    PubMed Central

    Shigefuku, Ryuta; Hattori, Nobuhiro; Watanabe, Tsunamasa; Matsunaga, Kotaro; Hiraishi, Tetsuya; Tamura, Tomohiro; Noguchi, Yohei; Fukuda, Yasunobu; Ishii, Toshiya; Okuse, Chiaki; Sato, Akira; Suzuki, Michihiro; Itoh, Fumio

    2016-01-01

    Background Decreased hemoglobin (Hb) level has been supposed to be a relatively rare side effect of a combination therapy against hepatitis C virus that consists of the NS5A inhibitor daclatasvir (DCV) and the NS3/4A protease inhibitor asunaprevir (ASV). Methods The study was conducted in 75 patients with genotype 1b chronic hepatitis C virus infection who had started combination therapy with DCV and ASV at St. Marianna University School of Medicine Hospital between September 2014 and December 2014. Results Among the patients examined, decreased Hb level by ≥1.5 g/dL from the values at treatment initiation was observed in 11 individuals. This was accompanied by decreased mean corpuscular volume, and iron and ferritin levels. Conclusions These findings suggest that the mechanism of the phenomenon is caused by iron deficiency. The underlying mechanism and clinical impacts will need to be further examined. PMID:26990758

  12. Alteration in lymphocyte responses, cytokine and chemokine profiles in chickens infected with genotype VII and VIII velogenic Newcastle disease virus.

    PubMed

    Rasoli, Mehdi; Yeap, Swee Keong; Tan, Sheau Wei; Moeini, Hassan; Ideris, Aini; Bejo, Mohd Hair; Alitheen, Noorjahan Banu Mohamed; Kaiser, Pete; Omar, Abdul Rahman

    2014-01-01

    Newcastle disease (ND) is a highly contagious avian disease and one of the major causes of economic losses in the poultry industry. The emergence of virulent NDV genotypes and repeated outbreaks of NDV in vaccinated chickens have raised the need for fundamental studies on the virus-host interactions. In this study, the profiles of B and T lymphocytes and macrophages and differential expression of 26 immune-related genes in the spleen of specific-pathogen-free (SPF) chickens, infected with either the velogenic genotype VII NDV strain IBS002 or the genotype VIII NDV strain AF2240, were evaluated. A significant reduction in T lymphocyte population and an increase in the infiltration of IgM+ B cells and KUL01+ macrophages were detected in the infected spleens at 1, 3 and 4 days post-infection (dpi) (P<0.05). The gene expression profiles showed an up-regulation of CCLi3, CXCLi1, CXCLi2 (IL-8), IFN-γ, IL-12α, IL-18, IL-1β, IL-6, iNOS, TLR7, MHCI, IL-17F and TNFSF13B (P<0.05). However, these two genotypes showed different cytokine expression patterns and viral load. IBS002 showed higher viral load than AF2240 in spleen at 3 and 4dpi and caused a more rapid up-regulation of CXCLi2, IFN-γ, IL-12α, IL-18, IL-1β, iNOS and IL-10 at 3dpi. Meanwhile, the expression levels of CCLI3, CXCLi1, IFN-γ, IL-12α, IL-1β and iNOS genes were significantly higher in AF2240 at 4dpi. In addition, the expression levels of IL-10 were significantly higher in the IBS002-infected chickens at 3 and 4dpi. Hence, infection with velogenic genotype VII and VIII NDV induced different viral load and production of cytokines and chemokines associated with inflammatory reactions. PMID:24225159

  13. Interactive Effects of Immunoglobulin Gamma and Human Leucocyte Antigen Genotypes on Response to Interferon Based Therapy of Hepatitis C Virus

    PubMed Central

    Gomaa, Howayda E.; Mahmoud, Mohamed; Saad, Nevine E.; Hussein, Amal S.; Ismail, Somaia; Thabet, Eman H.; Farouk, Hebatallah; Kandil, Dina; Heiba, Ahmed; Hafez, Wael

    2015-01-01

    AIM: We examined the role that immunoglobulin GM 23 and KM allotypes—genetic markers of γ and κ chains, respectively—play in response to treatment of hepatitis C virus (HCV) infection in Egyptian patients. MATERIAL AND METHODS: A total of 120 persons who had responded to HCV treatment and 125 with persistent HCV infection were genotyped for the presence of GM23 and KM determinants. HLA –C genotyping was also done. RESULTS: Association of GM 23+ and KM3 was significantly associated with non response to treatment (P < 0.0001). Individuals who lacked this GM genotype (but were positive for KM1,2 and 3) were likely to respond to treatment (P=0.045). Association of heterozygous GM23 (+/-) with KM 1,2 and 3 or KM3 alone was significantly associated with SVR (P = 0.001) and (P = 0.0001) respectively. Particular combinations of HLA and GM genotypes were associated significantly with the response to HCV treatment. The combination of HLAC2C2 and GM23+ was associated with persistence of infection (P = 0.027) while the association of HLAC2C2 and heterozygous GM23+/- was associated with SVR (P = 0.001). The association of HLAC1C1 and heterozygous GM23+/- was significantly associated with SVR (P = 0.001) and also subjects with HLA C1/C2 and heterozygous GM23+/- were likely to respond to treatment (P = 0.003) while subjects with HLA C1/C2 and GM23+ show tendency to resist to treatment (P = 0.0001). CONCLUSION: Our results didn’t support a role for KM allotypes, GM23 allotype plays a role in the persistence of HCV infection in the presence or absence of KM1,3. Interaction between certain GM and HLA-C genotypes may favor adequate response to interferon based therapies.

  14. Evolution and mutations of hepatitis B virus quasispecies in genotype B and C during vertical transmission.

    PubMed

    Wu, Quanxin; Xu, Cheng; Li, Junnan; Li, Li; Yan, Guohua; Yue, Liangliang; Zeng, Yi; Huang, Hongfei; Deng, Guohong; Wang, Yuming

    2016-06-01

    Evolution patterns of HBV QS between genotype B and C during vertical transmission are not well understood. In this study, we enrolled 10 HBV infected mother-infant pairs (four pairs with genotype B, four pairs with genotype C, and two with co-infection) without anti-viral therapy. Serum HBV DNA of mothers and infants were sequenced, HBV QS complexity and diversity were analyzed, polymorphisms and mutation sites were recorded, and phylogenetic trees were performed. Our result showed that the QS complexities in P (amino acid), C/PreC (amino acid), and PreS1 (nucleotide) gene were significantly higher in mothers than in infants in pairs with genotype C (P < 0.05), however, full-length and other genes showed non-significant differences (P > 0.05). Unlike genotype C, QS complexity of P gene (nucleotide) was significantly higher in infants than in mothers (P < 0.05) in pairs with genotype B, similarly, QS complexities of full-length and other genes (except Pre S2) were also higher in infants than in mothers but without significant differences (P > 0.05). QS diversities of full-length and most genes in genotype B were comparable between mothers and their infants (P > 0.05), in pairs with genotype C, dS of P, X, RT genes, genetic distance of Pre S1 gene (amino acid) and dN of Pre S1 gene were significant higher in mothers than in infants (P < 0.05). Several HBV mutations correlated with immune escape, e antigen loss and drug resistance were observed in infants. The results indicated that differences of HBV QS evolution patterns between genotype B and C during vertical transmission might contribute to distinct prognosis. J. Med. Virol. 88:1018-1026, 2016. © 2015 Wiley Periodicals, Inc. PMID:26531675

  15. Using NS5B Sequencing for Hepatitis C Virus Genotyping Reveals Discordances with Commercial Platforms

    PubMed Central

    Chueca, Natalia; Rivadulla, Isidro; Lovatti, Rubén; Reina, Gabriel; Blanco, Ana; Fernandez-Caballero, Jose Angel; Cardeñoso, Laura; Rodriguez-Granjer, Javier; Fernandez-Alonso, Miriam; Aguilera, Antonio; Alvarez, Marta

    2016-01-01

    We aimed to evaluate the correct assignment of HCV genotypes by three commercial methods—Trugene HCV genotyping kit (Siemens), VERSANT HCV Genotype 2.0 assay (Siemens), and Real-Time HCV genotype II (Abbott)—compared to NS5B sequencing. We studied 327 clinical samples that carried representative HCV genotypes of the most frequent geno/subtypes in Spain. After commercial genotyping, the sequencing of a 367 bp fragment in the NS5B gene was used to assign genotypes. Major discrepancies were defined, e.g. differences in the assigned genotype by one of the three methods and NS5B sequencing, including misclassification of subtypes 1a and 1b. Minor discrepancies were considered when differences at subtype levels, other than 1a and 1b, were observed. The overall discordance with the reference method was 34% for Trugene and 15% for VERSANT HCV2.0. The Abbott assay correctly identified all 1a and 1b subtypes, but did not subtype all the 2, 3, 4 and 5 (34%) genotypes. Major discordances were found in 16% of cases for Trugene HCV, and the majority were 1b- to 1a-related discordances; major discordances were found for VERSANT HCV 2.0 in 6% of cases, which were all but one 1b to 1a cases. These results indicated that the Trugene assay especially, and to a lesser extent, Versant HCV 2.0, can fail to differentiate HCV subtypes 1a and 1b, and lead to critical errors in clinical practice for correctly using directly acting antiviral agents. PMID:27097040

  16. Using NS5B Sequencing for Hepatitis C Virus Genotyping Reveals Discordances with Commercial Platforms.

    PubMed

    Chueca, Natalia; Rivadulla, Isidro; Lovatti, Rubén; Reina, Gabriel; Blanco, Ana; Fernandez-Caballero, Jose Angel; Cardeñoso, Laura; Rodriguez-Granjer, Javier; Fernandez-Alonso, Miriam; Aguilera, Antonio; Alvarez, Marta; Galán, Juan Carlos; García, Federico

    2016-01-01

    We aimed to evaluate the correct assignment of HCV genotypes by three commercial methods-Trugene HCV genotyping kit (Siemens), VERSANT HCV Genotype 2.0 assay (Siemens), and Real-Time HCV genotype II (Abbott)-compared to NS5B sequencing. We studied 327 clinical samples that carried representative HCV genotypes of the most frequent geno/subtypes in Spain. After commercial genotyping, the sequencing of a 367 bp fragment in the NS5B gene was used to assign genotypes. Major discrepancies were defined, e.g. differences in the assigned genotype by one of the three methods and NS5B sequencing, including misclassification of subtypes 1a and 1b. Minor discrepancies were considered when differences at subtype levels, other than 1a and 1b, were observed. The overall discordance with the reference method was 34% for Trugene and 15% for VERSANT HCV2.0. The Abbott assay correctly identified all 1a and 1b subtypes, but did not subtype all the 2, 3, 4 and 5 (34%) genotypes. Major discordances were found in 16% of cases for Trugene HCV, and the majority were 1b- to 1a-related discordances; major discordances were found for VERSANT HCV 2.0 in 6% of cases, which were all but one 1b to 1a cases. These results indicated that the Trugene assay especially, and to a lesser extent, Versant HCV 2.0, can fail to differentiate HCV subtypes 1a and 1b, and lead to critical errors in clinical practice for correctly using directly acting antiviral agents. PMID:27097040

  17. Latent viral infections in young patients with inflammatory diseases treated with biological agents: prevalence of JC virus genotype 2.

    PubMed

    Comar, Manola; Delbue, Serena; Lepore, Loredana; Martelossi, Stefano; Radillo, Oriano; Ronfani, Luca; D'Agaro, Pierlanfranco; Ferrante, Pasquale

    2013-04-01

    Treatment with biological drugs is associated with increased susceptibility to viral infections. Reactivation of JC virus (JCV) and human cytomegalovirus (HCMV) in adults after therapy has been documented. The long-term effects of biological and conventional therapy on human herpesviruses and polyomaviruses infections in young patients were assessed. One hundred eighty-six samples [urine, serum, and blood cells (PBMCs)] from 62 patients (15.8 ± 6.2 years old) with Crohn's disease, ulcerative rectocolitis or juvenile rheumatoid arthritis treated with immunotherapy or conventional therapy for over 12 months were tested by real time PCR. One hundred twenty-four samples (urine and blood) from 62 matched healthy volunteers (13.8 ± 8.6 years old) were included as controls. Sequencing of the JCV viral protein 1 (VP1) and transcriptional control region (TCR) was performed. Herpes simplex virus 1/2 and varicella zoster virus genomes were not detected in any patients, whereas Epstein-Barr virus, HCMV, and human herpesvirus-6 genomes were detected in 4.8%, 3.2%, and 1.6% of the patients, respectively. JCV was detected in 22.6% (14/62) of urine samples from patients and in 8% (5/62) from controls, in 50% (7/14) of sera from patients shedding JCV, and in 71.4% (5/7) of matched PBMCs. There was a significant association between infliximab treatment and excretion of JCV genotype 2. Subclinical infection/reactivation of JCV genotype 2 in young patients during infliximab therapy was demonstrated. Conversely, increased susceptibility to herpesviruses infection was not shown. Future studies are warranted to investigate the effects of JCV reactivation on the health of young patients treated with infliximab. PMID:23364870

  18. A fast and low-cost genotyping method for hepatitis B virus based on pattern recognition in point-of-care settings

    PubMed Central

    Qiu, Xianbo; Song, Liuwei; Yang, Shuo; Guo, Meng; Yuan, Quan; Ge, Shengxiang; Min, Xiaoping; Xia, Ningshao

    2016-01-01

    A fast and low-cost method for HBV genotyping especially for genotypes A, B, C and D was developed and tested. A classifier was used to detect and analyze a one-step immunoassay lateral flow strip functionalized with genotype-specific monoclonal antibodies (mAbs) on multiple capture lines in the form of pattern recognition for point-of-care (POC) diagnostics. The fluorescent signals from the capture lines and the background of the strip were collected via multiple optical channels in parallel. A digital HBV genotyping model, whose inputs are the fluorescent signals and outputs are a group of genotype-specific digital binary codes (0/1), was developed based on the HBV genotyping strategy. Meanwhile, a companion decoding table was established to cover all possible pairing cases between the states of a group of genotype-specific digital binary codes and the HBV genotyping results. A logical analyzing module was constructed to process the detected signals in parallel without program control, and its outputs were used to drive a set of LED indicators, which determine the HBV genotype. Comparing to the nucleic acid analysis to HBV viruses, much faster HBV genotyping with significantly lower cost can be obtained with the developed method. PMID:27306485

  19. Characterization of a VHS virus genotype III isolated from rainbow trout (Oncorhychus mykiss) at a marine site on the west coast of Norway

    PubMed Central

    2010-01-01

    Background Norwegian production of rainbow trout (Oncorhynchus mykiss) has been without any outbreaks of VHS for many years until the disease emerged in a farm in western Norway in November 2007. The fish were, in addition to VHS virus, positive for gill chlamydia-like bacteria, Flavobacterium psychrophilum, and a microsporidian. A new VHS virus genotype III was isolated from the fish in RTgill-W1 cells and the complete coding region (11,065 nucleotides) was sequenced. This virus was also used in a challenge experiment to see if it could cause any mortality in rainbow trout in sea water. Results This is the first time a nearly complete sequence of a genotype III virus isolate has been presented. The organization of the genes is the same as in the other VHS virus genotypes studied (GI and GIV). Between the ORFs are nontranslated regions that contain highly conserved sequences encompassing the polyadenylation signal for one gene, and the putative transcription initiation site of the next gene. The intergenic regions vary in length from 74 nt to 128 nt. The nucleotide sequence is more similar to genotype I isolates compared to isolates from genotype II and IV. Analyses of the sequences of the N and G protein genes show that this new isolate is distinct from other VHS virus isolates and groups closely together with isolates from genotype III. In a challenge experiment, using intraperitoneal (ip) injection of the isolate, co-habitation with infected fish, and bath challenge, mortalities slightly above 40% were obtained. There was no significant difference in mortality between the bath challenged group and the ip injected group, while the mortality in the co-habitation group was as low as 30%. Conclusions All VHS virus isolates in genotype III are from marine fish in the North East Atlantic. Unlike the other known genotype III isolates, which are of low virulence, this new isolate is moderately virulent. It was not possible to detect any changes in the virus genome that

  20. Immune responses against hepatitis C virus genotype 3a virus-like particles in mice: A novel VLP prime-adenovirus boost strategy.

    PubMed

    Kumar, Anuj; Das, Soma; Mullick, Ranajoy; Lahiri, Priyanka; Tatineni, Ranjitha; Goswami, Debashree; Bhat, Prasanna; Torresi, Joseph; Gowans, Eric James; Karande, Anjali Anoop; Das, Saumitra

    2016-02-17

    Chronic hepatitis C virus (HCV) infection represents a major health threat to global population. In India, approximately 15-20% of cases of chronic liver diseases are caused by HCV infection. Although, new drug treatments hold great promise for HCV eradication in infected individuals, the treatments are highly expensive. A vaccine for preventing or treating HCV infection would be of great value, particularly in developing countries. Several preclinical trials of virus-like particle (VLP) based vaccine strategies are in progress throughout the world. Previously, using baculovirus based system, we have reported the production of hepatitis C virus-like particles (HCV-LPs) encoding structural proteins for genotype 3a, which is prevalent in India. In the present study, we have generated HCV-LPs using adenovirus based system and tried different immunization strategies by using combinations of both kinds of HCV-LPs with other genotype 3a-based immunogens. HCV-LPs and peptides based ELISAs were used to evaluate antibody responses generated by these combinations. Cell-mediated immune responses were measured by using T-cell proliferation assay and intracellular cytokine staining. We observed that administration of recombinant adenoviruses expressing HCV structural proteins as final booster enhances both antibody as well as T-cell responses. Additionally, reduction of binding of VLP and JFH1 virus to human hepatocellular carcinoma cells demonstrated the presence of neutralizing antibodies in immunized sera. Taken together, our results suggest that the combined regimen of VLP followed by recombinant adenovirus could more effectively inhibit HCV infection, endorsing the novel vaccine strategy. PMID:26700891

  1. Daclatasvir vs telaprevir plus peginterferon alfa/ribavirin for hepatitis C virus genotype 1

    PubMed Central

    Jacobson, Ira; Zeuzem, Stefan; Flisiak, Robert; Knysz, Brygida; Lueth, Stefan; Zarebska-Michaluk, Dorota; Janczewska, Ewa; Ferenci, Peter; Diago, Moises; Zignego, Anna Linda; Safadi, Rifaat; Baruch, Yaacov; Abdurakhmanov, Dzhamal; Shafran, Stephen; Thabut, Dominique; Bruck, Rafael; Gadano, Adrian; Thompson, Alexander James; Kopit, Justin; McPhee, Fiona; Michener, Tracy; Hughes, Eric A; Yin, Philip D; Noviello, Stephanie

    2016-01-01

    AIM: To evaluate daclatasvir vs telaprevir, each combined with peginterferon alfa-2a/ribavirin (pegIFN/RBV), in treatment-naive hepatitis C virus (HCV) genotype (GT) 1-infected patients. METHODS: In this phase 3, randomized, open-label, noninferiority study, 602 patients were randomly assigned (2:1) to daclatasvir vs telaprevir, stratified by IL28B rs12979860 host genotype (CC vs non-CC), cirrhosis status (compensated cirrhosis vs no cirrhosis), and HCV GT1 subtype (GT1a vs GT1b). Patients were selected by study inclusion criteria from a total of 793 enrolled patients. Patients received daclatasvir 60 mg once daily or telaprevir 750 mg 3 times daily plus pegIFN/RBV. Daclatasvir recipients received 24 wk of daclatasvir plus pegIFN/RBV; those without an extended rapid virologic response (eRVR; undetectable HCV-RNA at weeks 4 and 12) received an additional 24 wk of pegIFN/RBV. Telaprevir-treated patients received 12 wk of telaprevir plus pegIFN/RBV followed by 12 (with eRVR) or 36 (no eRVR) wk of pegIFN/RBV. The primary objective was to compare for noninferiority of sustained virologic response rates at posttreatment week 12 (SVR12) in GT1b-infected patients. Key secondary objectives were to demonstrate that the rates of anemia (hemoglobin < 10 g/dL) and rash-related events, through week 12, were lower with daclatasvir + pegIFN/RBV than with telaprevir + pegIFN/RBV among GT1b-infected patients. Resistance testing was performed using population-based sequencing of the NS5A region for all patients at baseline, and for patients with virologic failure or relapse and HCV-RNA ≥ 1000 IU/mL, to investigate any link between NS5A polymorphisms associated with daclatasvir resistance and virologic outcome. RESULTS: Patient demographics and disease characteristics were generally balanced across treatment arms; however, there was a higher proportion of black/African Americans in the daclatasvir groups (6.0% and 8.2% in the GT1b and GT1a groups, respectively) than in the

  2. Reverse restriction fragment length polymorphism (RRFLP): A novel technique for genotyping infectious laryngotracheitis virus (ILTV) live attenuated vaccines.

    PubMed

    Callison, Scott A; Riblet, Sylva M; Rodríguez-Avila, Andres; García, Maricarmen

    2009-09-01

    A novel technique, the reverse restriction fragment length polymorphism (RRFLP) assay, was developed as a means of detecting specific informative polymorphic sites in the infectious laryngotracheitis virus (ILTV) genome. During the RRFLP procedure, DNA is digested with restriction enzymes targeting an informative polymorphic site and then used as template in a real-time polymerase chain reaction (PCR) with primers flanking the informative region. The analysis of the DeltaC(t) values obtained from digested and undigested template DNA provides the genotype of the DNA. In this study, the RRFLP assay was applied as a method to differentiate between the two types of infectious laryngotracheitis virus attenuated live vaccines. Sequence analysis of ILTV vaccines revealed an informative polymorphic site in the 5'-non-coding region of the infected cell protein (ICP4) gene. Unique AvaI and AlwI restriction enzyme sites were identified in the tissue culture origin and chicken embryo origin attenuated vaccines, respectively. These two informative polymorphic sites were used in a RRFLP assay to genotype rapidly and reproducibly ILTV attenuated live vaccines. PMID:19433109

  3. Interferon Lambda 4 Genotype Is Associated With Jaundice and Elevated Aminotransferase Levels During Acute Hepatitis C Virus Infection: Findings From the InC3 Collaborative

    PubMed Central

    Page, Kimberly; Mirzazadeh, Ali; Rice, Thomas M.; Grebely, Jason; Kim, Arthur Y.; Cox, Andrea L.; Morris, Meghan D.; Hellard, Margaret; Bruneau, Julie; Shoukry, Naglaa H.; Dore, Gregory J.; Maher, Lisa; Lloyd, Andrew R.; Lauer, Georg; Prins, Maria; McGovern, Barbara H.

    2016-01-01

    Symptomatic acute HCV infection and interferon lambda 4 (IFNL4) genotypes are important predictors of spontaneous viral clearance. Using data from a multicohort database (Injecting Cohorts [InC3] Collaborative), we establish an independent association between host IFNL4 genotype and symptoms of acute hepatitis C virus infection. This association potentially explains the higher spontaneous clearance observed in some patients with symptomatic disease. PMID:26973850

  4. Genotypes of Canine Distemper Virus Determined by Analysis of the Hemagglutinin Genes of Recent Isolates from Dogs in Japan

    PubMed Central

    Mochizuki, Masami; Hashimoto, Michiru; Hagiwara, Shigeyuki; Yoshida, Yoshio; Ishiguro, Shinryo

    1999-01-01

    Canine distemper of domestic dogs is caused by canine distemper virus (CDV), a member of the morbilliviruses. It has been a highly contagious disease of great veterinary importance for centuries, but for the last several decades it has been controlled satisfactorily by modified live vaccines. In the 1990s, however, it was described that CDV strains genetically different from vaccine strains may have caused the disease in vaccinated dogs. The highest antigenic variation is found in the H protein. Therefore, in the present study, hemagglutinin (H) genes obtained from current vaccines and field isolates and amplified directly from clinical specimens were genetically analyzed by restriction fragment length polymorphism assay and sequencing. Phylogenetic analysis of the H-gene amino acid sequences revealed that at least two CDV genotypes are circulating among dogs in Japan; one is a genotype to which almost all Japanese CDV isolates belong and the other has not been previously described. Both are separate and independent from the other lineages or genotypes of vaccine strains, as well as European and U.S. CDV isolates. The results suggest that CDV has also evolved in Japan, and further studies will be needed for an evaluation and possible improvement of the efficacies of current CDV vaccines. PMID:10449479

  5. A Linear Surface Epitope in a Proline-Rich Region of ORF3 Product of Genotype 1 Hepatitis E Virus.

    PubMed

    Yang, Yonglin; Lin, Shaoli; Nan, Yuchen; Ma, Zexu; Yang, Liping; Zhang, Yanjin

    2016-01-01

    Hepatitis E virus (HEV) is one of the viral pathogens causing hepatitis in humans. HEV open reading frame 3 (ORF3) encodes a small multifunctional protein (VP13), which is essential for HEV infection. In this study, a linear epitope was identified in a polyproline (PXXP) motif from VP13 of genotype 1 HEV by using a monoclonal antibody. The epitope was detected in enzyme-linked immunosorbent assay (ELISA), immunoblotting and immunofluorescence assays. Epitope mapping showed that the epitope locates in a proline-rich region containing a PXXP motif in amino acid residues 66-75 of VP13. The epitope was also detected in HEV-infected liver cells and reacted with genotype 1-specific antibodies in an HEV-positive human serum sample. The results demonstrated that the epitope in the PXXP motif of the genotype 1 VP13 is linear and surface-oriented, which should facilitate in-depth studies on the viral protein and HEV biology. PMID:27548202

  6. Hepatitis C virus genotype 3: Meta-analysis on sustained virologic response rates with currently available treatment options

    PubMed Central

    Ampuero, Javier; Reddy, K Rajender; Romero-Gomez, Manuel

    2016-01-01

    AIM: To address the therapeutic efficacy of various treatment regimens in genotype 3 selecting randomized clinical trials and prospective National Cohort Studies. METHODS: (1) PEG-INF-based therapy including sofosbuvir (SOF) + RBV for 12 wk vs SOF + RBV 24 wk; (2) SOF + RBV therapy 12 wk/16 wk vs 24 wk; and (3) the role of RBV in SOF + daclatasvir (DCV) and SOF + ledipasvir (LDV) combinations. This meta-analysis provides robust information with the intention of addressing treatment strategy for hepatitis C virus genotype 3. RESULTS: A combination treatment including SOF + RBV + PEG-IFN for 12 wk notes better SVR than with only SOF + RBV for 12 wk, although its association with more frequent adverse effects may be a limiting factor. Longer duration therapy with SOF + RBV (24 wk) has achieved higher SVR rates than shorter durations (12 or 16 wk). SOF + LDV are not an ideal treatment for genotype 3. CONCLUSION: Lastly, SOF + DCV combination is probably the best oral therapy option and the addition of RBV does not appear to be needed to increase SVR rates substantially. PMID:27298572

  7. A Linear Surface Epitope in a Proline-Rich Region of ORF3 Product of Genotype 1 Hepatitis E Virus

    PubMed Central

    Yang, Yonglin; Lin, Shaoli; Nan, Yuchen; Ma, Zexu; Yang, Liping; Zhang, Yanjin

    2016-01-01

    Hepatitis E virus (HEV) is one of the viral pathogens causing hepatitis in humans. HEV open reading frame 3 (ORF3) encodes a small multifunctional protein (VP13), which is essential for HEV infection. In this study, a linear epitope was identified in a polyproline (PXXP) motif from VP13 of genotype 1 HEV by using a monoclonal antibody. The epitope was detected in enzyme-linked immunosorbent assay (ELISA), immunoblotting and immunofluorescence assays. Epitope mapping showed that the epitope locates in a proline-rich region containing a PXXP motif in amino acid residues 66-75 of VP13. The epitope was also detected in HEV-infected liver cells and reacted with genotype 1-specific antibodies in an HEV-positive human serum sample. The results demonstrated that the epitope in the PXXP motif of the genotype 1 VP13 is linear and surface-oriented, which should facilitate in-depth studies on the viral protein and HEV biology. PMID:27548202

  8. Novel approach to differentiate subclades of varicella-zoster virus genotypes E1 and E2 in Germany.

    PubMed

    Schmidt-Chanasit, Jonas; Olschläger, Stephan; Bialonski, Alexandra; Heinemann, Patrick; Bleymehl, Karoline; Gross, Gerd; Günther, Stephan; Ulrich, Rainer G; Doerr, Hans Wilhelm

    2009-11-01

    Varicella-zoster virus (VZV) is the causative agent of chicken pox (varicella) in children and reactivation of VZV in elderly or immunocompromised persons can cause shingles (zoster). A subclade differentiation of the most prevalent VZV genotypes E1 and E2 in Germany was not possible with the current genotyping methods in use, but is highly important to understand the VZV molecular evolution in more detail and especially to follow up the routes of infection. Therefore the objective of this study was to develop a simple PCR-based method for differentiation of E1 and E2 subclades. Viral DNA was isolated from vesicle fluid samples of six selected German zoster patients and used to amplify nine complete open reading frames (ORFs) of the VZV genome by different PCR assays. Phylogenetic analysis was performed by a Bayesian approach. Based on the analysis of a total of nine ORFs, a 7482 bp stretch consisting of ORFs 5, 37 and 62 contained informative sites for identification of novel subclades E1a, E2a and E2b for VZV genotypes E1 and E2. Specific single nucleotide polymorphisms (SNPs) were demonstrated for subclades E2a and E2b within the ORFs 5, 37 and 62, whereas a subclade E1a-specific SNP was found in ORF 56. The classification of E1 and E2 subclades may facilitate a more exact and in-depth monitoring of the molecular evolution of VZV in Germany in the future. PMID:19712712

  9. Frequency and genotypic distribution of GB virus C (GBV-C) among Colombian population with Hepatitis B (HBV) or Hepatitis C (HCV) infection

    PubMed Central

    2011-01-01

    Background GB virus C (GBV-C) is an enveloped positive-sense ssRNA virus belonging to the Flaviviridae family. Studies on the genetic variability of the GBV-C reveals the existence of six genotypes: genotype 1 predominates in West Africa, genotype 2 in Europe and America, genotype 3 in Asia, genotype 4 in Southwest Asia, genotype 5 in South Africa and genotype 6 in Indonesia. The aim of this study was to determine the frequency and genotypic distribution of GBV-C in the Colombian population. Methods Two groups were analyzed: i) 408 Colombian blood donors infected with HCV (n = 250) and HBV (n = 158) from Bogotá and ii) 99 indigenous people with HBV infection from Leticia, Amazonas. A fragment of 344 bp from the 5' untranslated region (5' UTR) was amplified by nested RT PCR. Viral sequences were genotyped by phylogenetic analysis using reference sequences from each genotype obtained from GenBank (n = 160). Bayesian phylogenetic analyses were conducted using Markov chain Monte Carlo (MCMC) approach to obtain the MCC tree using BEAST v.1.5.3. Results Among blood donors, from 158 HBsAg positive samples, eight 5.06% (n = 8) were positive for GBV-C and from 250 anti-HCV positive samples, 3.2%(n = 8) were positive for GBV-C. Also, 7.7% (n = 7) GBV-C positive samples were found among indigenous people from Leticia. A phylogenetic analysis revealed the presence of the following GBV-C genotypes among blood donors: 2a (41.6%), 1 (33.3%), 3 (16.6%) and 2b (8.3%). All genotype 1 sequences were found in co-infection with HBV and 4/5 sequences genotype 2a were found in co-infection with HCV. All sequences from indigenous people from Leticia were classified as genotype 3. The presence of GBV-C infection was not correlated with the sex (p = 0.43), age (p = 0.38) or origin (p = 0.17). Conclusions It was found a high frequency of GBV-C genotype 1 and 2 in blood donors. The presence of genotype 3 in indigenous population was previously reported from Santa Marta region in Colombia and

  10. Molecular evolution of the hypervariable region of the attachment glycoprotein gene in human respiratory syncytial virus subgroup B genotypes BA9 and BA10.

    PubMed

    Nagasawa, Koo; Hirano, Eiko; Kobayashi, Miho; Ryo, Akihide; Oishi, Kazunori; Obuchi, Masatsugu; Ishiwada, Naruhiko; Noda, Masahiro; Kuroda, Makoto; Shimojo, Naoki; Kimura, Hirokazu

    2015-12-01

    We studied the molecular evolution of the C-terminal 3rd hypervariable region in the attachment glycoprotein gene of human respiratory syncytial virus subgroup B (HRSV-B) genotypes BA9 and BA10. We performed time-scaled phylogenetic analyses using Bayesian Markov chain Monte Carlo methods. We also performed a genetic distance analysis (p-distance analysis), positive and negative selection analyses, and a Bayesian skyline plot (BSP) analysis. We found that genotype BA9 diverged from the common ancestor of genotypes BA7, BA8, and BA10, while genotype BA10 diverged from the ancestor of genotypes BA7 and BA8. Strains of both genotypes were distributed worldwide. BA9 and BA10 diverged between 1999 and 2001. Both BA9 and BA10 evolved rapidly (about 4.8×10(-3)substitutions/site/year) and formed three distinct lineages in a 10-year period. BA10 strains belonging to lineage 3 had large genetic distances (p-distance>0.07). Thus, it may be possible to classify these strains as a new genotype, BA11. No positive selection site was detected in either genotype. Phylodynamic analyses showed that the effective population size of BA10 decreased gradually since 2010 and BA9 slightly decreased since 2009. The results suggested that the recently prevalent HRSV-B genotypes BA9 and BA10 evolved uniquely, leading to epidemics of HRSV-B worldwide over a 15-year period. PMID:26408340

  11. Epidemiology of respiratory syncytial virus in children in Cyprus during three consecutive winter seasons (2010-2013): age distribution, seasonality and association between prevalent genotypes and disease severity.

    PubMed

    Panayiotou, C; Richter, J; Koliou, M; Kalogirou, N; Georgiou, E; Christodoulou, C

    2014-11-01

    This study reports the epidemiology of respiratory syncytial virus (RSV) in hospitalized children in Cyprus over three successive seasons (2010-2013) and the association between prevalent genotypes and disease severity. RSV infections had a circulation pattern from December to March. Most RSV-positive children (83%) were aged <2 years. Genotyping of RSV isolates showed that during the first winter season of the study (2010-2011), the only RSV genotype circulating was GA2 (RSV-A), followed by genotype BA (RSV-B) in the next winter season with only few sporadic cases of GA2. During the last winter season of the study (2012-2013) the newly emerged RSV genotype ON1 (RSV-A) was virtually the only circulating genotype. Children infected with genotype ON1 suffered a significantly milder illness compared to infections with genotypes GA2 and BA with a higher percentage of BA-infected children requiring oxygen. Our findings are in contrast to the majority of published reports that suggest RSV-A causes more severe illness than RSV-B. Therefore, further investigation of the association between RSV genotypes and disease severity is required, as it might affect treatment strategies in the future. PMID:24476750

  12. Genotype patterns of contemporary reassorted H3N2 virus in U.S. swine

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To understand the evolution of H3N2v influenza viruses that have infected 288 humans since July 2011, we performed the largest phylogenetic analysis at a whole genome scale of influenza viruses from North American swine to date (n = 200). At least ten distinct reassorted H3N2/pandemic H1N1 (rH3N2p)...

  13. Field Performance of Cowpea Genotypes Grown under Virus Pressure in Puerto Rico

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cowpea [Vigna unguiculata (L.) Walp.] is an important grain legume in many regions of the tropics. However, viral diseases, particularly Cucumber mosaic virus (CMV) and Blackeye cowpea mosaic virus (BlCMV), can be a limiting factor in cowpea production. We evaluated in replicated field plots and un...

  14. Characterization of a novel citrus tristeza virus genotype within three cross-protecting source GFMS12 sub-isolates in South Africa by means of Illumina sequencing.

    PubMed

    Zablocki, Olivier; Pietersen, Gerhard

    2014-08-01

    Tristeza disease (caused by citrus tristeza virus, CTV) is currently controlled in South Africa by means of cross-protection. In this study, we characterized the CTV populations of three grapefruit mild strain 12 (GFMS12) single-aphid-transmission-derived sub-isolates at the whole-genome level using Illumina sequencing technology. A novel South African isolate (CT-ZA3, of the T68 genotype) was shown to be the dominant genotype in all GFMS12 sub-isolates tested, along with reads unique to various other genotypes occurring as minor components. Uncertainty remains as to the significance of these minor components. PMID:24623089

  15. Isolation of Multiple TT Virus Genotypes from Spleen Biopsy Tissue from a Hodgkin's Disease Patient: Genome Reorganization and Diversity in the Hypervariable Region

    PubMed Central

    Jelcic, Ilijas; Hotz-Wagenblatt, Agnes; Hunziker, Andreas; zur Hausen, Harald; de Villiers, Ethel-Michele

    2004-01-01

    We report the isolation of 24 novel genotypes of TT viruses from a surgically removed spleen of a patient with Hodgkin's disease. The sequence analysis of our 24 isolates revealed the remarkable heterogeneity of TT virus isolates not only from the same patient but also from the same biopsy material. These isolates belong to four phylogenetic groups of TT viruses. Nucleotide sequence analyses revealed five distinct genotypes (tth3, tth4, tth5, tth6, and tth7). The limited variation in sequence identity of the other isolates defines the latter as variants of four of these genotypes. A group of 6 isolates (the tth7 group) revealed a reorganization of open reading frame 1 (ORF1) leading to one larger and a varying number of smaller ORFs. The nucleotide difference of the full-length genomes was less than 1%. A variation of 69 to 97% in amino acids of a second group of 8 isolates (the tth3 group) was restricted to the hypervariable region of ORF1, indicating the existence of a quasi-species. These isolates differed by less than 2% in the remainder of their nucleotide sequences. An alignment of these isolates with 79 previously reported TT virus genotypes permits the proposal of TT virus genera and species within the family Anelloviridae in analogy to a previous proposal for the papillomaviruses (family Papillomaviridae). PMID:15220423

  16. Correlation of phylogenetic clade diversification and in vitro infectivity differences among Cosmopolitan genotype strains of Chikungunya virus.

    PubMed

    Abraham, Rachy; Manakkadan, Anoop; Mudaliar, Prashant; Joseph, Iype; Sivakumar, Krishnankutty Chandrika; Nair, Radhakrishnan Reghunathan; Sreekumar, Easwaran

    2016-01-01

    Cosmopolitan genotypes of Chikungunya virus caused the large-scale febrile disease outbreaks in the last decade in Asian and African continents. Molecular analyses of these strains had revealed significant genetic diversification and occurrence of novel mosquito-adaptive mutations. In the present study we looked into whether the genetic diversification has implications in the infectivity phenotype. A detailed sequence and phylogenetic analyses of these virus strains of Indian Ocean lineage from Kerala, South India from the years 2008 to 2013 identified three distinct genetic clades (I, II and III), which had presence of clade-specific amino acid changes. The E2 envelope protein of the strains from the years 2012 to 2013 had a K252Q or a novel K252H change. This site is reported to affect mosquito cell infectivity. Most of these strains also had the E2 G82R mutation, a mutation previously identified to increase mammalian cell infectivity, and a novel mutation E2 N72S. Positive selection was identified in four sites in the envelope proteins (E1 K211E, A226V and V291I; E2 K252Q/H). In infectivity analysis, we found that strains from clade III had enhanced cytopathogenicity in HEK293 and Vero cells than by strains representing other two clades. These two strains formed smaller sized plaques and had distinctly higher viral protein expression, infectious virus production and apoptosis induction in HEK293 cells. They had novel mutations R171Q in the nsP1; I539S in nsP2; N409T in nsP3; and N72S in E2. Our study identifies a correlation between phylogenetic clade diversification and differences in mammalian cell infectivity phenotype among Cosmopolitan genotype CHIKV strains. PMID:26611825

  17. Profile of paritaprevir/ritonavir/ombitasvir plus dasabuvir in the treatment of chronic hepatitis C virus genotype 1 infection

    PubMed Central

    Smith, Michael A; Lim, Alice

    2015-01-01

    Over the last several years, many advances have been made in the treatment of chronic hepatitis C virus (HCV) infection with the development of direct-acting antivirals. Paritaprevir/ritonavir/ombitasvir with dasabuvir (PrOD) is a novel combination of a nonstructural (NS) 3/4A protein inhibitor boosted by ritonavir, an NS5A protein inhibitor, and an NS5B nonnucleoside polymerase inhibitor. This review aims to discuss the pharmacology, efficacy, safety, drug interactions, and viral drug resistance of PrOD in the treatment of HCV genotype 1 infections. Phase I, II, and III human and animal studies that describe the pharmacology, pharmacokinetics, efficacy, and safety of PrOD for HCV were identified and included. Studies that evaluated patients without cirrhosis (n=2,249) and with cirrhosis (n=422) demonstrated that PrOD for 12 or 24 weeks was effective at achieving sustained virologic response rates (>90%) in patients with genotype 1a or 1b HCV infection. Although indicated for the treatment of HCV genotype 1 infection, PrOD is also recommended for the treatment of HCV in patients coinfected with HIV. Additionally, promising data exist for the use of PrOD in liver-transplant recipients. The most common adverse drug events associated with PrOD included nausea, pruritus, insomnia, diarrhea, asthenia, dry skin, vomiting, and anemia. The high efficacy rates seen coupled with a favorable side effect profile seen with PrOD with or without ribavirin have led to its addition as a recommended treatment regimen for HCV genotype 1 infection. PMID:26622169

  18. Profile of paritaprevir/ritonavir/ombitasvir plus dasabuvir in the treatment of chronic hepatitis C virus genotype 1 infection.

    PubMed

    Smith, Michael A; Lim, Alice

    2015-01-01

    Over the last several years, many advances have been made in the treatment of chronic hepatitis C virus (HCV) infection with the development of direct-acting antivirals. Paritaprevir/ritonavir/ombitasvir with dasabuvir (PrOD) is a novel combination of a nonstructural (NS) 3/4A protein inhibitor boosted by ritonavir, an NS5A protein inhibitor, and an NS5B nonnucleoside polymerase inhibitor. This review aims to discuss the pharmacology, efficacy, safety, drug interactions, and viral drug resistance of PrOD in the treatment of HCV genotype 1 infections. Phase I, II, and III human and animal studies that describe the pharmacology, pharmacokinetics, efficacy, and safety of PrOD for HCV were identified and included. Studies that evaluated patients without cirrhosis (n=2,249) and with cirrhosis (n=422) demonstrated that PrOD for 12 or 24 weeks was effective at achieving sustained virologic response rates (>90%) in patients with genotype 1a or 1b HCV infection. Although indicated for the treatment of HCV genotype 1 infection, PrOD is also recommended for the treatment of HCV in patients coinfected with HIV. Additionally, promising data exist for the use of PrOD in liver-transplant recipients. The most common adverse drug events associated with PrOD included nausea, pruritus, insomnia, diarrhea, asthenia, dry skin, vomiting, and anemia. The high efficacy rates seen coupled with a favorable side effect profile seen with PrOD with or without ribavirin have led to its addition as a recommended treatment regimen for HCV genotype 1 infection. PMID:26622169

  19. Alcohol consumption among patients with hepatitis B infection in northern Portugal considering gender and hepatitis B virus genotype differences.

    PubMed

    Mota, Ana; Guedes, Fátima; Areias, Jorge; Pinho, Luciana; Cardoso, Margarida Fonseca

    2010-03-01

    Alcohol abuse is an important public health problem. In Portugal with a population of 10 millions of inhabitants, there are around 10% of alcoholics or excessive alcohol drinkers and 1% of chronically infected patients with hepatitis B virus (HBV). To examine the characteristics of patients with higher levels of alcohol consumption and to investigate the association between alcohol consumption and liver damage a total of 298 chronically infected individuals, with HBV genotyped and submitted to liver biopsy, were classified with Child's grading and separated by habits of alcohol intake, less and greater than 20g/day. No significant differences were observed about genotype but genotypes A and D were predominant in both of them. A higher percentage of males (P<.001) were observed in the group with alcohol intake above 20g/day, as well a lower proportion of patients with HBeAg negativity (P< or =.035). In this group, biochemistry parameters, such as alanine aminotransferase (P=.006), aspartate aminotransferase (P=.001), gamma-glutamyl transferase (P<.001) were elevated in a significantly higher proportion than in the other group. The analysis of hematological parameters showed significantly lower values of platelets (P=.042) and mean corpuscular volume (P<.001) and significantly higher values of prothrombin time (P<.001) in the group with higher levels of alcohol consumption. The characteristics of biopsy (P<.001) and Child-Phug's classification (P=.002) revealed more severe results in this group. Logistic regression showed a positive association between liver damage and alcohol intake, increasing with age. In female patients, a strong positive association between alcohol intake and liver damage was also found (odds ratio: 9.379; 95% confidence interval: 0.859-468.422; P = .037); however, the most severe cases were only observed in women older than 45 years. In patients with HBV infection, alcohol is associated with a more severe liver disease. No evidence was found

  20. Identification and retrospective validation of T-cell epitopes in the hepatitis C virus genotype 4 proteome

    PubMed Central

    Abdel-Hady, Karim M; Gutierrez, Andres H; Terry, Frances; Desrosiers, Joe; De Groot, Anne S; Azzazy, Hassan ME

    2014-01-01

    With over 150 million people chronically infected worldwide and millions more infected annually, hepatitis C continues to pose a burden on the global healthcare system. The standard therapy of hepatitis C remains expensive, with severe associated side effects and inconsistent cure rates. Vaccine development against the hepatitis C virus has been hampered by practical and biological challenges posed by viral evasion mechanisms. Despite these challenges, HCV vaccine research has presented a number of candidate vaccines that progressed to phase II trials. However, those efforts focused mainly on HCV genotypes 1 and 2 as vaccine targets and barely enough attention was given to genotype 4, the variant most prevalent in the Middle East and central Africa. We describe herein the in silico identification of highly conserved and immunogenic T-cell epitopes from the HCV genotype 4 proteome, using the iVAX immunoinformatics toolkit, as targets for an epitope-driven vaccine. We also describe a fast and inexpensive approach for results validation using the empirical data on the Immune Epitope Database (IEDB) as a reference. Our analysis identified 90 HLA class I epitopes of which 20 were found to be novel and 19 more had their binding predictions retrospectively validated; empirical data for the remaining 51 epitopes was insufficient to validate their binding predictions. Our analysis also identified 14 HLA class II epitopes, of which 8 had most of their binding predictions validated. Further investigation is required regarding the efficacy of the identified epitopes as vaccine targets in populations where HCV genotype 4 is most prevalent. PMID:25424944

  1. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes

    PubMed Central

    Fontaine, Albin; Ar Gouilh, Meriadeg; Moltini-Conclois, Isabelle

    2016-01-01

    Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution. PMID:27304978

  2. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes.

    PubMed

    Lequime, Sebastian; Fontaine, Albin; Ar Gouilh, Meriadeg; Moltini-Conclois, Isabelle; Lambrechts, Louis

    2016-06-01

    Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution. PMID:27304978

  3. Correlation between histologic staging, hepatitis C virus genotypes and clinical features in HCV chronic hepatitis: evidence of a new pattern.

    PubMed

    Di Tommaso, L; Macchia, S; Morandi, L; Leoncini, S; Pession, A; Dal Monte, P R; Foschini, M P

    2003-07-01

    Genome heterogeneity may be related to the wide variability of clinical and pathological features in hepatitis C virus (HCV)-related chronic liver disease. This paper addresses the possible association between HCV subtypes and clinical and histological features of chronically infected patients. Sixty-eight consecutive liver biopsies of chronic hepatitis constituted the basis of the study. HCV genotyping was performed on frozen tissue. Grading of necroinflammatory activity and staging of fibrosis were histologically assessed. Serologic HCV-RNA and liver function were assessed at the same time. All information was compared with clinical data including age, sex, HCV serology, and probable data and route of infection. Two cases were excluded as inadequate tissue was available. Five cases were negative to HCV-RNA in both serum and tissue. In 61 cases HCV RNA was present at the same time in serum and liver tissue. Forty-four patients were men (72%) and 17 (28%) were women. Two peaks of age were observed: 1 in the 4th decade of life, the 2nd in the 7th. The 2 groups had different HCV genotypes. Patients with genotypes 1b (mean age 50.7 years), 2c (mean age 61.3 years), and a subgroup of coinfections (mean age 60 years) were older than patients with genotypes 1a (mean age 35.5 years), 3 (mean age 36 years), and a subgroup of coinfections (mean age 33 years). Patients with genotypes 1b, 2, or 2c and a subgroup of coinfections more frequently had a history of blood transfusion and or surgical intervention dating up to 49 years previously. Patients with HCV 1a, 3, and a subgroup of coinfections frequently admitted a period of intravenous drug abuse. Patients with advanced liver disease, i.e., severe fibrosis and cirrhosis, showed the same 2 peaks of incidence: in the 4th and 7th decades of life, the first group mainly comprising patients with HCV types 1a and 3, the second, patients with HCV types 1b and 2c. Both these groups shared a clinical history of a long

  4. [Distribution of hepatitis C virus genotypes among patients with chronic hepatitis C infection in Akdeniz University Hospital, Antalya, Turkey: a five-year evaluation].

    PubMed

    Sağlik, İmran; Mutlu, Derya; Öngut, Gözde; İnan, Dilara; Öğünç, Dilara; Can Sarinoğlu, Rabia; Özhak Baysan, Betil; Gültekin, Meral; Çolak, Dilek

    2014-07-01

    Hepatitis C virus (HCV) is one of the major causes of chronic hepatitis. It is important to know the genotypes of HCV in the decision of the HCV related chronic hepatitis therapy. The aim of this study was to evaluate the HCV genotypes determined at the Microbiology Laboratory of Akdeniz University Hospital, and to evaluate the changes in the distribution of the genotypes within the last five years. A total of 422 blood samples from HCV-RNA positive chronic hepatitis C patients (219 male, 203 female; age range: 8-79 yrs, mean age 46.3 ± 15.5 yrs) which were sent to our laboratory for genotyping between 2009-2013 period, were analyzed retrospectively. HCV-RNA extractions were performed in an automated system (EZ1 Virus Mini Kit v2.0, Qiagen, Germany), and a commercial reverse hybridization line probe-based assay (LIPA; GEN-C RT-PCR, Italy) was carried out for genotyping, For viral load determinations, a real-time PCR method (Cobas TaqMan HCV, Roche Diagnostics, Germany) was used. Demographic data of the patients were obtained from the hospital information systems and electronic patients' files. Out of the 422 patients, genotype 1b was detected in 63.3% (n= 267), genotype 1a in 14.7% (n= 62), genotype 3a in 11.1% (n= 47), genotype 2b in 0.9% (n= 4), genotype 4e in 0.2% (n= 1). The subtypes couldn't be determined for 5.4% (n= 23), 2.6% (n= 11) and 1.4% (n= 6) of the patients infected with genotype 1, 2 and 4, respectively. One (0.2%) patient, was coinfected with genotype 1 and 4. Of the patients, 40 were foreign-born (16 cases from Russia; 4 of each from Ukraine and Georgia; 3 of each from Turkmenistan, Kyrgyzstan, and Germany; one of each from Tajikistan, Azerbaijan, Uzbekistan, Chechnya, Moldova, Switzerland and Romania) and among these patients genotype 3a (19/40; 47.5%) was the most common genotype followed by genotype 1b (17/40; 42.5%). Median values of HCV viral load were 668.500 IU/ml (range: 2.000-9.630.000) in the whole group; while it was 732.000 IU

  5. Prevalence of HPV High-Risk Genotypes in Three Cohorts of Women in Ouagadougou (Burkina Faso)

    PubMed Central

    Zohoncon, Theodora M.; Bisseye, Cyrille; Djigma, Florencia W.; Yonli, Albert T.; Compaore, Tegwinde R.; Sagna, Tani; Ouermi, Djeneba; Ouédraogo, Charlemagne M.R.; Pietra, Virginio; Nikiéma, Jean-Baptiste; Akpona, Simon A.; Simpore, Jacques

    2013-01-01

    The development of cervical cancer is associated with high-risk Human papilloma viruses (HPV-HR). In sub-Saharan Africa cervical cancer is the most common cancer among women and the leading cause of death attributed to malignant tumors. This study aims to identify HPV genotypes within the 30′S and 50′S HPV families found in two previous studies from our laboratory, and to determine the prevalence of twelve HPV-HR genotypes in a population of women in Ouagadougou. The twelve HPV-HR genotypes were determined by real-time multiplex PCR, in 180 samples from the general population and among a group of HIV-1 infected women. The most common genotypes found were HPV-35 (29.4%) and HPV-31 (26.1%) of the 30′S family, and HPV-52 (29.4%) and HPV-58 (20.6%) of the 50′S family. Multiple infections of HPV-HR were observed in 78.03% of infected women. The frequencies of HPV genotypes from the 30′S and 50′S families were higher, while the genotypes HPV-16 and18 were lower among the women in our study. PMID:24106609

  6. Induction of skin papillomas in the rabbit, Oryctologus cuniculus, by bites of a blood-sucking insect, Cimex lectularius, irradiated by gamma rays

    SciTech Connect

    el-Mofty, M.M.; Sakr, S.A.; Younis, M.W. )

    1989-11-01

    Bed bugs, Cimex lectularius, irradiated with gamma rays were allowed to suck blood from shaved areas of the skin of rabbits, Oryctolagus cuniculus, 2 times/week for 5 months and then once weekly for another 5 months. This significantly induced the formation of skin papillomas and sweat gland hyperplasia in five out of nine experimental animals. It is speculated that the saliva of the irradiated bugs was activated by gamma rays and was responsible for the induction of skin papillomas. Because bed bugs play a significant role in the transmission of virus, it is also speculated that there is a virus in the saliva of bugs; this virus may be activated by gamma radiation and causes the development of papillomas in the skin.

  7. Induction of skin papillomas in the rabbit, Oryctologus cuniculus, by bites of a blood-sucking insect, Cimex lectularius, irradiated by gamma rays.

    PubMed

    el-Mofty, M M; Sakr, S A; Younis, M W

    1989-11-01

    Bed bugs, Cimex lectularius, irradiated with gamma rays were allowed to suck blood from shaved areas of the skin of rabbits, Oryctolagus cuniculus, 2 times/week for 5 months and then once weekly for another 5 months. This significantly induced the formation of skin papillomas and sweat gland hyperplasia in five out of nine experimental animals. It is speculated that the saliva of the irradiated bugs was activated by gamma rays and was responsible for the induction of skin papillomas. Because bed bugs play a significant role in the transmission of virus, it is also speculated that there is a virus in the saliva of bugs; this virus may be activated by gamma radiation and causes the development of papillomas in the skin. PMID:2794550

  8. Genotyping of Korean isolates of infectious hematopoietic necrosis virus (IHNV) based on the glycoprotein gene

    USGS Publications Warehouse

    Kim, W.-S.; Oh, M.-J.; Nishizawa, T.; Park, J.-W.; Kurath, G.; Yoshimizu, M.

    2007-01-01

    Glycoprotein (G) gene nucleotide sequences of four Korean isolates of infectious hematopoietic necrosis virus (IHNV) were analyzed to evaluate their genetic relatedness to worldwide isolates. All Korean isolates were closely related to Japanese isolates of genogroup JRt rather than to those of North American and European genogroups. It is believed that Korean IHNV has been most likely introduced from Japan to Korea by the movement of contaminated fish eggs. Among the Korean isolates, phylogenetically distinct virus types were obtained from sites north and south of a large mountain range, suggesting the possibility of more than one introduction of virus from Japan. ?? 2007 Springer-Verlag.

  9. Antibody to E1 peptide of hepatitis C virus genotype 4 inhibits virus binding and entry to HepG2 cells in vitro

    PubMed Central

    EL-Awady, Mostafa K; Tabll, Ashraf A; Atef, Khaled; Yousef, Samar S; Omran, Moataza H; El-Abd, Yasmin; Bader-Eldin, Noha G; Salem, Ahmad M; Zohny, Samir F; El-Garf, Wael T

    2006-01-01

    AIM: To analyze the neutralizing activity of antibodies against E1 region of hepatitis C virus (HCV). Specific polyclonal antibody was raised via immunization of New Zealand rabbits with a synthetic peptide that had been derived from the E1 region of HCV and was shown to be highly conserved among HCV published genotypes. METHODS: Hyper-immune HCV E1 antibodies were incubated over night at 4 °C with serum samples positive for HCV RNA, with viral loads ranging from 615 to 3.2 million IU/ mL. Treated sera were incubated with HepG2 cells for 90 min. Blocking of viral binding and entry into cells by anti E1 antibody were tested by means of RT-PCR and flow cytometry. RESULTS: Direct immunostaining using FITC conjugated E1 antibody followed by Flow cytometric analysis showed reduced mean fluorescence intensity in samples pre-incubated with E1 antibody compared with untreated samples. Furthermore, 13 out of 18 positive sera (72%) showed complete inhibition of infectivity as detected by RT-PCR. CONCLUSION: In house produced E1 antibody, blocks binding and entry of HCV virion infection to target cells suggesting the involvement of this epitope in virus binding and entry. Isolation of these antibodies that block virus attachment to human cells are useful as therapeutic reagents. PMID:16688798

  10. Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa

    PubMed Central

    Rajhi, Mouna; Ghedira, Kais; Chouikha, Anissa; Djebbi, Ahlem; Cheikh, Imed; Ben Yahia, Ahlem; Sadraoui, Amel; Hammami, Walid; Azouz, Msaddek; Ben Mami, Nabil; Triki, Henda

    2016-01-01

    HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869–1902) before the introduction of HCV-2k in 1901 (1867–1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization. PMID:27100294

  11. Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa.

    PubMed

    Rajhi, Mouna; Ghedira, Kais; Chouikha, Anissa; Djebbi, Ahlem; Cheikh, Imed; Ben Yahia, Ahlem; Sadraoui, Amel; Hammami, Walid; Azouz, Msaddek; Ben Mami, Nabil; Triki, Henda

    2016-01-01

    HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869-1902) before the introduction of HCV-2k in 1901 (1867-1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization. PMID:27100294

  12. Genotypic Differences in Dengue Virus Neutralization Are Explained by a Single Amino Acid Mutation That Modulates Virus Breathing

    PubMed Central

    Dowd, Kimberly A.; DeMaso, Christina R.

    2015-01-01

    ABSTRACT Flaviviruses sample an ensemble of virion conformations resulting from the conformational flexibility of their structural proteins. To investigate how sequence variation among strains impacts virus breathing, we performed studies with the monoclonal antibody (MAb) E111, which binds an inaccessible domain III envelope (E) protein epitope of dengue virus serotype 1 (DENV1). Prior studies indicated that an observed ~200-fold difference in neutralization between the DENV1 strains Western Pacific-74 (West Pac-74) and 16007 could not be explained by differences in the affinity of MAb E111 for each strain. Through neutralization studies with wild-type and variant viruses carrying genes encoding reciprocal mutations at all 13 amino acid differences between the E proteins of West Pac-74 and 16007, we found that E111 neutralization susceptibility mapped solely to the presence of a lysine or arginine at E domain II residue 204, located distally from the E111 epitope. This same residue correlated with neutralization differences observed for MAbs specific for epitopes distinct from E111, suggesting that this amino acid dictates changes in the conformational ensembles sampled by the virus. Furthermore, an observed twofold difference in the stability of infectious West Pac-74 versus 16007 in solution also mapped to E residue 204. Our results demonstrate that neutralization susceptibility can be altered in an epitope-independent manner by natural strain variation that influences the structures sampled by DENV. That different conformational ensembles of flaviviruses may affect the landscape available for antibody binding, as well as virus stability, has important implications for functional studies of antibody potency, a critical aspect of vaccine development. PMID:26530385

  13. Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013.

    PubMed

    Kotaki, Tomohiro; Yamanaka, Atsushi; Mulyatno, Kris Cahyo; Churrotin, Siti; Labiqah, Amaliah; Sucipto, Teguh Hari; Soegijanto, Soegeng; Kameoka, Masanori; Konishi, Eiji

    2014-12-01

    Four serotypes of dengue virus (DENV-1 to DENV-4) and their genotypes are distributed in tropical and subtropical regions. Indonesia has been recently suggested as the origin of some dengue virus genotypes. In Surabaya, the second biggest city of Indonesia, we previously reported a shift of the predominantly circulating serotype from DENV-2 to DENV-1 in November 2008, followed by a genotype shift of DENV-1 from genotype IV (GIV) to genotype I (GI) in September 2009, based on nucleotide sequences in the envelope protein coding region. Since then, GI strains had predominantly circulated until December 2010. In this report, we investigated further DENV-1 transitions in Surabaya during 2011-2013 in order to comprehend dengue dynamics during 2008-2013 in more detail. From January 2011 through December 2011, only GIV strains were isolated, indicating that a genotype shift again took place from GI to GIV. In January 2012, GI and GIV strains started co-circulating, which continued until June 2013. To further investigate this phenomenon, analysis was performed at a clade level. GI and GIV strains isolated in Surabaya formed four and three distinct clades, respectively. Concomitant with co-circulation, new clade strains appeared in both genotypes. In contrast, some previously circulating clades were not isolated during co-circulation, indicating clade shifts. Among our Surabaya isolates, nucleotide and amino acid differences in the E region were, respectively, 1.0-2.3% and 0.2-1.0% for GI isolates and 2.0-6.3% and 0.0-1.8% for GIV isolates. Several characteristic amino acid substitutions in the envelope ectodomain were observed in some clades. After July 2013, DENV-1 strains were not isolated and were replaced with DENV-2. This study showed that continuous shifts of more than one genotype resulted in their co-circulation and subsequent disappearance and suggested the relevance of clade replacement to genotype co-circulation and disappearance in Surabaya. PMID:25219342

  14. Genetic diversity and phylogenetic analysis revealed Pepino Mosaic Virus in North-America has shifted to a more aggressive CH2 genotype

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In nearly a decade, Pepino mosaic virus (PepMV) has become endemic on greenhouse tomatoes in North America. Several distinct genotypes of PepMV have been identified and three of them confirmed, including EU, US1, and CH2. Previous population genetic studies conducted in 2006-2007 revealed a predom...

  15. De Novo Polymerase Activity and Oligomerization of Hepatitis C Virus RNA-Dependent RNA-Polymerases from Genotypes 1 to 5

    PubMed Central

    Bellón-Echeverría, Itxaso; Encinar, José Antonio; Martínez-Alfaro, Elisa; Pérez-Flores, Ricardo; Mas, Antonio

    2011-01-01

    Hepatitis C virus (HCV) shows a great geographical diversity reflected in the high number of circulating genotypes and subtypes. The response to HCV treatment is genotype specific, with the predominant genotype 1 showing the lowest rate of sustained virological response. Virally encoded enzymes are candidate targets for intervention. In particular, promising antiviral molecules are being developed to target the viral NS3/4A protease and NS5B polymerase. Most of the studies with the NS5B polymerase have been done with genotypes 1b and 2a, whilst information about other genotypes is scarce. Here, we have characterized the de novo activity of NS5B from genotypes 1 to 5, with emphasis on conditions for optimum activity and kinetic constants. Polymerase cooperativity was determined by calculating the Hill coefficient and oligomerization through a new FRET-based method. The Vmax/Km ratios were statistically different between genotype 1 and the other genotypes (p<0.001), mainly due to differences in Vmax values, but differences in the Hill coefficient and NS5B oligomerization were noted. Analysis of sequence changes among the studied polymerases and crystal structures show the αF helix as a structural component probably involved in NS5B-NS5B interactions. The viability of the interaction of αF and αT helixes was confirmed by docking studies and calculation of electrostatic surface potentials for genotype 1 and point mutants corresponding to mutations from different genotypes. Results presented in this study reveal the existence of genotypic differences in NS5B de novo activity and oligomerization. Furthermore, these results allow us to define two regions, one consisting of residues Glu128, Asp129, and Glu248, and the other consisting of residues of αT helix possibly involved in NS5B-NS5B interactions. PMID:21490973

  16. Analysis of the entire nucleotide sequence of hepatitis B virus genotype B in the Philippines reveals a new subgenotype of genotype B.

    PubMed

    Nagasaki, Futoshi; Niitsuma, Hirofumi; Cervantes, Julieta G; Chiba, Masanori; Hong, Shan; Ojima, Toshiaki; Ueno, Yoshiyuki; Bondoc, Edgardo; Kobayashi, Koju; Ishii, Motoyasu; Shimosegawa, Tooru

    2006-05-01

    The entire nucleotide sequences were determined for hepatitis B virus (HBV) genotype B (HBV/B) genomes extracted from five patients in the Philippines and designated GenBank AB219426, AB219427, AB219428, AB219429 and AB219430. The serotype of the first four isolates was ayw and that of GenBank AB219430 was adw. Divergences of entire sequences were 1.0-2.0 % between the first four isolates and 3.8-4.2 % between these four and GenBank AB219430. Phylogenetic-tree analysis revealed that, worldwide, HBV/B comprises five subgenotypes: B1, B2, B3, B4 and the new Philippines group, designated B5. Divergences of the entire genome sequences between four isolates in subgenotype B5 and isolates from other countries (subgenotypes) were 4.4-4.8 % with Vietnam (B4), 2.9-3.5 % with Indonesia (B3), 4.7-5.1 % with China (B2) and 5.4-6.0 % with Japan (B1). Similarly, GenBank AB219430 showed the lowest divergences: 3.4 % with the isolate from Indonesia (B3), 5.0 % with Vietnam (B4), 5.4 % with China (B2) and 6.1 % with Japan (B1). This is the first report of entire nucleotide sequences of HBV/B from the Philippines and the results show that these sequences belong to a new subgenotype, B5. The present study identified that HBV/B isolates throughout the world are divided genetically into five subgenotypes, the relationships between geographical distances and the genetic distances of HBV/B being well-correlated. PMID:16603518

  17. Next-Generation Sequencing-Based HPV Genotyping Assay Validated in Formalin-Fixed, Paraffin-Embedded Oropharyngeal and Cervical Cancer Specimens

    PubMed Central

    Ambulos, Nicholas P.; Schumaker, Lisa M.; Mathias, Trevor J.; White, Ruth; Troyer, Jennifer; Wells, David

    2016-01-01

    Available clinical human papilloma virus (HPV) diagnostics for head and neck cancer have limited sensitivity and/or fail to define the HPV genotype. Common HPV genotyping assays are costly and labor intensive. We sought to develop a next-generation sequencing (NGS)-based HPV genotyping assay that was sensitive enough to work on formalin-fixed paraffin-embedded (FFPE) samples. We developed an ion torrent NGS HPV genotyping assay using barcoded HPV PCR broad-spectrum general primers 5+/6+ (BSGP)5+/6+. To validate genotype specificity and use in archived clinical FFPE tumor samples, we compared NGS HPV genotyping at 2 sequencing centers with typing by Roche Linear Array assay in 42 oropharyngeal and cervical cancer specimens representing 10 HPV genotypes, as well as HPV-negative cases. To demonstrate the detection of a broad range of HPV genotypes, we genotyped a cohort of 266 cervical cancers. A comparison of NGS genotyping of FFPE cancer specimens with genotyping by Linear Array showed concordant results in 34/37 samples (92%) at sequencing site 1 and 39/42 samples (93%) at sequencing site 2. Concordance between sites was 92%. Designed for use with 10 ng genomic DNA, the assay detected HPV using as little as 1.25 ng FFPE-derived genomic DNA. In 266 cervical cancer specimens, the NGS assay identified 20 different HPV genotypes, including all 13 carcinogenic genotypes. This novel NGS assay provides a sensitive and specific high-throughput method to detect and genotype HPV in a range of clinical specimens derived from FFPE with low per-sample cost. PMID:27006646

  18. Next-Generation Sequencing-Based HPV Genotyping Assay Validated in Formalin-Fixed, Paraffin-Embedded Oropharyngeal and Cervical Cancer Specimens.

    PubMed

    Ambulos, Nicholas P; Schumaker, Lisa M; Mathias, Trevor J; White, Ruth; Troyer, Jennifer; Wells, David; Cullen, Kevin J

    2016-07-01

    Available clinical human papilloma virus (HPV) diagnostics for head and neck cancer have limited sensitivity and/or fail to define the HPV genotype. Common HPV genotyping assays are costly and labor intensive. We sought to develop a next-generation sequencing (NGS)-based HPV genotyping assay that was sensitive enough to work on formalin-fixed paraffin-embedded (FFPE) samples. We developed an ion torrent NGS HPV genotyping assay using barcoded HPV PCR broad-spectrum general primers 5(+)/6(+) (BSGP)5(+)/6(+). To validate genotype specificity and use in archived clinical FFPE tumor samples, we compared NGS HPV genotyping at 2 sequencing centers with typing by Roche Linear Array assay in 42 oropharyngeal and cervical cancer specimens representing 10 HPV genotypes, as well as HPV-negative cases. To demonstrate the detection of a broad range of HPV genotypes, we genotyped a cohort of 266 cervical cancers. A comparison of NGS genotyping of FFPE cancer specimens with genotyping by Linear Array showed concordant results in 34/37 samples (92%) at sequencing site 1 and 39/42 samples (93%) at sequencing site 2. Concordance between sites was 92%. Designed for use with 10 ng genomic DNA, the assay detected HPV using as little as 1.25 ng FFPE-derived genomic DNA. In 266 cervical cancer specimens, the NGS assay identified 20 different HPV genotypes, including all 13 carcinogenic genotypes. This novel NGS assay provides a sensitive and specific high-throughput method to detect and genotype HPV in a range of clinical specimens derived from FFPE with low per-sample cost. PMID:27006646

  19. Clinical and laboratorial findings in pregnant ewes and their progeny infected with Border disease virus (BDV-4 genotype).

    PubMed

    García-Pérez, A L; Minguijón, E; Estévez, L; Barandika, J F; Aduriz, G; Juste, R A; Hurtado, A

    2009-04-01

    To evaluate the pathogenicity of local isolates of ovine pestiviruses (BDV-4 genotype), 13 virus- and antibody-negative, artificially inseminated pregnant ewes were challenged on days 108 (5 ewes), 76 (5 ewes) and 55 of pregnancy (3 ewes) with 2 ml of ovine pestivirus containing 10(6) TCID(50). Viraemia was detected by RT-PCR from 2 to 15 days pi in most ewes. No abortion due to the infection was observed but the number of stillbirths was high (32%), and bodyweight at lambing was significantly reduced compared to the experimental flock of origin used as control. Clinical symptoms in live lambs consisted on tremors, gait anomalies and inability to stand unaided. Skeletal abnormalities (brachygnathia, prognathia, arthrogryposis) were present in 44% of the lambs. Only 20% of the lambs were clinically normal. RT-PCR was a very sensitive technique compared to antigen ELISA in detecting viral presence in experimentally infected ewes and their progeny. PMID:18755485

  20. Cytokine profiles and phenotype regulation of antigen presenting cells by genotype-I porcine reproductive and respiratory syndrome virus isolates

    PubMed Central

    2011-01-01

    The present study examined the immunological response of antigen presenting cells (APC) to genotype-I isolates of porcine reproductive and respiratory syndrome virus (PRRSV) infection by analysing the cytokine profile induced and evaluating the changes taking place upon infection on immunologically relevant cell markers (MHCI, MHCII, CD80/86, CD14, CD16, CD163, CD172a, SWC9). Several types of APC were infected with 39 PRRSV isolates. The results show that different isolates were able to induce different patterns of IL-10 and TNF-α. The four possible phenotypes based on the ability to induce IL-10 and/or TNF-α were observed, although different cell types seemed to have different capabilities. In addition, isolates inducing different cytokine-release profiles on APC could induce different expression of cell markers. PMID:21314968

  1. Cytokine profiles and phenotype regulation of antigen presenting cells by genotype-I porcine reproductive and respiratory syndrome virus isolates.

    PubMed

    Gimeno, Mariona; Darwich, Laila; Diaz, Ivan; de la Torre, Eugenia; Pujols, Joan; Martín, Marga; Inumaru, Shigeki; Cano, Esmeralda; Domingo, Mariano; Montoya, Maria; Mateu, Enric

    2011-01-01

    The present study examined the immunological response of antigen presenting cells (APC) to genotype-I isolates of porcine reproductive and respiratory syndrome virus (PRRSV) infection by analysing the cytokine profile induced and evaluating the changes taking place upon infection on immunologically relevant cell markers (MHCI, MHCII, CD80/86, CD14, CD16, CD163, CD172a, SWC9). Several types of APC were infected with 39 PRRSV isolates. The results show that different isolates were able to induce different patterns of IL-10 and TNF-α. The four possible phenotypes based on the ability to induce IL-10 and/or TNF-α were observed, although different cell types seemed to have different capabilities. In addition, isolates inducing different cytokine-release profiles on APC could induce different expression of cell markers. PMID:21314968

  2. Choroid plexus papilloma with a hyperdiploid karyotype

    SciTech Connect

    Roland, B.; Pinto, A.

    1994-09-01

    An 11-month-old male underwent surgery for a choroid plexus neoplasm, which on histologic examination was diagnosed as a benign papilloma. Chromosome analysis showed a karyotype of 55,XY,+7+7,+8,+9,+12,+12,+15,+20,+21 in all 20 metaphases analyzed. This is only the third benign choroid plexus papilloma that has been karyotyped, with the others being normal and hypodiploid (33 chromosomes). Three malignant choroid plexus carcinomas have also been analyzed, two with normal karyotypes and one hypodiploid (34 - 35 chromosomes). The two hypoidiploid neoplasms lack chromosomes 2, 3, 4, 5, 10, 13, 14, 17 and 18. Since the chromosomes that are lost in the hypodiploid neoplasms are different from the chromosomes gained in our tumor, it appears that the dosage of specific chromosomes is important in the origin of choroid plexus neoplasms. Benign choroid plexus papillomas can be difficult to differentiate from choroid plexus carcinomas. With the data available so far, it does not appear that cytogenetics can assist in making the diagnosis.

  3. Genogeography and Immune Epitope Characteristics of Hepatitis B Virus Genotype C Reveals Two Distinct Types: Asian and Papua-Pacific.

    PubMed

    Thedja, Meta Dewi; Muljono, David Handojo; Ie, Susan Irawati; Sidarta, Erick; Turyadi; Verhoef, Jan; Marzuki, Sangkot

    2015-01-01

    Distribution of hepatitis B virus (HBV) genotypes/subgenotypes is geographically and ethnologically specific. In the Indonesian archipelago, HBV genotype C (HBV/C) is prevalent with high genome variability, reflected by the presence of 13 of currently existing 16 subgenotypes. We investigated the association between HBV/C molecular characteristics with host ethnicity and geographical distribution by examining various subgenotypes of HBV/C isolates from the Asia and Pacific region, with further analysis on the immune epitope characteristics of the core and surface proteins. Phylogenetic tree was constructed based on complete HBV/C genome sequences from Asia and Pacific region, and genetic distance between isolates was also examined. HBV/C surface and core immune epitopes were analyzed and grouped by comparing the amino acid residue characteristics and geographical origins. Based on phylogenetic tree and geographical origins of isolates, two major groups of HBV/C isolates--East-Southeast Asia and Papua-Pacific--were identified. Analysis of core and surface immune epitopes supported these findings with several amino acid substitutions distinguishing the East-Southeast Asia isolates from the Papua-Pacific isolates. A west-to-east gradient of HBsAg subtype distribution was observed with adrq+ prominent in the East and Southeast Asia and adrq- in the Pacific, with several adrq-indeterminate subtypes observed in Papua and Papua New Guinea (PNG). This study indicates that HBV/C isolates can be classified into two types, the Asian and the Papua-Pacific, based on the virus genome diversity, immune epitope characteristics, and geographical distribution, with Papua and PNG as the molecular evolutionary admixture region in the switching from adrq+ to adrq-. PMID:26162099

  4. Hepatitis C Virus Genotype 4 Replication in the Hepatocellular Carcinoma Cell Line HepG2/C3A

    PubMed Central

    Shier, Medhat K.; El-Wetidy, Mohammad S.; Ali, Hebatallah H.; Al-Qattan, Mohammad M.

    2016-01-01

    Background/Aims: The lack of a reliable cell culture system allowing persistent in vitro hepatitis C virus (HCV) propagation is still restraining the search for novel antiviral strategies. HepG2 cells transfection with HCV allows for viral replication. However, the replication is weak presumably because of HepG2 lack of miRNA-122, which is essential for viral replication. Other agents such as polyethylene glycol (PEG) and dimethyl sulfoxide (DMSO) have been shown to increase the efficiency of infection with other viruses. This study included comparison of HCV genotype 4 5′UTR and core RNA levels and HCV core protein expression at different time intervals in the absence or presence of PEG and/or DMSO postinfection. Materials and Methods: We used serum with native HCV particles in infecting HepG2 cells in vitro. HCV replication was assessed by reverse transcriptase polymerase chain reaction for detection of HCV RNA and immunofluorescence and flow cytometry for detection of HCV core protein. Results: HCV 5′UTR and core RNA expression was evident at different time intervals after viral infection, especially after cells were treated with PEG. HCV core protein was also evident at different time intervals using both immunofluorescence and flow cytometry. PEG, not DMSO, has increased the HCV core protein expression in the treated cells, similar to its effect on viral RNA expression. Conclusions: These expression profiles suggest that the current model of cultured HepG2 cells allows the study of HCV genotype 4 replication and different stages of the viral life cycle. PMID:27184644

  5. Genogeography and Immune Epitope Characteristics of Hepatitis B Virus Genotype C Reveals Two Distinct Types: Asian and Papua-Pacific

    PubMed Central

    Thedja, Meta Dewi; Muljono, David Handojo; Ie, Susan Irawati; Sidarta, Erick; Turyadi; Verhoef, Jan; Marzuki, Sangkot

    2015-01-01

    Distribution of hepatitis B virus (HBV) genotypes/subgenotypes is geographically and ethnologically specific. In the Indonesian archipelago, HBV genotype C (HBV/C) is prevalent with high genome variability, reflected by the presence of 13 of currently existing 16 subgenotypes. We investigated the association between HBV/C molecular characteristics with host ethnicity and geographical distribution by examining various subgenotypes of HBV/C isolates from the Asia and Pacific region, with further analysis on the immune epitope characteristics of the core and surface proteins. Phylogenetic tree was constructed based on complete HBV/C genome sequences from Asia and Pacific region, and genetic distance between isolates was also examined. HBV/C surface and core immune epitopes were analyzed and grouped by comparing the amino acid residue characteristics and geographical origins. Based on phylogenetic tree and geographical origins of isolates, two major groups of HBV/C isolates—East-Southeast Asia and Papua-Pacific—were identified. Analysis of core and surface immune epitopes supported these findings with several amino acid substitutions distinguishing the East-Southeast Asia isolates from the Papua-Pacific isolates. A west-to-east gradient of HBsAg subtype distribution was observed with adrq+ prominent in the East and Southeast Asia and adrq- in the Pacific, with several adrq-indeterminate subtypes observed in Papua and Papua New Guinea (PNG). This study indicates that HBV/C isolates can be classified into two types, the Asian and the Papua-Pacific, based on the virus genome diversity, immune epitope characteristics, and geographical distribution, with Papua and PNG as the molecular evolutionary admixture region in the switching from adrq+ to adrq-. PMID:26162099

  6. Simeprevir and sofosbuvir with or without ribavirin to treat recurrent genotype 1 hepatitis C virus infection after orthotopic liver transplantation.

    PubMed

    Crittenden, Neil E; Buchanan, Laura A; Pinkston, Christina M; Cave, Barbra; Barve, Ashutosh; Marsano, Luis; McClain, Craig James; Jones, Christopher M; Marvin, Michael R; Davis, Eric G; Kuns-Adkins, Candice B; Gedaly, Roberto; Brock, Guy; Shah, Malay B; Rosenau, Jens; Cave, Matthew C

    2016-05-01

    Although combination simeprevir (SIM) plus sofosbuvir (SOF) is an approved regimen for genotype 1 chronic hepatitis C virus (HCV), data regarding its safety and efficacy in liver transplant recipients remain limited. A multicenter retrospective study was performed to determine the efficacy and tolerability of a 12-week regimen of SIM/SOF with or without ribavirin (RBV) in 56 consecutive liver transplant recipients in 2014; 79% of patients had genotype 1a, 14% had cirrhosis, and 73% were treatment experienced. Sustained virological response at 12 weeks (SVR12) was 88% by intention to treat analysis (95% confidence interval, 84%-90%). Four patients relapsed, but no on-treatment virological failures occurred. The Q80K polymorphism did not impact SVR12, but there was a trend toward decreased sustained virological response with advanced fibrosis (P = 0.18). HCV RNA was detectable at treatment week 4 in 21% of patients, and those who had detectable levels were less likely to achieve SVR12 (58% versus 95%; P = 0.003). Five patients had baseline Child-Pugh class B cirrhosis, and 2 of them died (1 following early discontinuation of therapy). An additional discontinuation resulted from a severe photosensitivity reaction in a patient on concomitant cyclosporine. Seven patients receiving RBV developed progressive anemia requiring intervention. Immunosuppression dose modifications were minimal. SIM/SOF for 12 weeks was effective and well tolerated by compensated liver transplant recipients especially when administered without concomitant RBV or cyclosporine. SIM/SOF appears to have a niche as the only 12-week RBV-free treatment regimen currently recommended by guidelines for compensated transplant recipients. However, 12 weeks may not be the optimal duration of therapy for those with detectable virus at week 4 or possibly for those with cirrhosis. These data require confirmation by prospective randomized clinical trials. Liver Transplantation 22 635-643 2016 AASLD. PMID

  7. Virus Genotype Distribution and Virus Burden in Children and Adults Hospitalized for Norovirus Gastroenteritis, 2012–2014, Hong Kong

    PubMed Central

    Chan, Martin C.W.; Leung, Ting F.; Chung, Tracy W.S.; Kwok, Angela K.; Nelson, E. Anthony S.; Lee, Nelson; Chan, Paul K.S.

    2015-01-01

    We conducted a 2-year hospital-based study on norovirus gastroenteritis among children and adults between August 2012 and September 2014. A total of 1,146 norovirus cases were identified. Young children (aged ≤ 5 years) accounted for a majority (53.3%) of cases. Hospitalization incidence exhibited a U-shaped pattern with the highest rate in young children (1,475 per 100,000 person-years), followed by the elderly aged > 84 years (581 per 100,000 person-years). A subset (n = 395, 34.5%) of cases were selected for norovirus genotyping and noroviral load measurement. Non-GII.4 infections were more commonly observed in young children than in older adults (aged > 65 years) (20.5% versus 9.2%; p < 0.05). In young children, the median noroviral load of GII.4 and non-GII.4 cases was indistinguishably high (cycle threshold value, median [interquartile range]: 16.6 [15.2–19.3] versus 16.6 [14.9–21.6]; p = 0.45). Two age-specific non-GII.4 genotypes (GII.3 and GII.6) were identified among young children. These findings may have implications in norovirus vaccination strategy. PMID:26082165

  8. Genotypic Characterization of Herpes Simplex Virus Type 1 Isolates in Immunocompromised Patients in Rio de Janeiro, Brazil

    PubMed Central

    Perse da Silva, Amanda; Lopes, Amanda de Oliveira; Vieira, Yasmine Rangel; de Almeida, Adilson José; Sion, Fernando Samuel; Grinsztejn, Beatriz; Wagner, Sandra; de Paula, Vanessa Salete

    2015-01-01

    Herpes simplex virus type 1 (HSV-1) is a prevalent human pathogen that causes a variety of diseases, including an increased risk of developing more severe disease in HIV-infected individuals. In Brazil, there is no information about the molecular epidemiology of HSV-1 infection, especially in HIV-infected individuals. The aim of this study was to perform the genotypic characterization of HSV-1 among HIV-infected patients. A total of 214 serum samples from HIV-positive patients without HSV infection symptoms were enrolled in one of two reference hospitals for HIV infection managing in Rio de Janeiro. The gG and gI genes were analyzed by restriction fragment length polymorphism (RFLP) and full nucleotide sequencing of the US8 (1601 bp), UL44 (1996 bp), and UL23 (1244 bp) regions was performed. A total of 38.3% (82/214) and 32.7% (70/214) of the serum samples tested positive for gG and gI genes, respectively. RFLP analysis classified the HSV-1 as belonging to genotype A. Phylogenetic analysis of the Brazilian samples for the US8, UL44, and UL23 regions demonstrated that the nucleotide identity between Brazilian samples was higher than 97% for all genes. No acyclovir mutation was detected in the patients. The shedding of HSV in the serum samples from HIV-positive patients who were asymptomatic for HSV infection was detected in this work. This is the first report of molecular characterization of HSV-1 in Brazilian samples since there is no previous data available in the literature concerning the genotypic classification and stable distribution of Brazilian strains of HSV-1 in Rio de Janeiro, Brazil. PMID:26407292

  9. Micrococcin P1, a naturally occurring macrocyclic peptide inhibiting hepatitis C virus entry in a pan-genotypic manner.

    PubMed

    Lee, Myungeun; Yang, Jaewon; Park, Sanghyun; Jo, Eunji; Kim, Hee-Young; Bae, Yong-Soo; Windisch, Marc P

    2016-08-01

    Hepatitis C virus (HCV) is considered a major public health concern worldwide. Despite recent advances in curing chronic hepatitis C, unmet medical needs still remain, especially due to the high economic burden of therapies. Accordingly, our study aimed to identify affordable novel HCV inhibitors by screening of natural product compound libraries. We identified micrococcin P1, a macrocyclic peptide antibiotic, inhibiting HCV entry in a pan-genotypic manner with an EC50 range of 0.1-0.5 μM. Micrococcin P1 interfered with HCV entry at an attachment step. Furthermore, micrococcin P1 efficiently inhibited HCV spread by blocking cell-free infection as well as cell-to-cell transmission, without affecting the secretion of infectious virions. Interestingly, the putative molecular target of micrococcin P1 is glycoprotein E2 (IIe-630-Thr), as revealed by selection for viral drug resistance. In addition, micrococcin P1 inhibited sofosbuvir-resistant HCV strains and showed synergy in combination with selected HCV drugs, suggesting an alternative treatment paradigm for patients. In conclusion, we identified micrococcin P1 as specifically inhibiting entry of all HCV genotypes and demonstrated that micrococcin P1 potentially could add value to therapies in combination with current HCV interventions. PMID:27387825

  10. Rapid spread of the novel respiratory syncytial virus A ON1 genotype, central Italy, 2011 to 2013.

    PubMed

    Pierangeli, A; Trotta, D; Scagnolari, C; Ferreri, M L; Nicolai, A; Midulla, F; Marinelli, K; Antonelli, G; Bagnarelli, P

    2014-01-01

    Respiratory infections positive for human respiratory syncytial virus (RSV) subtype A were characterised in children admitted to hospitals in Rome and Ancona (Italy) over the last three epidemic seasons. Different strains of the novel RSV-A genotype ON1, first identified in Ontario (Canada) in December 2010, were detected for the first time in Italy in the following 2011/12 epidemic season. They bear an insertion of 24 amino acids in the G glycoprotein as well as amino acid changes likely to change antigenicity. By early 2013, ON1 strains had spread so efficiently that they had nearly replaced other RSV-A strains. Notably, the RSV peak in the 2012/13 epidemic season occurred earlier and, compared with the previous two seasons, influenza-like illnesses diagnoses were more frequent in younger children; bronchiolitis cases had a less severe clinical course. Nonetheless, the ON1-associated intensive care unit admission rate was similar, if not greater, than that attributable to other RSV-A strains. Improving RSV surveillance would allow timely understanding of the epidemiological and clinicopathological features of the novel RSV-A genotype. PMID:25011065

  11. Novel Atlantic bottlenose dolphin parainfluenza virus TtPIV-1 clusters with bovine PIV-3 genotype B strains.

    PubMed

    Eberle, Kirsten C; Neill, John D; Venn-Watson, Stephanie K; McGill, Jodi L; Sacco, Randy E

    2015-10-01

    Parainfluenza virus 3 (PIV-3) is a common viral infection not only in humans, but also in many other species. Serological evidence suggests that nearly 100 % of children in the United States have been infected with PIV-3 by 5 years of age. Similarly, in cattle, PIV-3 is commonly associated with bovine respiratory disease complex. A novel dolphin PIV-3 (TtPIV-1) was described by Nollens et al. in 2008 from a dolphin that was diagnosed with an unknown respiratory illness. At that time, TtPIV-1 was found to be most similar to, but distinct from, bovine PIV-3 (BPIV-3). In the present study, similar viral growth kinetics and pro-inflammatory cytokine (IL-1β, IL-6, and CXCL8) production were seen between BPIV-3 and TtPIV-1 in BEAS-2B, MDBK, and Vero cell lines. Initial nomenclature of TtPIV-1 was based on partial sequence of the fusion and RNA polymerase genes. Based on the similarities we saw with the in vitro work, it was important to examine the TtPIV-1 genome in more detail. Full genome sequencing and subsequent phylogenetic analysis revealed that all six viral genes of TtPIV-1 clustered within the recently described BPIV-3 genotype B strains, and it is proposed that TtPIV-1 be re-classified with BPIV-3 genotype B strains. PMID:26174699

  12. Hepatitis E Virus Genotype 3 Diversity: Phylogenetic Analysis and Presence of Subtype 3b in Wild Boar in Europe

    PubMed Central

    Vina-Rodriguez, Ariel; Schlosser, Josephine; Becher, Dietmar; Kaden, Volker; Groschup, Martin H.; Eiden, Martin

    2015-01-01

    An increasing number of indigenous cases of hepatitis E caused by genotype 3 viruses (HEV-3) have been diagnosed all around the word, particularly in industrialized countries. Hepatitis E is a zoonotic disease and accumulating evidence indicates that domestic pigs and wild boars are the main reservoirs of HEV-3. A detailed analysis of HEV-3 subtypes could help to determine the interplay of human activity, the role of animals as reservoirs and cross species transmission. Although complete genome sequences are most appropriate for HEV subtype determination, in most cases only partial genomic sequences are available. We therefore carried out a subtype classification analysis, which uses regions from all three open reading frames of the genome. Using this approach, more than 1000 published HEV-3 isolates were subtyped. Newly recovered HEV partial sequences from hunted German wild boars were also included in this study. These sequences were assigned to genotype 3 and clustered within subtype 3a, 3i and, unexpectedly, one of them within the subtype 3b, a first non-human report of this subtype in Europe. PMID:26008708

  13. Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus.

    PubMed

    Pu, Juan; Wang, Shuoguo; Yin, Yanbo; Zhang, Guozhong; Carter, Robert A; Wang, Jinliang; Xu, Guanlong; Sun, Honglei; Wang, Min; Wen, Chu; Wei, Yandi; Wang, Dongdong; Zhu, Baoli; Lemmon, Gordon; Jiao, Yuannian; Duan, Susu; Wang, Qian; Du, Qian; Sun, Meng; Bao, Jinnan; Sun, Yipeng; Zhao, Jixun; Zhang, Hui; Wu, Gang; Liu, Jinhua; Webster, Robert G

    2015-01-13

    The emergence of human infection with a novel H7N9 influenza virus in China raises a pandemic concern. Chicken H9N2 viruses provided all six of the novel reassortant's internal genes. However, it is not fully understood how the prevalence and evolution of these H9N2 chicken viruses facilitated the genesis of the novel H7N9 viruses. Here we show that over more than 10 y of cocirculation of multiple H9N2 genotypes, a genotype (G57) emerged that had changed antigenicity and improved adaptability in chickens. It became predominant in vaccinated farm chickens in China, caused widespread outbreaks in 2010-2013 before the H7N9 viruses emerged in humans, and finally provided all of their internal genes to the novel H7N9 viruses. The prevalence and variation of H9N2 influenza virus in farmed poultry could provide an important early warning of the emergence of novel reassortants with pandemic potential. PMID:25548189

  14. Hepatitis A Virus Genotype Distribution during a Decade of Universal Vaccination of Preadolescents

    PubMed Central

    D’Andrea, Lucía; Pérez-Rodríguez, Francisco J.; de Castellarnau, Montserrat; Manzanares, Sandra; Lite, Josep; Guix, Susana; Bosch, Albert; Pintó, Rosa M.

    2015-01-01

    A universal vaccination program among preadolescents was implemented in Catalonia, Spain, during the period of 1999–2013 and its effectiveness has been clearly demonstrated by an overall significant attack rate reduction. However, reductions were not constant over time, and increases were again observed in 2002–2009 due to the occurrence of huge outbreaks. In the following years, in the absence of large outbreaks, the attack rate decreased again to very low levels. However, an increase of symptomatic cases in the <5 age group has recently been observed. This is an unexpected observation since children younger than 6 are mostly asymptomatic. Such a long vaccination campaign offers the opportunity to analyze not only the effectiveness of vaccination, but also the influence of the circulating genotypes on the incidence of hepatitis A among the different age groups. This study has revealed the emergence of genotype IC during a foodborne outbreak, the short-lived circulation of vaccine-escape variants isolated during an outbreak among the men-having-sex-with-men group, and the association of genotype IIIA with the increase of symptomatic cases among the very young. From a public health perspective, two conclusions may be drawn: vaccination is better at an early age, and the vaccination schedule must be complete and include all recommended vaccine doses. PMID:25815599

  15. Displacement of the Predominant Dengue Virus from Type 2 to Type 1 with a Subsequent Genotype Shift from IV to I in Surabaya, Indonesia 2008–2010

    PubMed Central

    Yamanaka, Atsushi; Mulyatno, Kris C.; Susilowati, Helen; Hendrianto, Eryk; Ginting, Amor P.; Sary, Dian D.; Rantam, Fedik A.; Soegijanto, Soegeng; Konishi, Eiji

    2011-01-01

    Indonesia has annually experienced approximately 100,000 reported cases of dengue fever (DF) and dengue hemorrhagic fever (DHF) in recent years. However, epidemiological surveys of dengue viruses (DENVs) have been limited in this country. In Surabaya, the second largest city, a single report indicated that dengue virus type 2 (DENV2) was the predominant circulating virus in 2003–2005. We conducted three surveys in Surabaya during: (i) April 2007, (ii) June 2008 to April 2009, and (iii) September 2009 to December 2010. A total of 231 isolates were obtained from dengue patients and examined by PCR typing. We found that the predominant DENV shifted from type 2 to type 1 between October and November 2008. Another survey using wild-caught mosquitoes in April 2009 confirmed that dengue type 1 virus (DENV1) was the predominant type in Surabaya. Phylogenetic analyses of the nucleotide sequences of the complete envelope gene of DENV1 indicated that all 22 selected isolates in the second survey belonged to genotype IV and all 17 selected isolates in the third survey belonged to genotype I, indicating a genotype shift between April and September 2009. Furthermore, in December 2010, isolates were grouped into a new clade of DENV1 genotype I, suggesting clade shift between September and December 2010. According to statistics reported by the Surabaya Health Office, the proportion of DHF cases among the total number of dengue cases increased about three times after the type shift in 2008. In addition, the subsequent genotype shift in 2009 was associated with the increased number of total dengue cases. This indicates the need for continuous surveillance of circulating viruses to predict the risk of DHF and DF. PMID:22087290

  16. Chronic hepatitis C virus infections: predictive value of genotype and level of viraemia on disease progression and response to interferon alpha.

    PubMed Central

    Booth, J C; Foster, G R; Kumar, U; Galassini, R; Goldin, R D; Brown, J L; Thomas, H C

    1995-01-01

    The effects of hepatitis C virus genotype and viraemia on disease outcome in patients with chronic hepatitis C virus infection were studied. Patients infected with genotype 1 tended to develop more severe disease, and to respond less well to interferon (IFN) treatment, but no pretreatment variable successfully predicted either the severity of the disease or the response to IFN. Failure to eliminate the virus during the first three months of therapy, however, predicted a failure to derive long term benefit from the current IFN regime. Hence pretreatment variables cannot be used to determine whether individual patients will respond to IFN, but observations during the first three months of therapy can be used to decide which patients will not respond to prolonged therapy. In these patients consideration should be given to changing the IFN dosing regime or using alternative treatments. PMID:7698703

  17. Isolation of two non-A genotypes of Bovine parainfluenza virus 3 in the United States.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine parainfluenza virus type 3 (bPI3) is a member of the Paramyxoviridae, genus Respirovirus. bPI3 are pathogens commonly associated with bovine respiratory disease complex. Most infections are subclinical but they can cause acute respiratory disease characterized by cough, fever and nasal disc...

  18. Determining bovine viral diarrhea virus genotypes and biotypes circulating in cattle populations in Mexico

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine viral diarrhea (BVD) is the disease in cattle that results from infection with bovine viral diarrhea viruses (BVDV). BVDV is found in cattle populations throughout the world. While the term BVD encompasses a wide range of clinical manifestations, including severe respiratory disease, gastroe...

  19. Serologic evidence of infection with non-A genotypes of bovine parainfluenza 3 virus in Alabama

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine parainfluenza 3 virus (BPI3V) is a member of the Respirovirus genus in the Paramyxoviridae family. Infection with BPI3V often results in mild or subclinical disease but can also result in acute respiratory disease either alone, or in conjunction with other respiratory pathogens in the develop...

  20. Sensitive detection of multiple hepatitis A virus genotypes with a single polony-based assay

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hepatitis A virus (HAV) is one of the major causes of non-bacterial gastroenteritis in humans worldwide. HAV is mostly transmitted via direct person-to-person contact, or by consumption of contaminated foods and water. Since only a few viral particles may cause disease, detection of low levels of HA...

  1. Phylogenetic clades of ovine progressive pneumonia virus (OPPV) associate with sheep TMEM154 genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ovine progressive pneumonia virus (OPPV) is a lentivirus within the Retroviridae family that infects sheep. OPPV-induced clinical disease progresses slowly over time and manifests primarily in the lungs and central nervous system. Symptoms include weight loss, respiratory distress, and inevitably ...

  2. Phenotypic and genotypic characterization of clinical isolates of herpes simplex virus resistant to aciclovir.

    PubMed

    Harris, Wendy; Collins, Peter; Fenton, Rob J; Snowden, Wendy; Sowa, Mike; Darby, Graham

    2003-06-01

    A panel of 10 clinical isolates of herpes simplex virus (HSV) deficient in the expression of thymidine kinase (TK) and phenotypically resistant to aciclovir was characterized. Sequence analysis revealed a variety of mutations in TK (nucleotide substitutions, insertions and deletions), most of which resulted in truncated TK polypeptides. In line with previous reports, the most common mutation was a single G insertion in the 'G-string' motif. One HSV-1 isolate and two HSV-2 isolates appeared to encode full-length polypeptides and, in each case, an amino acid substitution likely to be responsible for the phenotype was identified. Pathogenicity was determined using a zosteriform model of HSV infection in BALB/c mice. The majority of isolates appeared to show impaired growth at the inoculation site compared with wild-type virus. They also showed poor replication in the peripheral nervous system and little evidence of zosteriform spread. One exception was isolate 4, which had a double G insertion in the G-string but, nevertheless, exhibited zosteriform spread. These studies confirmed that TK-deficient viruses display a range of neurovirulence with respect to latency and zosteriform spread. These results are discussed in the light of previous experience with TK-deficient viruses. PMID:12771406

  3. Microsatellite Diversity of Soybean Genotypes Differing in Bean Pod Mottle Virus Leaf Symptom

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean, Glycine max (L.) Merr, is the most important source of vegetable oil and protein meal in the world. Bean pod mottle virus (BPMV) is a threat to soybean yield and productivity in most soybean growing states of the USA. In the absence of complete resistance to BPMV, partial resistance of so...

  4. Hepatitis C virus genotype and HIV coinfection affect cytokine mRNA levels in unstimulated PBMC but do not shift the T1/T2 balance.

    PubMed

    Lee, Silvia; Watson, Mark W; Clark, Ben; Flexman, James P; Cheng, Wendy; French, Martyn A H; Price, Patricia

    2006-08-01

    Rapid progression of hepatitis C virus (HCV) disease in patients with HIV/HCV may reflect different cytokine responses and be influenced by HCV genotype. This is addressed by a study of patients with HIV/HCV coinfection and infection with HCV genotype 2 or 3 (2/3). They are compared with coinfected patients infected with genotype 1 and HCV monoinfected patients matched for HCV genotype. IFN-gamma, IL-10, IL-4 and IL-4delta2 mRNA were quantified by real-time PCR in unstimulated PBMC and after in vitro stimulation with HCV core or nonstructural 3/4A antigen. In unstimulated PBMC, levels of IFN-gamma and IL-4 mRNA were lowest in HIV/HCV genotype 1 patients, intermediate in HIV/HCV genotype 2/3 patients and highest in HCV genotype 2/3 patients. Neither HCV genotype nor HIV affected levels of IL-10 mRNA in unstimulated PBMC or IFN-gamma, IL-4 and IL-10 mRNA in PBMC stimulated with HCV antigens. Levels of IL-4 and IL-4delta2 mRNA correlated in mitogen-stimulated PBMC from all patient groups but both were low in HIV/HCV genotype 1 patients. Serum soluble CD30 levels (a putative marker of a T2 cytokine environment) did not differ between patient groups. The data do not suggest a shift in the T1/T2 balance driven by HIV coinfection or HCV genotype but either may affect IL-4 bioavailability. PMID:16834574

  5. Naturally occurring NS3 resistance-associated variants in hepatitis C virus genotype 1: Their relevance for developing countries.

    PubMed

    Echeverría, Natalia; Betancour, Gabriela; Gámbaro, Fabiana; Hernández, Nelia; López, Pablo; Chiodi, Daniela; Sánchez, Adriana; Boschi, Susana; Fajardo, Alvaro; Sóñora, Martín; Moratorio, Gonzalo; Cristina, Juan; Moreno, Pilar

    2016-09-01

    Hepatitis C virus (HCV) is a major cause of global morbidity and mortality, with an estimated 130-150 million infected individuals worldwide. HCV is a leading cause of chronic liver diseases including cirrhosis and hepatocellular carcinoma. Current treatment options in developing countries involve pegylated interferon-α and ribavirin as dual therapy or in combination with one or more direct-acting antiviral agents (DAA). The emergence of resistance-associated variants (RAVs) after treatment reveals the great variability of this virus leading to a great difficulty in developing effective antiviral strategies. Baseline RAVs detected in DAA treatment-naïve HCV-infected patients could be of great importance for clinical management and outcome prediction. Although the frequency of naturally occurring HCV NS3 protease inhibitor mutations has been addressed in many countries, there are only a few reports on their prevalence in South America. In this study, we investigated the presence of RAVs in the HCV NS3 serine protease region by analysing a cohort of Uruguayan patients with chronic hepatitis C who had not been treated with any DAAs and compare them with the results found for other South American countries. The results of these studies revealed that naturally occurring mutations conferring resistance to NS3 inhibitors exist in a substantial proportion of Uruguayan treatment-naïve patients infected with HCV genotype 1 enrolled in these studies. The identification of these baseline RAVs could be of great importance for patients' management and outcome prediction in developing countries. PMID:27449600

  6. Rapid detection of duck hepatitis A virus genotype C using reverse transcription loop-mediated isothermal amplification.

    PubMed

    Li, Chuanfeng; Chen, Zongyan; Meng, Chunchun; Liu, Guangqing

    2014-02-01

    A one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was used and optimized to develop a rapid and sensitive detection system for duck hepatitis A virus genotype C (DHAV-C) RNA. A set of four specific primers was designed against highly conserved sequences located within the 3D gene from DHAV (strain GX1201). Under optimal reaction conditions, the sensitivity of DHAV-C-specific RT-LAMP was 100-fold higher than that of reverse transcriptase-polymerase chain reaction (RT-PCR), with a detection limit of 0.3pg (6.59×10(4) copies) per reaction. No cross-reactivity was observed from the samples of other duck viruses, which is in good accordance with RT-PCR. Furthermore, a positive reaction can be visually inspected by observing turbidity or color change after the addition of SYBR green I dye. The DHAV-C-specific RT-LAMP assay was applied to the samples and compared with RT-PCR. The positive-sample ratios were 26.7%