The Classroom, Board Room, Chat Room, and Court Room: School Computers at the Crossroads.

ERIC Educational Resources Information Center

Stewart, Michael

2000-01-01

In schools' efforts to maximize technology's benefits, ethical considerations have often taken a back seat. Computer misuse is growing exponentially and assuming many forms: unauthorized data access, hacking, piracy, information theft, fraud, virus creation, harassment, defamation, and discrimination. Integrated-learning activities will help…

Computer Viruses: Pathology and Detection.

ERIC Educational Resources Information Center

Maxwell, John R.; Lamon, William E.

1992-01-01

Explains how computer viruses were originally created, how a computer can become infected by a virus, how viruses operate, symptoms that indicate a computer is infected, how to detect and remove viruses, and how to prevent a reinfection. A sidebar lists eight antivirus resources. (four references) (LRW)

Spyware

ERIC Educational Resources Information Center

Bergren, Martha Dewey

2004-01-01

School nurses access an enormous amount of information through the Internet. Although most avid computer users are savvy to the threat of viruses to the integrity of data, many who surf the Web do not know that their data and the functioning of their computer is at risk to another hidden threat--spyware. This article will describe spyware, why it…

An overview of computer viruses in a research environment

NASA Technical Reports Server (NTRS)

Bishop, Matt

1991-01-01

The threat of attack by computer viruses is in reality a very small part of a much more general threat, specifically threats aimed at subverting computer security. Here, computer viruses are examined as a malicious logic in a research and development environment. A relation is drawn between the viruses and various models of security and integrity. Current research techniques aimed at controlling the threats posed to computer systems by threatening viruses in particular and malicious logic in general are examined. Finally, a brief examination of the vulnerabilities of research and development systems that malicious logic and computer viruses may exploit is undertaken.

Safe Computing: An Overview of Viruses.

ERIC Educational Resources Information Center

Wodarz, Nan

2001-01-01

A computer virus is a program that replicates itself, in conjunction with an additional program that can harm a computer system. Common viruses include boot-sector, macro, companion, overwriting, and multipartite. Viruses can be fast, slow, stealthy, and polymorphic. Anti-virus products are described. (MLH)

Virus Database and Online Inquiry System Based on Natural Vectors.

PubMed

Dong, Rui; Zheng, Hui; Tian, Kun; Yau, Shek-Chung; Mao, Weiguang; Yu, Wenping; Yin, Changchuan; Yu, Chenglong; He, Rong Lucy; Yang, Jie; Yau, Stephen St

2017-01-01

We construct a virus database called VirusDB (http://yaulab.math.tsinghua.edu.cn/VirusDB/) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research.

Protecting Your Computer from Viruses

ERIC Educational Resources Information Center

Descy, Don E.

2006-01-01

A computer virus is defined as a software program capable of reproducing itself and usually capable of causing great harm to files or other programs on the same computer. The existence of computer viruses--or the necessity of avoiding viruses--is part of using a computer. With the advent of the Internet, the door was opened wide for these…

Infotech. Cyber security. Health care learns to share scares and solutions.

PubMed

Colias, Mike

2004-05-01

Health care information technology leaders and others are coming together to share scary experiences and develop best practices to guard against crippling computer viruses, scheming hackers and other cyber threats.

Technology for Libraries.

ERIC Educational Resources Information Center

Phenix, Katharine; And Others

1990-01-01

Five articles discuss information technology in libraries: (1) "Software for Libraries" (Katharine Phenix); (2) "Online Update: European Online Services" (Martin Kesselman); (3) "Connect Time: Online Pricing Breakthroughs" (Barbara Quint); (4) "Microcomputing: Micro Biology Computer Viruses" (James LaRue);…

pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC.

PubMed

Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen

2017-09-10

Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computational tools for timely annotating their subcellular locations based on the sequence information alone. The current study is focused on virus proteins. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions. This kind of multiplex proteins is particularly important for both basic research and drug design. Using the multi-label theory, we present a new predictor called "pLoc-mVirus" by extracting the optimal GO (Gene Ontology) information into the general PseAAC (Pseudo Amino Acid Composition). Rigorous cross-validation on a same stringent benchmark dataset indicated that the proposed pLoc-mVirus predictor is remarkably superior to iLoc-Virus, the state-of-the-art method in predicting virus protein subcellular localization. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mVirus/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. Copyright © 2017 Elsevier B.V. All rights reserved.

Computer Bytes, Viruses and Vaccines.

ERIC Educational Resources Information Center

Palmore, Teddy B.

1989-01-01

Presents a history of computer viruses, explains various types of viruses and how they affect software or computer operating systems, and describes examples of specific viruses. Available vaccines are explained, and precautions for protecting programs and disks are given. (nine references) (LRW)

"Glitch Logic" and Applications to Computing and Information Security

NASA Technical Reports Server (NTRS)

Stoica, Adrian; Katkoori, Srinivas

2009-01-01

This paper introduces a new method of information processing in digital systems, and discusses its potential benefits to computing and information security. The new method exploits glitches caused by delays in logic circuits for carrying and processing information. Glitch processing is hidden to conventional logic analyses and undetectable by traditional reverse engineering techniques. It enables the creation of new logic design methods that allow for an additional controllable "glitch logic" processing layer embedded into a conventional synchronous digital circuits as a hidden/covert information flow channel. The combination of synchronous logic with specific glitch logic design acting as an additional computing channel reduces the number of equivalent logic designs resulting from synthesis, thus implicitly reducing the possibility of modification and/or tampering with the design. The hidden information channel produced by the glitch logic can be used: 1) for covert computing/communication, 2) to prevent reverse engineering, tampering, and alteration of design, and 3) to act as a channel for information infiltration/exfiltration and propagation of viruses/spyware/Trojan horses.

Email networks and the spread of computer viruses

NASA Astrophysics Data System (ADS)

Newman, M. E.; Forrest, Stephanie; Balthrop, Justin

2002-09-01

Many computer viruses spread via electronic mail, making use of computer users' email address books as a source for email addresses of new victims. These address books form a directed social network of connections between individuals over which the virus spreads. Here we investigate empirically the structure of this network using data drawn from a large computer installation, and discuss the implications of this structure for the understanding and prevention of computer virus epidemics.

METHODOLOGICAL NOTES: Computer viruses and methods of combatting them

NASA Astrophysics Data System (ADS)

Landsberg, G. L.

1991-02-01

This article examines the current virus situation for personal computers and time-sharing computers. Basic methods of combatting viruses are presented. Specific recommendations are given to eliminate the most widespread viruses. A short description is given of a universal antiviral system, PHENIX, which has been developed.

[Birth and death process of computer viruses].

PubMed

Segawa, Katsunori; Nakano, Tatsuya; Nakata, Kotoko; Hayashi, Yuzuru

2006-01-01

The daily variations in the number of computer viruses found attaching to e-mails and the number of accesses to the home page of a national institute in Japan are examined. The power spectral densities (PSD) of the variation in the computer viruses show a time-correlation characteristic of Markov process, but the daily access number does not (identified as white noise). Like biological viruses, the variation in the computer viruses can be described by the birth-and-death model known as a Markov process.

Zika Virus: Medical Countermeasure Development Challenges

PubMed Central

Malone, Robert W.; Homan, Jane; Callahan, Michael V.; Glasspool-Malone, Jill; Damodaran, Lambodhar; Schneider, Adriano De Bernardi; Zimler, Rebecca; Talton, James; Cobb, Ronald R.; Ruzic, Ivan; Smith-Gagen, Julie; Janies, Daniel; Wilson, James

2016-01-01

Introduction Reports of high rates of primary microcephaly and Guillain–Barré syndrome associated with Zika virus infection in French Polynesia and Brazil have raised concerns that the virus circulating in these regions is a rapidly developing neuropathic, teratogenic, emerging infectious public health threat. There are no licensed medical countermeasures (vaccines, therapies or preventive drugs) available for Zika virus infection and disease. The Pan American Health Organization (PAHO) predicts that Zika virus will continue to spread and eventually reach all countries and territories in the Americas with endemic Aedes mosquitoes. This paper reviews the status of the Zika virus outbreak, including medical countermeasure options, with a focus on how the epidemiology, insect vectors, neuropathology, virology and immunology inform options and strategies available for medical countermeasure development and deployment. Methods Multiple information sources were employed to support the review. These included publically available literature, patents, official communications, English and Lusophone lay press. Online surveys were distributed to physicians in the US, Mexico and Argentina and responses analyzed. Computational epitope analysis as well as infectious disease outbreak modeling and forecasting were implemented. Field observations in Brazil were compiled and interviews conducted with public health officials. PMID:26934531

Spyware.

PubMed

Bergren, Martha Dewey

2004-10-01

School nurses access an enormous amount of information through the Internet. Although most avid computer users are savvy to the threat of viruses to the integrity of data, many who surf the Web do not know that their data and the functioning of their computer is at risk to another hidden threat--spyware. This article will describe spyware, why it is a problem, how it is transmitted to a personal or business computer, how to prevent spyware infestation, and how to delete it.

The Computer Virus Threat and What You Can Do about It.

ERIC Educational Resources Information Center

Lateulere, John

1992-01-01

Discussion of computer viruses describes two types of viruses and how they work; suggests ways to prevent or minimize virus risk; and explains how to recognize a virus and limit damage once a virus attacks. A sidebar lists several antivirus software products. (two references) (NRP)

Epstein-Barr virus: a paradigm for persistent infection - for real and in virtual reality.

PubMed

Thorley-Lawson, David A; Duca, Karen A; Shapiro, Michael

2008-04-01

The really interesting thing about herpesviruses is that they can establish lifelong persistant infections in immunocompetent hosts. At first glance, they would seem to have very different ways of doing this. Here we will use as a model our current understanding of how the human herpesvirus Epstein-Barr virus establishes and maintains such an infection. We apply information from a wide range of sources including laboratory experimentation, clinical observation, animal models and a new computer simulation. We propose that the detailed mechanisms for establishing infection are dependent on the virus and tissues involved, but the strategy is the same - to persist in a long-lived cell type where the virus is invisible to the immune system and nonpathogenic.

Computer Virus Protection

ERIC Educational Resources Information Center

Rajala, Judith B.

2004-01-01

A computer virus is a program--a piece of executable code--that has the unique ability to replicate. Like biological viruses, computer viruses can spread quickly and are often difficult to eradicate. They can attach themselves to just about any type of file, and are spread by replicating and being sent from one individual to another. Simply having…

Preliminary Classification of Novel Hemorrhagic Fever-Causing Viruses Using Sequence-Based PAirwise Sequence Comparison (PASC) Analysis.

PubMed

Bào, Yīmíng; Kuhn, Jens H

2018-01-01

During the last decade, genome sequence-based classification of viruses has become increasingly prominent. Viruses can be even classified based on coding-complete genome sequence data alone. Nevertheless, classification remains arduous as experts are required to establish phylogenetic trees to depict the evolutionary relationships of such sequences for preliminary taxonomic placement. Pairwise sequence comparison (PASC) of genomes is one of several novel methods for establishing relationships among viruses. This method, provided by the US National Center for Biotechnology Information as an open-access tool, circumvents phylogenetics, and yet PASC results are often in agreement with those of phylogenetic analyses. Computationally inexpensive, PASC can be easily performed by non-taxonomists. Here we describe how to use the PASC tool for the preliminary classification of novel viral hemorrhagic fever-causing viruses.

Computer Virus Bibliography, 1988-1989.

ERIC Educational Resources Information Center

Bologna, Jack, Comp.

This bibliography lists 14 books, 154 journal articles, 34 newspaper articles, and 3 research papers published during 1988-1989 on the subject of computer viruses, software protection and 'cures', virus hackers, and other related issues. Some of the sources listed include Computers and Security, Computer Security Digest, PC Week, Time, the New…

Advanced information society(7)

NASA Astrophysics Data System (ADS)

Chiba, Toshihiro

Various threats are hiding in advanced informationalized society. As we see car accident problems in motorization society light aspects necessarily accompy shady ones. Under the changing circumstances of advanced informationalization added values of information has become much higher. It causes computer crime, hacker, computer virus to come to the surface. In addition it can be said that infringement of intellectual property and privacy are threats brought by advanced information. Against these threats legal, institutional and insurance measures have been progressed, and newly security industry has been established. However, they are not adequate individually or totally. The future vision should be clarified, and countermeasures according to the visions have to be considered.

Coping with Computer Viruses: General Discussion and Review of Symantec Anti-Virus for the Macintosh.

ERIC Educational Resources Information Center

Primich, Tracy

1992-01-01

Discusses computer viruses that attack the Macintosh and describes Symantec AntiVirus for Macintosh (SAM), a commercial program designed to detect and eliminate viruses; sample screen displays are included. SAM is recommended for use in library settings as well as two public domain virus protection programs. (four references) (MES)

Modelling the human immunodeficiency virus (HIV) epidemic: A review of the substance and role of models in South Africa

PubMed Central

2018-01-01

We review key mathematical models of the South African human immunodeficiency virus (HIV) epidemic from the early 1990s onwards. In our descriptions, we sometimes differentiate between the concepts of a model world and its mathematical or computational implementation. The model world is the conceptual realm in which we explicitly declare the rules – usually some simplification of ‘real world’ processes as we understand them. Computing details of informative scenarios in these model worlds is a task requiring specialist knowledge, but all other aspects of the modelling process, from describing the model world to identifying the scenarios and interpreting model outputs, should be understandable to anyone with an interest in the epidemic. PMID:29568647

Cyberethics: Identifying the Moral, Legal and Social Issues of Cybertechnology in K-12 Classrooms

ERIC Educational Resources Information Center

Brown, David S.; Wang, Tao

2008-01-01

Two computer viruses that have caused hundreds of millions of dollars in damage over the past four years are the Melissa and the Sasser virus. In March of 1999, the Melissa virus first appeared on the Internet and spread rapidly throughout computer systems in the United States and Europe. The virus made its way through 1.2 million computers in the…

Computer Viruses: An Epidemic Real or Imagined?

ERIC Educational Resources Information Center

Chaffin, Ellen

1989-01-01

Discusses the current problems associated with computer viruses that affect system and software users and the frequency with which they occur. System security is discussed, steps to take to safeguard against damage by computer viruses are suggested, and anti-viral programs, or vaccines, are described. (LRW)

Discovering Deeply Divergent RNA Viruses in Existing Metatranscriptome Data with Machine Learning

NASA Astrophysics Data System (ADS)

Rivers, A. R.

2016-02-01

Most sampling of RNA viruses and phages has been directed toward a narrow range of hosts and environments. Several marine metagenomic studies have examined the RNA viral fraction in aquatic samples and found a number of picornaviruses and uncharacterized sequences. The lack of homology to known protein families has limited the discovery of new RNA viruses. We developed a computational method for identifying RNA viruses that relies on information in the codon transition probabilities of viral sequences to train a classifier. This approach does not rely on homology, but it has higher information content than other reference-free methods such as tetranucleotide frequency. Training and validation with RefSeq data gave true positive and true negative rates of 99.6% and 99.5% on the highly imbalanced validation sets (0.2% viruses) that, like the metatranscriptomes themselves, contain mostly non-viral sequences. To further test the method, a validation dataset of putative RNA virus genomes were identified in metatransciptomes by the presence of RNA dependent RNA polymerase, an essential gene for RNA viruses. The classifier successfully identified 99.4% of those contigs as viral. This approach is currently being extended to screen all metatranscriptome data sequenced at the DOE Joint Genome Institute, presently 4.5 Gb of assembled data from 504 public projects representing a wide range of marine, aquatic and terrestrial environments.

Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology.

PubMed

Poon, Art F Y

2015-09-01

The shapes of phylogenetic trees relating virus populations are determined by the adaptation of viruses within each host, and by the transmission of viruses among hosts. Phylodynamic inference attempts to reverse this flow of information, estimating parameters of these processes from the shape of a virus phylogeny reconstructed from a sample of genetic sequences from the epidemic. A key challenge to phylodynamic inference is quantifying the similarity between two trees in an efficient and comprehensive way. In this study, I demonstrate that a new distance measure, based on a subset tree kernel function from computational linguistics, confers a significant improvement over previous measures of tree shape for classifying trees generated under different epidemiological scenarios. Next, I incorporate this kernel-based distance measure into an approximate Bayesian computation (ABC) framework for phylodynamic inference. ABC bypasses the need for an analytical solution of model likelihood, as it only requires the ability to simulate data from the model. I validate this "kernel-ABC" method for phylodynamic inference by estimating parameters from data simulated under a simple epidemiological model. Results indicate that kernel-ABC attained greater accuracy for parameters associated with virus transmission than leading software on the same data sets. Finally, I apply the kernel-ABC framework to study a recent outbreak of a recombinant HIV subtype in China. Kernel-ABC provides a versatile framework for phylodynamic inference because it can fit a broader range of models than methods that rely on the computation of exact likelihoods. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Virus Alert: Ten Steps to Safe Computing.

ERIC Educational Resources Information Center

Gunter, Glenda A.

1997-01-01

Discusses computer viruses and explains how to detect them; discusses virus protection and the need to update antivirus software; and offers 10 safe computing tips, including scanning floppy disks and commercial software, how to safely download files from the Internet, avoiding pirated software copies, and backing up files. (LRW)

Entering the Dragon’s Lair: Chinese Antiaccess Strategies and Their Implications for the United States

DTIC Science & Technology

2007-01-01

possible expansion of electronic warfare into outer space in future conflicts (Peng and Yao, 2001, p. 363): As a result of the continuous development of...information warfare units to develop viruses to attack enemy computer systems and networks .” Potential Effects of Chinese Antiaccess Measures 87...computers, enhanced user identi- fication measures, and monitoring of network activity. Given the possibility that China could nonetheless succeed in

The impact of countermeasure propagation on the prevalence of computer viruses.

PubMed

Chen, Li-Chiou; Carley, Kathleen M

2004-04-01

Countermeasures such as software patches or warnings can be effective in helping organizations avert virus infection problems. However, current strategies for disseminating such countermeasures have limited their effectiveness. We propose a new approach, called the Countermeasure Competing (CMC) strategy, and use computer simulation to formally compare its relative effectiveness with three antivirus strategies currently under consideration. CMC is based on the idea that computer viruses and countermeasures spread through two separate but interlinked complex networks-the virus-spreading network and the countermeasure-propagation network, in which a countermeasure acts as a competing species against the computer virus. Our results show that CMC is more effective than other strategies based on the empirical virus data. The proposed CMC reduces the size of virus infection significantly when the countermeasure-propagation network has properties that favor countermeasures over viruses, or when the countermeasure-propagation rate is higher than the virus-spreading rate. In addition, our work reveals that CMC can be flexibly adapted to different uncertainties in the real world, enabling it to be tuned to a greater variety of situations than other strategies.

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

PubMed Central

Squires, R. Burke; Noronha, Jyothi; Hunt, Victoria; García‐Sastre, Adolfo; Macken, Catherine; Baumgarth, Nicole; Suarez, David; Pickett, Brett E.; Zhang, Yun; Larsen, Christopher N.; Ramsey, Alvin; Zhou, Liwei; Zaremba, Sam; Kumar, Sanjeev; Deitrich, Jon; Klem, Edward; Scheuermann, Richard H.

2012-01-01

Please cite this paper as: Squires et al. (2012) Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respiratory Viruses 6(6), 404–416. Background  The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. Design  The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly‐accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user‐friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in‐protected ‘workbench’ spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. Results  To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross‐protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. Conclusions  The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics. PMID:22260278

Do potential SETI signals need to be decontaminated?

NASA Astrophysics Data System (ADS)

Carrigan, Richard A., Jr.

2006-01-01

Biological contamination from space samples is a remote but accepted possibility. Signals received by searches for extraterrestrial intelligence (SETI) could also contain harmful information in the spirit of a computer virus, the so-called "SETI Hacker" hypothesis. Over the last four decades extraterrestrial intelligence searches have given little consideration to this possibility. Some argue that information in an extraterrestrial signal could not attack a terrestrial computer because the computer logic and code is idiosyncratic and constitutes an impenetrable firewall. Suggestions are given on how to probe these arguments. Measures for decontaminating extraterrestrial intelligence signals (ETI) are discussed. Modifications to the current SETI detection protocol may be appropriate. Beyond that, the potential character of ETI message content requires much broader discussion.

Workshop Report: The Future of ROK Navy-US Navy Cooperation

DTIC Science & Technology

2007-10-01

vulnerability also increases. Cyber attacks to paralyze information and communication systems through hacking , virus attacks on computers, and jamming...Pacific Fleet (N5) 250 Makalpa Dr. Pearl Harbor, HI 96860-7000 Ms. Ariane L. Whitemore Chief of Staff, Strategic Planning and Policy HQ USPACOM/ J5 COS

Overreaction to External Attacks on Computer Systems Could Be More Harmful than the Viruses Themselves.

ERIC Educational Resources Information Center

King, Kenneth M.

1988-01-01

Discussion of the recent computer virus attacks on computers with vulnerable operating systems focuses on the values of educational computer networks. The need for computer security procedures is emphasized, and the ethical use of computer hardware and software is discussed. (LRW)

Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research.

PubMed

Chang, Suhua; Zhang, Jiajie; Liao, Xiaoyun; Zhu, Xinxing; Wang, Dahai; Zhu, Jiang; Feng, Tao; Zhu, Baoli; Gao, George F; Wang, Jian; Yang, Huanming; Yu, Jun; Wang, Jing

2007-01-01

Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have established the Influenza Virus Database (IVDB) to integrate information and create an analysis platform for genetic, genomic, and phylogenetic studies of the virus. IVDB hosts complete genome sequences of influenza A virus generated by Beijing Institute of Genomics (BIG) and curates all other published IV sequences after expert annotation. Our Q-Filter system classifies and ranks all nucleotide sequences into seven categories according to sequence content and integrity. IVDB provides a series of tools and viewers for comparative analysis of the viral genomes, genes, genetic polymorphisms and phylogenetic relationships. A search system has been developed for users to retrieve a combination of different data types by setting search options. To facilitate analysis of global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) has been developed to display the worldwide geographic distribution of chosen viral genotypes and to couple genomic data with epidemiological data. The BLAST, multiple sequence alignment and phylogenetic analysis tools were integrated for online data analysis. Furthermore, IVDB offers instant access to pre-computed alignments and polymorphisms of IV genes and proteins, and presents the results as SNP distribution plots and minor allele distributions. IVDB is publicly available at http://influenza.genomics.org.cn.

Virus evolution and transmission in an ever more connected world

PubMed Central

Pybus, Oliver G.; Tatem, Andrew J.; Lemey, Philippe

2015-01-01

The frequency and global impact of infectious disease outbreaks, particularly those caused by emerging viruses, demonstrate the need for a better understanding of how spatial ecology and pathogen evolution jointly shape epidemic dynamics. Advances in computational techniques and the increasing availability of genetic and geospatial data are helping to address this problem, particularly when both information sources are combined. Here, we review research at the intersection of evolutionary biology, human geography and epidemiology that is working towards an integrated view of spatial incidence, host mobility and viral genetic diversity. We first discuss how empirical studies have combined viral spatial and genetic data, focusing particularly on the contribution of evolutionary analyses to epidemiology and disease control. Second, we explore the interplay between virus evolution and global dispersal in more depth for two pathogens: human influenza A virus and chikungunya virus. We discuss the opportunities for future research arising from new analyses of human transportation and trade networks, as well as the associated challenges in accessing and sharing relevant spatial and genetic data. PMID:26702033

Structural Transition and Antibody Binding of EBOV GP and ZIKV E Proteins from Pre-Fusion to Fusion-Initiation State.

PubMed

Lappala, Anna; Nishima, Wataru; Miner, Jacob; Fenimore, Paul; Fischer, Will; Hraber, Peter; Zhang, Ming; McMahon, Benjamin; Tung, Chang-Shung

2018-05-10

Membrane fusion proteins are responsible for viral entry into host cells—a crucial first step in viral infection. These proteins undergo large conformational changes from pre-fusion to fusion-initiation structures, and, despite differences in viral genomes and disease etiology, many fusion proteins are arranged as trimers. Structural information for both pre-fusion and fusion-initiation states is critical for understanding virus neutralization by the host immune system. In the case of Ebola virus glycoprotein (EBOV GP) and Zika virus envelope protein (ZIKV E), pre-fusion state structures have been identified experimentally, but only partial structures of fusion-initiation states have been described. While the fusion-initiation structure is in an energetically unfavorable state that is difficult to solve experimentally, the existing structural information combined with computational approaches enabled the modeling of fusion-initiation state structures of both proteins. These structural models provide an improved understanding of four different neutralizing antibodies in the prevention of viral host entry.

Computer Intrusions and Attacks.

ERIC Educational Resources Information Center

Falk, Howard

1999-01-01

Examines some frequently encountered unsolicited computer intrusions, including computer viruses, worms, Java applications, trojan horses or vandals, e-mail spamming, hoaxes, and cookies. Also discusses virus-protection software, both for networks and for individual users. (LRW)

The impact of neighboring infection on the computer virus spread in packets on scale-free networks

NASA Astrophysics Data System (ADS)

Lazfi, S.; Lamzabi, S.; Rachadi, A.; Ez-Zahraouy, H.

2017-12-01

In this paper, we introduce the effect of neighbors on the infection of packets by computer virus in the SI and SIR models using the minimal traffic routing protocol. We have applied this model to the Barabasi-Albert network to determine how intrasite and extrasite infection rates affect virus propagation through the traffic flow of information packets in both the free-flow and the congested phases. The numerical results show that when we change the intrasite infection rate λ1 while keeping constant the extrasite infection rate λ2, we get normal behavior in the congested phase: in the network, the proportion of infected packets increases to reach a peak and then decreases resulting in a simultaneous increase of the recovered packets. In contrast, when the intrasite infection rate λ1 is kept fixed, an increase of the extrasite infection rate results in two regimes: The first one is characterized by an increase of the proportion of infected packets until reaching some peak value and then decreases smoothly. The second regime is characterized by an increase of infected packets to some stationary value.

Securing PCs and Data in Libraries and Schools: A Handbook with Menuing, Anti-Virus, and Other Protective Software.

ERIC Educational Resources Information Center

Benson, Allen C.

This handbook is designed to help readers identify and eliminate security risks, with sound recommendations and library-tested security software. Chapter 1 "Managing Your Facilities and Assessing Your Risks" addresses fundamental management responsibilities including planning for a secure system, organizing computer-related information, assessing…

Information Warfare: Issues Associated with the Defense of DOD Computers and Computer Networks

DTIC Science & Technology

2002-04-12

professionals; any mistakes that remain are mine and mine alone. Finally, I wish to thank my family, my wife Cecilia , my daughters Leslie and Marguerite, and my...Accessed 15 January 2002. Malicious Activity Continues to Climb Virus Growth Per Month (Internet - “Wild List”) J a n May NovS e pJul 130 140 150 160...28 Original brief previously unpublished. Briefing is currently held in Operation Directorate ( J -3) of the Joint Task

Identifying Challenges to the Integration of Computer-Based Surveillance Information Systems in a Large City Health Department: A Case Study.

PubMed

Jennings, Jacky M; Stover, Jeffrey A; Bair-Merritt, Megan H; Fichtenberg, Caroline; Munoz, Mary Grace; Maziad, Rafiq; Ketemepi, Sherry Johnson; Zenilman, Jonathan

2009-01-01

Integrated infectious disease surveillance information systems have the potential to provide important new surveillance capacities and business efficiencies for local health departments. We conducted a case study at a large city health department of the primary computer-based infectious disease surveillance information systems during a 10-year period to identify the major challenges for information integration across the systems. The assessment included key informant interviews and evaluations of the computer-based surveillance information systems used for acute communicable diseases, human immunodeficiency virus/acquired immunodeficiency syndrome, sexually transmitted diseases, and tuberculosis. Assessments were conducted in 1998 with a follow-up in 2008. Assessments specifically identified and described the primary computer-based surveillance information system, any duplicative information systems, and selected variables collected. Persistent challenges to information integration across the information systems included the existence of duplicative data systems, differences in the variables used to collect similar information, and differences in basic architecture. The assessments identified a number of challenges for information integration across the infectious disease surveillance information systems at this city health department. The results suggest that local disease control programs use computer-based surveillance information systems that were not designed for data integration. To the extent that integration provides important new surveillance capacities and business efficiencies, we recommend that patient-centric information systems be designed that provide all the epidemiologic, clinical, and research needs in one system. In addition, the systems should include a standard system of elements and fields across similar surveillance systems.

Computer Viruses. Legal and Policy Issues Facing Colleges and Universities.

ERIC Educational Resources Information Center

Johnson, David R.; And Others

Compiled by various members of the higher educational community together with risk managers, computer center managers, and computer industry experts, this report recommends establishing policies on an institutional level to protect colleges and universities from computer viruses and the accompanying liability. Various aspects of the topic are…

Stopping computer crimes

NASA Technical Reports Server (NTRS)

Denning, Peter J.

1989-01-01

Two new books about intrusions and computer viruses remind us that attacks against our computers on networks are the actions of human beings. Cliff Stoll's book about the hacker who spent a year, beginning in Aug. 1986, attempting to use the Lawrence Berkeley Computer as a stepping-stone for access to military secrets is a spy thriller that illustrates the weaknesses of our password systems and the difficulties in compiling evidence against a hacker engaged in espionage. Pamela Kane's book about viruses that attack IBM PC's shows that viruses are the modern version of the old problem of a Trojan horse attack. It discusses the most famous viruses and their countermeasures, and it comes with a floppy disk of utility programs that will disinfect your PC and thwart future attack.

Protecting computer-based medical devices: defending against viruses and other threats.

PubMed

2005-07-01

The increasing integration of computer hardware has exposed medical devices to greater risks than ever before. More and more devices rely on commercial off-the-shelf software and operating systems, which are vulnerable to the increasing proliferation of viruses and other malicious programs that target computers. Therefore, it is necessary for hospitals to take steps such as those outlined in this article to ensure that their computer-based devices are made safe and continue to remain safe in the future. Maintaining the security of medical devices requires planning, careful execution, and a commitment of resources. A team should be created to develop a process for surveying the security status of all computerized devices in the hospital and making sure that patches and other updates are applied as needed. These patches and updates should be approved by the medical system supplier before being implemented. The team should consider using virtual local area networks to isolate susceptible devices on the hospital's network. All security measures should be carefully documented, and the documentation should be kept up-to-date. Above all, care must be taken to ensure that medical device security involves a collaborative, supportive partnership between the hospital's information technology staff and biomedical engineering personnel.

Computer synthesis of high resolution electron micrographs

NASA Technical Reports Server (NTRS)

Nathan, R.

1976-01-01

Specimen damage, spherical aberration, low contrast and noisy sensors combine to prevent direct atomic viewing in a conventional electron microscope. The paper describes two methods for obtaining ultra-high resolution in biological specimens under the electron microscope. The first method assumes the physical limits of the electron objective lens and uses a series of dark field images of biological crystals to obtain direct information on the phases of the Fourier diffraction maxima; this information is used in an appropriate computer to synthesize a large aperture lens for a 1-A resolution. The second method assumes there is sufficient amplitude scatter from images recorded in focus which can be utilized with a sensitive densitometer and computer contrast stretching to yield fine structure image details. Cancer virus characterization is discussed as an illustrative example. Numerous photographs supplement the text.

Protein sequences clustering of herpes virus by using Tribe Markov clustering (Tribe-MCL)

NASA Astrophysics Data System (ADS)

Bustamam, A.; Siswantining, T.; Febriyani, N. L.; Novitasari, I. D.; Cahyaningrum, R. D.

2017-07-01

The herpes virus can be found anywhere and one of the important characteristics is its ability to cause acute and chronic infection at certain times so as a result of the infection allows severe complications occurred. The herpes virus is composed of DNA containing protein and wrapped by glycoproteins. In this work, the Herpes viruses family is classified and analyzed by clustering their protein-sequence using Tribe Markov Clustering (Tribe-MCL) algorithm. Tribe-MCL is an efficient clustering method based on the theory of Markov chains, to classify protein families from protein sequences using pre-computed sequence similarity information. We implement the Tribe-MCL algorithm using an open source program of R. We select 24 protein sequences of Herpes virus obtained from NCBI database. The dataset consists of three types of glycoprotein B, F, and H. Each type has eight herpes virus that infected humans. Based on our simulation using different inflation factor r=1.5, 2, 3 we find a various number of the clusters results. The greater the inflation factor the greater the number of their clusters. Each protein will grouped together in the same type of protein.

Stability and Hopf bifurcation for a delayed SLBRS computer virus model.

PubMed

Zhang, Zizhen; Yang, Huizhong

2014-01-01

By incorporating the time delay due to the period that computers use antivirus software to clean the virus into the SLBRS model a delayed SLBRS computer virus model is proposed in this paper. The dynamical behaviors which include local stability and Hopf bifurcation are investigated by regarding the delay as bifurcating parameter. Specially, direction and stability of the Hopf bifurcation are derived by applying the normal form method and center manifold theory. Finally, an illustrative example is also presented to testify our analytical results.

Evolution and Vaccination of Influenza Virus.

PubMed

Lam, Ham Ching; Bi, Xuan; Sreevatsan, Srinand; Boley, Daniel

2017-08-01

In this study, we present an application paradigm in which an unsupervised machine learning approach is applied to the high-dimensional influenza genetic sequences to investigate whether vaccine is a driving force to the evolution of influenza virus. We first used a visualization approach to visualize the evolutionary paths of vaccine-controlled and non-vaccine-controlled influenza viruses in a low-dimensional space. We then quantified the evolutionary differences between their evolutionary trajectories through the use of within- and between-scatter matrices computation to provide the statistical confidence to support the visualization results. We used the influenza surface Hemagglutinin (HA) gene for this study as the HA gene is the major target of the immune system. The visualization is achieved without using any clustering methods or prior information about the influenza sequences. Our results clearly showed that the evolutionary trajectories between vaccine-controlled and non-vaccine-controlled influenza viruses are different and vaccine as an evolution driving force cannot be completely eliminated.

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

NASA Astrophysics Data System (ADS)

Shekhar, Karthik; Ruberman, Claire F.; Ferguson, Andrew L.; Barton, John P.; Kardar, Mehran; Chakraborty, Arup K.

2013-12-01

Mutational escape from vaccine-induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine-induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of nonequilibrium viral evolution driven by patient-specific immune responses and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory á la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses.

Workshop on Education in Computer Security (WECS6) (6th): Avoiding Fear, Uncertainty and Doubt Through Effective Security Education, Held in Monterey, California on 12-16 July 2004

DTIC Science & Technology

2004-07-01

Melissa ) is created in the controlled environment and propagated. The students learn how viruses are written, how they are propagated via mediums like...vulnerabilities and threats, establishing disaster response and recovery procedures. Joseph Giordano , Technical Advisor, Information Warfare Branch, AFRL 60 The

Computer Viruses and Related Threats: A Management Guide.

ERIC Educational Resources Information Center

Wack, John P.; Carnahan, Lisa J.

This document contains guidance for managing the threats of computer viruses, Trojan horses, network worms, etc. and related software along with unauthorized use. It is geared towards managers of end-user groups, managers dealing with multi-user systems, personal computers, and networks. The guidance is general and addresses the vulnerabilities…

Modeling the state dependent impulse control for computer virus propagation under media coverage

NASA Astrophysics Data System (ADS)

Liang, Xiyin; Pei, Yongzhen; Lv, Yunfei

2018-02-01

A state dependent impulsive control model is proposed to model the spread of computer virus incorporating media coverage. By the successor function, the sufficient conditions for the existence and uniqueness of order-1 periodic solution are presented first. Secondly, for two classes of periodic solutions, the geometric property of successor function and the analogue of the Poincaré criterion are employed to obtain the stability results. These results show that the number of the infective computers is under the threshold all the time. Finally, the theoretic and numerical analysis show that media coverage can delay the spread of computer virus.

Stability and Hopf Bifurcation for a Delayed SLBRS Computer Virus Model

PubMed Central

Yang, Huizhong

2014-01-01

By incorporating the time delay due to the period that computers use antivirus software to clean the virus into the SLBRS model a delayed SLBRS computer virus model is proposed in this paper. The dynamical behaviors which include local stability and Hopf bifurcation are investigated by regarding the delay as bifurcating parameter. Specially, direction and stability of the Hopf bifurcation are derived by applying the normal form method and center manifold theory. Finally, an illustrative example is also presented to testify our analytical results. PMID:25202722

EPIPOX: Immunoinformatic Characterization of the Shared T-Cell Epitome between Variola Virus and Related Pathogenic Orthopoxviruses.

PubMed

Molero-Abraham, Magdalena; Glutting, John-Paul; Flower, Darren R; Lafuente, Esther M; Reche, Pedro A

2015-01-01

Concerns that variola viruses might be used as bioweapons have renewed the interest in developing new and safer smallpox vaccines. Variola virus genomes are now widely available, allowing computational characterization of the entire T-cell epitome and the use of such information to develop safe and yet effective vaccines. To this end, we identified 124 proteins shared between various species of pathogenic orthopoxviruses including variola minor and major, monkeypox, cowpox, and vaccinia viruses, and we targeted them for T-cell epitope prediction. We recognized 8,106, and 8,483 unique class I and class II MHC-restricted T-cell epitopes that are shared by all mentioned orthopoxviruses. Subsequently, we developed an immunological resource, EPIPOX, upon the predicted T-cell epitome. EPIPOX is freely available online and it has been designed to facilitate reverse vaccinology. Thus, EPIPOX includes key epitope-focused protein annotations: time point expression, presence of leader and transmembrane signals, and known location on outer membrane structures of the infective viruses. These features can be used to select specific T-cell epitopes suitable for experimental validation restricted by single MHC alleles, as combinations thereof, or by MHC supertypes.

EPIPOX: Immunoinformatic Characterization of the Shared T-Cell Epitome between Variola Virus and Related Pathogenic Orthopoxviruses

PubMed Central

Molero-Abraham, Magdalena; Glutting, John-Paul; Flower, Darren R.; Lafuente, Esther M.; Reche, Pedro A.

2015-01-01

Concerns that variola viruses might be used as bioweapons have renewed the interest in developing new and safer smallpox vaccines. Variola virus genomes are now widely available, allowing computational characterization of the entire T-cell epitome and the use of such information to develop safe and yet effective vaccines. To this end, we identified 124 proteins shared between various species of pathogenic orthopoxviruses including variola minor and major, monkeypox, cowpox, and vaccinia viruses, and we targeted them for T-cell epitope prediction. We recognized 8,106, and 8,483 unique class I and class II MHC-restricted T-cell epitopes that are shared by all mentioned orthopoxviruses. Subsequently, we developed an immunological resource, EPIPOX, upon the predicted T-cell epitome. EPIPOX is freely available online and it has been designed to facilitate reverse vaccinology. Thus, EPIPOX includes key epitope-focused protein annotations: time point expression, presence of leader and transmembrane signals, and known location on outer membrane structures of the infective viruses. These features can be used to select specific T-cell epitopes suitable for experimental validation restricted by single MHC alleles, as combinations thereof, or by MHC supertypes. PMID:26605344

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus

PubMed Central

Karp, Peter D.; Berger, Bonnie; Kovats, Diane; Lengauer, Thomas; Linial, Michal; Sabeti, Pardis; Hide, Winston; Rost, Burkhard

2015-01-01

Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola strains as well as 3-D protein modeling. Other computational approaches to Ebola may include large-scale docking studies of Ebola proteins with human proteins and with small-molecule libraries, computational modeling of the spread of the virus, computational mining of the Ebola literature, and creation of a curated Ebola database. Taken together, such computational efforts could significantly accelerate traditional scientific approaches. In recognition of the need for important and immediate solutions from the field of computational biology against Ebola, the International Society for Computational Biology (ISCB) announces a prize for an important computational advance in fighting the Ebola virus. ISCB will confer the ISCB Fight against Ebola Award, along with a prize of US$2,000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology (ISMB) 2016, Orlando, Florida). PMID:26097686

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.

PubMed

Karp, Peter D; Berger, Bonnie; Kovats, Diane; Lengauer, Thomas; Linial, Michal; Sabeti, Pardis; Hide, Winston; Rost, Burkhard

2015-01-01

Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola strains as well as 3-D protein modeling. Other computational approaches to Ebola may include large-scale docking studies of Ebola proteins with human proteins and with small-molecule libraries, computational modeling of the spread of the virus, computational mining of the Ebola literature, and creation of a curated Ebola database. Taken together, such computational efforts could significantly accelerate traditional scientific approaches. In recognition of the need for important and immediate solutions from the field of computational biology against Ebola, the International Society for Computational Biology (ISCB) announces a prize for an important computational advance in fighting the Ebola virus. ISCB will confer the ISCB Fight against Ebola Award, along with a prize of US$2,000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology (ISMB) 2016, Orlando, Florida).

Computational approaches to predict bacteriophage–host relationships

PubMed Central

Edwards, Robert A.; McNair, Katelyn; Faust, Karoline; Raes, Jeroen; Dutilh, Bas E.

2015-01-01

Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications. PMID:26657537

Optimizing Targeting of Intrusion Detection Systems in Social Networks

NASA Astrophysics Data System (ADS)

Puzis, Rami; Tubi, Meytal; Elovici, Yuval

Internet users communicate with each other in various ways: by Emails, instant messaging, social networking, accessing Web sites, etc. In the course of communicating, users may unintentionally copy files contaminated with computer viruses and worms [1, 2] to their computers and spread them to other users [3]. (Hereafter we will use the term "threats", rather than computer viruses and computer worms). The Internet is the chief source of these threats [4].

Laboratory preparedness in EU/EEA countries for detection of novel avian influenza A(H7N9) virus, May 2013

PubMed Central

Broberg, E; Pereyaslov, D; Struelens, M; Palm, D; Meijer, A; Ellis, J; Zambon, M; McCauley, J; Daniels, R

2015-01-01

Following human infections with novel avian influenza A(H7N9) viruses in China, the European Centre for Disease Prevention and Control, the World Health Organization (WHO) Regional Office for Europe and the European Reference Laboratory Network for Human Influenza (ERLI-Net) rapidly posted relevant information, including real-time RT-PCR protocols. An influenza RNA sequence-based computational assessment of detection capabilities for this virus was conducted in 32 national influenza reference laboratories in 29 countries, mostly WHO National Influenza Centres participating in the WHO Global Influenza Surveillance and Response System (GISRS). Twenty-seven countries considered their generic influenza A virus detection assay to be appropriate for the novel A(H7N9) viruses. Twenty-two countries reported having containment facilities suitable for its isolation and propagation. Laboratories in 27 countries had applied specific H7 real-time RT-PCR assays and 20 countries had N9 assays in place. Positive control virus RNA was provided by the WHO Collaborating Centre in London to 34 laboratories in 22 countries to allow evaluation of their assays. Performance of the generic influenza A virus detection and H7 and N9 subtyping assays was good in 24 laboratories in 19 countries. The survey showed that ERLI-Net laboratories had rapidly developed and verified good capability to detect the novel A(H7N9) influenza viruses. PMID:24507469

World Reference Center for Arboviruses.

DTIC Science & Technology

1997-07-01

reagent bank, to identify emerging viruses by antigenic and genetic methods, and (d) ordering and cataloguing the virus collection into a computer...encephalitis viruses in mosquitoes collected in Rhode Island and Connecticut. Eastern equine encephalitis (EKE) virus was isolated from 93 of 1800...Results of ri state mosquito- virus isolation studies Viruses identified Date of first isolation Number of isolations Date of last isolation Other

VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs

USDA-ARS?s Scientific Manuscript database

Accurate detection of viruses in plants and animals is critical for agriculture production and human health. Deep sequencing and assembly of virus-derived siRNAs has proven to be a highly efficient approach for virus discovery. However, to date no computational tools specifically designed for both k...

Optimal control strategy for a novel computer virus propagation model on scale-free networks

NASA Astrophysics Data System (ADS)

Zhang, Chunming; Huang, Haitao

2016-06-01

This paper aims to study the combined impact of reinstalling system and network topology on the spread of computer viruses over the Internet. Based on scale-free network, this paper proposes a novel computer viruses propagation model-SLBOSmodel. A systematic analysis of this new model shows that the virus-free equilibrium is globally asymptotically stable when its spreading threshold is less than one; nevertheless, it is proved that the viral equilibrium is permanent if the spreading threshold is greater than one. Then, the impacts of different model parameters on spreading threshold are analyzed. Next, an optimally controlled SLBOS epidemic model on complex networks is also studied. We prove that there is an optimal control existing for the control problem. Some numerical simulations are finally given to illustrate the main results.

Personal computer security: part 1. Firewalls, antivirus software, and Internet security suites.

PubMed

Caruso, Ronald D

2003-01-01

Personal computer (PC) security in the era of the Health Insurance Portability and Accountability Act of 1996 (HIPAA) involves two interrelated elements: safeguarding the basic computer system itself and protecting the information it contains and transmits, including personal files. HIPAA regulations have toughened the requirements for securing patient information, requiring every radiologist with such data to take further precautions. Security starts with physically securing the computer. Account passwords and a password-protected screen saver should also be set up. A modern antivirus program can easily be installed and configured. File scanning and updating of virus definitions are simple processes that can largely be automated and should be performed at least weekly. A software firewall is also essential for protection from outside intrusion, and an inexpensive hardware firewall can provide yet another layer of protection. An Internet security suite yields additional safety. Regular updating of the security features of installed programs is important. Obtaining a moderate degree of PC safety and security is somewhat inconvenient but is necessary and well worth the effort. Copyright RSNA, 2003

Effects of maximum node degree on computer virus spreading in scale-free networks

NASA Astrophysics Data System (ADS)

Bamaarouf, O.; Ould Baba, A.; Lamzabi, S.; Rachadi, A.; Ez-Zahraouy, H.

2017-10-01

The increase of the use of the Internet networks favors the spread of viruses. In this paper, we studied the spread of viruses in the scale-free network with different topologies based on the Susceptible-Infected-External (SIE) model. It is found that the network structure influences the virus spreading. We have shown also that the nodes of high degree are more susceptible to infection than others. Furthermore, we have determined a critical maximum value of node degree (Kc), below which the network is more resistible and the computer virus cannot expand into the whole network. The influence of network size is also studied. We found that the network with low size is more effective to reduce the proportion of infected nodes.

Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

PubMed

Jones, Susan; Baizan-Edge, Amanda; MacFarlane, Stuart; Torrance, Lesley

2017-01-01

Viruses cause significant yield and quality losses in a wide variety of cultivated crops. Hence, the detection and identification of viruses is a crucial facet of successful crop production and of great significance in terms of world food security. Whilst the adoption of molecular techniques such as RT-PCR has increased the speed and accuracy of viral diagnostics, such techniques only allow the detection of known viruses, i.e., each test is specific to one or a small number of related viruses. Therefore, unknown viruses can be missed and testing can be slow and expensive if molecular tests are unavailable. Methods for simultaneous detection of multiple viruses have been developed, and (NGS) is now a principal focus of this area, as it enables unbiased and hypothesis-free testing of plant samples. The development of NGS protocols capable of detecting multiple known and emergent viruses present in infected material is proving to be a major advance for crops, nuclear stocks or imported plants and germplasm, in which disease symptoms are absent, unspecific or only triggered by multiple viruses. Researchers want to answer the question "how many different viruses are present in this crop plant?" without knowing what they are looking for: RNA-sequencing (RNA-seq) of plant material allows this question to be addressed. As well as needing efficient nucleic acid extraction and enrichment protocols, virus detection using RNA-seq requires fast and robust bioinformatics methods to enable host sequence removal and virus classification. In this review recent studies that use RNA-seq for virus detection in a variety of crop plants are discussed with specific emphasis on the computational methods implemented. The main features of a number of specific bioinformatics workflows developed for virus detection from NGS data are also outlined and possible reasons why these have not yet been widely adopted are discussed. The review concludes by discussing the future directions of this field, including the use of bioinformatics tools for virus detection deployed in analytical environments using cloud computing.

76 FR 37057 - Notice of Request for Extension of Approval of an Information Collection; Virus-Serum-Toxin Act...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-24

...] Notice of Request for Extension of Approval of an Information Collection; Virus-Serum-Toxin Act and... approval of an information collection associated with the Virus-Serum-Toxin Act and regulations. DATES: We...: For information on the Virus-Serum- Toxin Act and regulations, contact Dr. Albert Morgan, Section...

78 FR 32229 - Notice of Request for Revision to and Extension of Approval of an Information Collection; Virus...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-29

...] Notice of Request for Revision to and Extension of Approval of an Information Collection; Virus-Serum... associated with the Virus-Serum-Toxin Act and regulations. DATES: We will consider all comments that we... call (202) 799-7039 before coming. FOR FURTHER INFORMATION CONTACT: For information regarding the Virus...

PREDICTING ATTENUATION OF VIRUSES DURING PERCOLATION IN SOILS: 2. USER'S GUIDE TO THE VIRULO 1.0 COMPUTER MODEL

EPA Science Inventory

In the EPA document Predicting Attenuation of Viruses During Percolation in Soils 1. Probabilistic Model the conceptual, theoretical, and mathematical foundations for a predictive screening model were presented. In this current volume we present a User's Guide for the computer mo...

Evaluation of a Biometric Keystroke Typing Dynamics Computer Security System

DTIC Science & Technology

1992-03-01

intrusions, numerous computer systems have been threatened or destroyed by virus attacks. A recent example was the virus called " Michelangelo ," which...threatened to destroy all data on infected hard disks on the birthday of the artist Michelangelo , 6 March, in 1992. During the 1991 Persian Gulf War

[4 years' experience with use of the "Ambulancia, Oddelenie, Sklad" software made by Softprogress Piestany installed on the local computer network in the Ophthalmology Department of the Trnava Hospital].

PubMed

Gavorník, P; Kristofovicová, A

1997-10-01

The authors give information about their positive and negative experience at using computers connected to local network in ophthalmology department. They put the stress on a need to respect the requirements on hygiene of work at the beginning of the process of planning of suitable hardware choice software and workplace equipment. The need of sufficient number of workplace-terminals and software choice are considered to be necessary and the latter one allows a complex data processing and forming of the common database of patients for outpatient department, department and storage files. They refer to risks of local network switching over with other workplaces and possibility of undesirable information escapes and virus penetration into the network.

Structure and sequence based functional annotation of Zika virus NS2b protein: Computational insights.

PubMed

Aguilera-Pesantes, Daniel; Méndez, Miguel A

2017-10-28

While Zika virus (ZIKV) outbreaks are a growing concern for global health, a deep understanding about the virus is lacking. Here we report a contribution to the basic science on the virus- a detailed computational analysis of the non structural protein NS2b. This protein acts as a cofactor for the NS3 protease (NS3Pro) domain that is important on the viral life cycle, and is an interesting target for drug development. We found that ZIKV NS2b cofactor is highly similar to other virus within the Flavivirus genus, especially to West Nile Virus, suggesting that it is completely necessary for the protease complex activity. Furthermore, the ZIKV NS2b has an important role to the function and stability of the ZIKV NS3 protease domain even when presents a low conservation score. In addition, ZIKV NS2b is mostly rigid, which could imply a non dynamic nature in substrate recognition. Finally, by performing a computational alanine scanning mutagenesis, we found that residues Gly 52 and Asp 83 in the NS2b could be important in substrate recognition. Copyright © 2017 Elsevier Inc. All rights reserved.

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.

PubMed

Lim, Chun Shen; Brown, Chris M

2017-01-01

Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community.

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

PubMed Central

Lim, Chun Shen; Brown, Chris M.

2018-01-01

Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community. PMID:29354101

Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review.

PubMed

Kim, Kiyeon; Omori, Ryosuke; Ueno, Keisuke; Iida, Sayaka; Ito, Kimihito

2016-01-01

Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima's D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima's D values of viral sequences were different depending on hosts and gene segments. Tajima's D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima's D values in rapidly growing viral population were also observed in computer simulations. Tajima's D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima's D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.

Dynamic properties of epidemic spreading on finite size complex networks

NASA Astrophysics Data System (ADS)

Li, Ying; Liu, Yang; Shan, Xiu-Ming; Ren, Yong; Jiao, Jian; Qiu, Ben

2005-11-01

The Internet presents a complex topological structure, on which computer viruses can easily spread. By using theoretical analysis and computer simulation methods, the dynamic process of disease spreading on finite size networks with complex topological structure is investigated. On the finite size networks, the spreading process of SIS (susceptible-infected-susceptible) model is a finite Markov chain with an absorbing state. Two parameters, the survival probability and the conditional infecting probability, are introduced to describe the dynamic properties of disease spreading on finite size networks. Our results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks. Also, knowledge about the dynamic character of virus spreading is helpful for adopting immunity policy.

Guidelines for computer security in general practice.

PubMed

Schattner, Peter; Pleteshner, Catherine; Bhend, Heinz; Brouns, Johan

2007-01-01

As general practice becomes increasingly computerised, data security becomes increasingly important for both patient health and the efficient operation of the practice. To develop guidelines for computer security in general practice based on a literature review, an analysis of available information on current practice and a series of key stakeholder interviews. While the guideline was produced in the context of Australian general practice, we have developed a template that is also relevant for other countries. Current data on computer security measures was sought from Australian divisions of general practice. Semi-structured interviews were conducted with general practitioners (GPs), the medical software industry, senior managers within government responsible for health IT (information technology) initiatives, technical IT experts, divisions of general practice and a member of a health information consumer group. The respondents were asked to assess both the likelihood and the consequences of potential risks in computer security being breached. The study suggested that the most important computer security issues in general practice were: the need for a nominated IT security coordinator; having written IT policies, including a practice disaster recovery plan; controlling access to different levels of electronic data; doing and testing backups; protecting against viruses and other malicious codes; installing firewalls; undertaking routine maintenance of hardware and software; and securing electronic communication, for example via encryption. This information led to the production of computer security guidelines, including a one-page summary checklist, which were subsequently distributed to all GPs in Australia. This paper maps out a process for developing computer security guidelines for general practice. The specific content will vary in different countries according to their levels of adoption of IT, and cultural, technical and other health service factors. Making these guidelines relevant to local contexts should help maximise their uptake.

A tradeoff between the losses caused by computer viruses and the risk of the manpower shortage

PubMed Central

Bi, Jichao; Yang, Lu-Xing; Wu, Yingbo; Tang, Yuan Yan

2018-01-01

This article addresses the tradeoff between the losses caused by a new virus and the size of the team for developing an antivirus against the virus. First, an individual-level virus spreading model is proposed to capture the spreading process of the virus before the appearance of its natural enemy. On this basis, the tradeoff problem is modeled as a discrete optimization problem. Next, the influences of different factors, including the infection force, the infection function, the available manpower, the alarm threshold, the antivirus development effort and the network topology, on the optimal team size are examined through computer simulations. This work takes the first step toward the tradeoff problem, and the findings are instructive to the decision makers of network security companies. PMID:29370222

A tradeoff between the losses caused by computer viruses and the risk of the manpower shortage.

PubMed

Bi, Jichao; Yang, Lu-Xing; Yang, Xiaofan; Wu, Yingbo; Tang, Yuan Yan

2018-01-01

This article addresses the tradeoff between the losses caused by a new virus and the size of the team for developing an antivirus against the virus. First, an individual-level virus spreading model is proposed to capture the spreading process of the virus before the appearance of its natural enemy. On this basis, the tradeoff problem is modeled as a discrete optimization problem. Next, the influences of different factors, including the infection force, the infection function, the available manpower, the alarm threshold, the antivirus development effort and the network topology, on the optimal team size are examined through computer simulations. This work takes the first step toward the tradeoff problem, and the findings are instructive to the decision makers of network security companies.

3D image reconstruction algorithms for cryo-electron-microscopy images of virus particles

NASA Astrophysics Data System (ADS)

Doerschuk, Peter C.; Johnson, John E.

2000-11-01

A statistical model for the object and the complete image formation process in cryo electron microscopy of viruses is presented. Using this model, maximum likelihood reconstructions of the 3D structure of viruses are computed using the expectation maximization algorithm and an example based on Cowpea mosaic virus is provided.

Zika Virus-Associated Cognitive Impairment in Adolescent, 2016.

PubMed

Zucker, Jason; Neu, Natalie; Chiriboga, Claudia A; Hinton, Veronica J; Leonardo, Marc; Sheikh, Arif; Thakur, Kiran

2017-06-01

Incidence of neurologic manifestations associated with Zika virus infection has been increasing. In 2016, neuropsychological and cognitive changes developed in an adolescent after travel to a Zika virus-endemic area. Single-photon emission computed tomography and neuropsychological testing raised the possibility that Zika virus infection may lead to neuropsychiatric and cognitive symptoms.

Computational 3D structures of drug-targeting proteins in the 2009-H1N1 influenza A virus

NASA Astrophysics Data System (ADS)

Du, Qi-Shi; Wang, Shu-Qing; Huang, Ri-Bo; Chou, Kuo-Chen

2010-01-01

The neuraminidase (NA) and M2 proton channel of influenza virus are the drug-targeting proteins, based on which several drugs were developed. However these once powerful drugs encountered drug-resistant problem to the H5N1 and H1N1 flu. To address this problem, the computational 3D structures of NA and M2 proteins of 2009-H1N1 influenza virus were built using the molecular modeling technique and computational chemistry method. Based on the models the structure features of NA and M2 proteins were analyzed, the docking structures of drug-protein complexes were computed, and the residue mutations were annotated. The results may help to solve the drug-resistant problem and stimulate designing more effective drugs against 2009-H1N1 influenza pandemic.

Crispen's Five Antivirus Rules.

ERIC Educational Resources Information Center

Crispen, Patrick Douglas

2000-01-01

Provides rules for protecting computers from viruses, Trojan horses, or worms. Topics include purchasing commercial antivirus programs and keeping them updated; updating virus definitions weekly; precautions before opening attached files; macro virus protection in Microsoft Word; and precautions with executable files. (LRW)

Stability of the Influenza Virus Hemagglutinin Protein Correlates with Evolutionary Dynamics.

PubMed

Klein, Eili Y; Blumenkrantz, Deena; Serohijos, Adrian; Shakhnovich, Eugene; Choi, Jeong-Mo; Rodrigues, João V; Smith, Brendan D; Lane, Andrew P; Feldman, Andrew; Pekosz, Andrew

2018-01-01

Protein thermodynamics are an integral determinant of viral fitness and one of the major drivers of protein evolution. Mutations in the influenza A virus (IAV) hemagglutinin (HA) protein can eliminate neutralizing antibody binding to mediate escape from preexisting antiviral immunity. Prior research on the IAV nucleoprotein suggests that protein stability may constrain seasonal IAV evolution; however, the role of stability in shaping the evolutionary dynamics of the HA protein has not been explored. We used the full coding sequence of 9,797 H1N1pdm09 HA sequences and 16,716 human seasonal H3N2 HA sequences to computationally estimate relative changes in the thermal stability of the HA protein between 2009 and 2016. Phylogenetic methods were used to characterize how stability differences impacted the evolutionary dynamics of the virus. We found that pandemic H1N1 IAV strains split into two lineages that had different relative HA protein stabilities and that later variants were descended from the higher-stability lineage. Analysis of the mutations associated with the selective sweep of the higher-stability lineage found that they were characterized by the early appearance of highly stabilizing mutations, the earliest of which was not located in a known antigenic site. Experimental evidence further suggested that H1N1 HA stability may be correlated with in vitro virus production and infection. A similar analysis of H3N2 strains found that surviving lineages were also largely descended from viruses predicted to encode more-stable HA proteins. Our results suggest that HA protein stability likely plays a significant role in the persistence of different IAV lineages. IMPORTANCE One of the constraints on fast-evolving viruses, such as influenza virus, is protein stability, or how strongly the folded protein holds together. Despite the importance of this protein property, there has been limited investigation of the impact of the stability of the influenza virus hemagglutinin protein-the primary antibody target of the immune system-on its evolution. Using a combination of computational estimates of stability and experiments, our analysis found that viruses with more-stable hemagglutinin proteins were associated with long-term persistence in the population. There are two potential reasons for the observed persistence. One is that more-stable proteins tolerate destabilizing mutations that less-stable proteins could not, thus increasing opportunities for immune escape. The second is that greater stability increases the fitness of the virus through increased production of infectious particles. Further research on the relative importance of these mechanisms could help inform the annual influenza vaccine composition decision process.

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.

PubMed

Karp, Peter D; Berger, Bonnie; Kovats, Diane; Lengauer, Thomas; Linial, Michal; Sabeti, Pardis; Hide, Winston; Rost, Burkhard

2015-02-15

Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola strains and three-dimensional protein modeling. Other computational approaches to Ebola may include large-scale docking studies of Ebola proteins with human proteins and with small-molecule libraries, computational modeling of the spread of the virus, computational mining of the Ebola literature and creation of a curated Ebola database. Taken together, such computational efforts could significantly accelerate traditional scientific approaches. In recognition of the need for important and immediate solutions from the field of computational biology against Ebola, the International Society for Computational Biology (ISCB) announces a prize for an important computational advance in fighting the Ebola virus. ISCB will confer the ISCB Fight against Ebola Award, along with a prize of US$2000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology 2016, Orlando, FL). dkovats@iscb.org or rost@in.tum.de. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

48 CFR 2452.239-71 - Information Technology Virus Security.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 6 2014-10-01 2014-10-01 false Information Technology... Provisions and Clauses 2452.239-71 Information Technology Virus Security. As prescribed in 2439.107(b), insert the following clause: Information Technology Virus Security (FEB 2006) (a) The contractor hereby...

48 CFR 2452.239-71 - Information Technology Virus Security.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 6 2013-10-01 2013-10-01 false Information Technology... Provisions and Clauses 2452.239-71 Information Technology Virus Security. As prescribed in 2439.107(b), insert the following clause: Information Technology Virus Security (FEB 2006) (a) The contractor hereby...

48 CFR 2452.239-71 - Information Technology Virus Security.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 6 2012-10-01 2012-10-01 false Information Technology... Provisions and Clauses 2452.239-71 Information Technology Virus Security. As prescribed in 2439.107(b), insert the following clause: Information Technology Virus Security (FEB 2006) (a) The contractor hereby...

48 CFR 2452.239-71 - Information Technology Virus Security.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 6 2011-10-01 2011-10-01 false Information Technology... Provisions and Clauses 2452.239-71 Information Technology Virus Security. As prescribed in 2439.107(b), insert the following clause: Information Technology Virus Security (FEB 2006) (a) The contractor hereby...

48 CFR 2452.239-71 - Information Technology Virus Security.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Information Technology... Provisions and Clauses 2452.239-71 Information Technology Virus Security. As prescribed in 2439.107(b), insert the following clause: Information Technology Virus Security (FEB 2006) (a) The contractor hereby...

Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice

PubMed Central

Jones, Susan; Baizan-Edge, Amanda; MacFarlane, Stuart; Torrance, Lesley

2017-01-01

Viruses cause significant yield and quality losses in a wide variety of cultivated crops. Hence, the detection and identification of viruses is a crucial facet of successful crop production and of great significance in terms of world food security. Whilst the adoption of molecular techniques such as RT-PCR has increased the speed and accuracy of viral diagnostics, such techniques only allow the detection of known viruses, i.e., each test is specific to one or a small number of related viruses. Therefore, unknown viruses can be missed and testing can be slow and expensive if molecular tests are unavailable. Methods for simultaneous detection of multiple viruses have been developed, and (NGS) is now a principal focus of this area, as it enables unbiased and hypothesis-free testing of plant samples. The development of NGS protocols capable of detecting multiple known and emergent viruses present in infected material is proving to be a major advance for crops, nuclear stocks or imported plants and germplasm, in which disease symptoms are absent, unspecific or only triggered by multiple viruses. Researchers want to answer the question “how many different viruses are present in this crop plant?” without knowing what they are looking for: RNA-sequencing (RNA-seq) of plant material allows this question to be addressed. As well as needing efficient nucleic acid extraction and enrichment protocols, virus detection using RNA-seq requires fast and robust bioinformatics methods to enable host sequence removal and virus classification. In this review recent studies that use RNA-seq for virus detection in a variety of crop plants are discussed with specific emphasis on the computational methods implemented. The main features of a number of specific bioinformatics workflows developed for virus detection from NGS data are also outlined and possible reasons why these have not yet been widely adopted are discussed. The review concludes by discussing the future directions of this field, including the use of bioinformatics tools for virus detection deployed in analytical environments using cloud computing. PMID:29123534

Understanding Virtual Epidemics: Children's Folk Conceptions of a Computer Virus

ERIC Educational Resources Information Center

Kafai, Yasmin B.

2008-01-01

Our work investigates the annual outbreak of Whypox, a virtual epidemic in Whyville.net, a virtual world with over 1.2 million registered players ages 8-16. We examined online and classroom participants' understanding of a computer virus using surveys and design activities. Our analyses reveal that students have a mostly naive understanding of a…

Knowledge levels of adolescent girls about human papilloma virus and its vaccine.

PubMed

Çetin, Orkun; Verit, Fatma Ferda; Keskin, Seda; Zebitay, Ali Galip; Deregözü, Ayşegül; Usta, Taner; Yücel, Oğuz

2014-06-01

The aim of our study was to evaluate the level of knowledge of the adolescent girls who presented to our clinic about human papilloma virus (HPV) infection and HPV vaccine. Five hundred and one adolescent girls aged between 13 and 18 years who presented to the gynecology outpatient clinic between March 2012 and March 2013 were asked to answer the questions of the questionnaire about HPV and HPV vaccine. The "Participant Information Form" and "HPV Information Assessment Form" were used by examination of the related literature by the investigators. The data obtained were entered into the computer using the SPSS 16.5 program and evaluated. Descriptive statistics were shown with mean, standard deviation, number and percentage values. The mean age of 501 subjects who were included into the study was 15.92 years. 390 subjects (77.8%) who were included in the study had no information about HPV. 111 subjects (22.2%) stated that they heard of HPV before or had information about HPV. The mean age of the subjects who had information about human papilloma virus was found to be 16.52 years. The mean age of 390 subjects (77.8%) who had no information about human papilloma virus was 15.75 years. It was found that only one of the subjects (0.9%) was vaccinated with HPV vaccine. When the subjects who did not wish to be vaccinated were asked for the reason, 40.9% stated that the reason was inadequate information, 26.4% stated that the reason was high cost, 16.4% stated that the reason was the fact that they did not consider themselves at risk and 16.4% stated that the reason was the fact that they were afraid of side effects. In our study, it was found that the adolescent girls who constituted our study group had insufficient information about HPV and HPV vaccine. Verbal, written and visual communication tools and internet should be used intensively and efficiently for the objective of introducing HPV vaccine and teaching the precautions related with prevention of cervix cancer in terms of public health. Primarily pediatrician and gynecologists and family physicians who give service for the adolescence age group should be supported to develop appropriate attitudes and behaviors related with HPV vaccine and infection.

Research Advances: DNA Computing Targets West Nile Virus, Other Deadly Diseases, and Tic-Tac-Toe; Marijuana Component May Offer Hope for Alzheimer's Disease Treatment; New Wound Dressing May Lead to Maggot Therapy--Without the Maggots

ERIC Educational Resources Information Center

King, Angela G.

2007-01-01

This article presents three reports of research advances. The first report describes a deoxyribonucleic acid (DNA)-based computer that could lead to faster, more accurate tests for diagnosing West Nile Virus and bird flu. Representing the first "medium-scale integrated molecular circuit," it is the most powerful computing device of its type to…

Identification of the transcriptional regulators by expression profiling infected with hepatitis B virus.

PubMed

Chai, Xiaoqiang; Han, Yanan; Yang, Jian; Zhao, Xianxian; Liu, Yewang; Hou, Xugang; Tang, Yiheng; Zhao, Shirong; Li, Xiao

2016-02-01

The molecular pathogenesis of infection by hepatitis B virus with human is extremely complex and heterogeneous. To date the molecular information is not clearly defined despite intensive research efforts. Thus, studies aimed at transcription and regulation during virus infection or combined researches of those already known to be beneficial are needed. With the purpose of identifying the transcriptional regulators related to infection of hepatitis B virus in gene level, the gene expression profiles from some normal individuals and hepatitis B patients were analyzed in our study. In this work, the differential expressed genes were selected primarily. The several genes among those were validated in an independent set by qRT-PCR. Then the differentially co-expression analysis was conducted to identify differentially co-expressed links and differential co-expressed genes. Next, the analysis of the regulatory impact factors was performed through mapping the links and regulatory data. In order to give a further insight to these regulators, the co-expression gene modules were identified using a threshold-based hierarchical clustering method. Incidentally, the construction of the regulatory network was generated using the computer software. A total of 137,284 differentially co-expressed links and 780 differential co-expressed genes were identified. These co-expressed genes were significantly enriched inflammatory response. The results of regulatory impact factors revealed several crucial regulators related to hepatocellular carcinoma and other high-rank regulators. Meanwhile, more than one hundred co-expression gene modules were identified using clustering method. In our study, some important transcriptional regulators were identified using a computational method, which may enhance the understanding of disease mechanisms and lead to an improved treatment of hepatitis B. However, further experimental studies are required to confirm these findings. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Prediction of common epitopes on hemagglutinin of the influenza A virus (H1 subtype).

PubMed

Guo, Chunyan; Xie, Xin; Li, Huijin; Zhao, Penghua; Zhao, Xiangrong; Sun, Jingying; Wang, Haifang; Liu, Yang; Li, Yan; Hu, Qiaoxia; Hu, Jun; Li, Yuan

2015-02-01

Influenza A virus infection is a persistent threat to public health worldwide due to hemagglutinin (HA) variation. Current vaccines against influenza A virus provide immunity to viral isolates similar to vaccine strains. Antibodies against common epitopes provide immunity to diverse influenza virus strains and protect against future pandemic influenza. Therefore, it is vital to analyze common HA antigenic epitopes of influenza virus. In this study, 14 strains of monoclonal antibodies with high sensitivity to common epitopes of influenza virus antigens identified in our previous study were selected as the tool to predict common HA epitopes. The common HA antigenic epitopes were divided into four categories by ELISA blocking experiments, and separately, into three categories according to the preliminary results of computer simulation. Comparison between the results of computer simulations and ELISA blocking experiments indicated that at least two classes of common epitopes are present in influenza virus HA. This study provides experimental data for improving the prediction of HA epitopes of influenza virus (H1 subtype) and the development of a potential universal vaccine as well as a novel approach for the prediction of epitopes on other pathogenic microorganisms. Copyright © 2014 Elsevier Inc. All rights reserved.

QPSO-Based Adaptive DNA Computing Algorithm

PubMed Central

Karakose, Mehmet; Cigdem, Ugur

2013-01-01

DNA (deoxyribonucleic acid) computing that is a new computation model based on DNA molecules for information storage has been increasingly used for optimization and data analysis in recent years. However, DNA computing algorithm has some limitations in terms of convergence speed, adaptability, and effectiveness. In this paper, a new approach for improvement of DNA computing is proposed. This new approach aims to perform DNA computing algorithm with adaptive parameters towards the desired goal using quantum-behaved particle swarm optimization (QPSO). Some contributions provided by the proposed QPSO based on adaptive DNA computing algorithm are as follows: (1) parameters of population size, crossover rate, maximum number of operations, enzyme and virus mutation rate, and fitness function of DNA computing algorithm are simultaneously tuned for adaptive process, (2) adaptive algorithm is performed using QPSO algorithm for goal-driven progress, faster operation, and flexibility in data, and (3) numerical realization of DNA computing algorithm with proposed approach is implemented in system identification. Two experiments with different systems were carried out to evaluate the performance of the proposed approach with comparative results. Experimental results obtained with Matlab and FPGA demonstrate ability to provide effective optimization, considerable convergence speed, and high accuracy according to DNA computing algorithm. PMID:23935409

Investigations in space-related molecular biology. [cryo-electron microscopic and diffraction studies on terrestrial and extraterrestrial specimens

NASA Technical Reports Server (NTRS)

Fernandez-Moran, H.; Pritzker, A. N.

1974-01-01

Improved instrumentation and preparation techniques for high resolution, high voltage cryo-electron microscopic and diffraction studies on terrestrial and extraterrestrial specimens are reported. Computer correlated ultrastructural and biochemical work on hydrated and dried cell membranes and related biological systems provided information on membrane organization, ice crystal formation and ordered water, RNA virus linked to cancer, lunar rock samples, and organometallic superconducting compounds. Apollo 11, 12, 14, and 15 specimens were analyzed

Emulation of the Active Immune Response in a Computer Network

DTIC Science & Technology

2009-01-15

the Code Red worm propagated faster than the Melissa virus in 1999 and much faster than Morris’ worm in 1988. In the case of the Code Red worm, only...report to AFRL on contract #30602-01-0509, Binghamton NY, 2002, 2. Skormin, V.A., Delgado-Frias, J.G., McGee, D.L., Giordano , J.V., Popyack, L.J...V., Delgado-Frias J., McGee D., Giordano J., Popyack L.. Tarakanov A., "BASIS: A Biological Approach to System Information Security," ^2

Evolutionary conservation of Ebola virus proteins predicts important functions at residue level.

PubMed

Arslan, Ahmed; van Noort, Vera

2017-01-15

The recent outbreak of Ebola virus disease (EVD) resulted in a large number of human deaths. Due to this devastation, the Ebola virus has attracted renewed interest as model for virus evolution. Recent literature on Ebola virus (EBOV) has contributed substantially to our understanding of the underlying genetics and its scope with reference to the 2014 outbreak. But no study yet, has focused on the conservation patterns of EBOV proteins. We analyzed the evolution of functional regions of EBOV and highlight the function of conserved residues in protein activities. We apply an array of computational tools to dissect the functions of EBOV proteins in detail: (i) protein sequence conservation, (ii) protein-protein interactome analysis, (iii) structural modeling and (iv) kinase prediction. Our results suggest the presence of novel post-translational modifications in EBOV proteins and their role in the modulation of protein functions and protein interactions. Moreover, on the basis of the presence of ATM recognition motifs in all EBOV proteins we postulate a role of DNA damage response pathways and ATM kinase in EVD. The ATM kinase is put forward, for further evaluation, as novel potential therapeutic target. http://www.biw.kuleuven.be/CSB/EBOV-PTMs CONTACT: vera.vannoort@biw.kuleuven.beSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape

PubMed Central

Soubeyrand, Samuel; Dallot, Sylvie; Labonne, Gérard; Chadœuf, Joël; Jacquot, Emmanuel

2018-01-01

Characterising the spatio-temporal dynamics of pathogens in natura is key to ensuring their efficient prevention and control. However, it is notoriously difficult to estimate dispersal parameters at scales that are relevant to real epidemics. Epidemiological surveys can provide informative data, but parameter estimation can be hampered when the timing of the epidemiological events is uncertain, and in the presence of interactions between disease spread, surveillance, and control. Further complications arise from imperfect detection of disease and from the huge number of data on individual hosts arising from landscape-level surveys. Here, we present a Bayesian framework that overcomes these barriers by integrating over associated uncertainties in a model explicitly combining the processes of disease dispersal, surveillance and control. Using a novel computationally efficient approach to account for patch geometry, we demonstrate that disease dispersal distances can be estimated accurately in a patchy (i.e. fragmented) landscape when disease control is ongoing. Applying this model to data for an aphid-borne virus (Plum pox virus) surveyed for 15 years in 605 orchards, we obtain the first estimate of the distribution of flight distances of infectious aphids at the landscape scale. About 50% of aphid flights terminate beyond 90 m, which implies that most infectious aphids leaving a tree land outside the bounds of a 1-ha orchard. Moreover, long-distance flights are not rare–10% of flights exceed 1 km. By their impact on our quantitative understanding of winged aphid dispersal, these results can inform the design of management strategies for plant viruses, which are mainly aphid-borne. PMID:29708968

Adjoint equations and analysis of complex systems: Application to virus infection modelling

NASA Astrophysics Data System (ADS)

Marchuk, G. I.; Shutyaev, V.; Bocharov, G.

2005-12-01

Recent development of applied mathematics is characterized by ever increasing attempts to apply the modelling and computational approaches across various areas of the life sciences. The need for a rigorous analysis of the complex system dynamics in immunology has been recognized since more than three decades ago. The aim of the present paper is to draw attention to the method of adjoint equations. The methodology enables to obtain information about physical processes and examine the sensitivity of complex dynamical systems. This provides a basis for a better understanding of the causal relationships between the immune system's performance and its parameters and helps to improve the experimental design in the solution of applied problems. We show how the adjoint equations can be used to explain the changes in hepatitis B virus infection dynamics between individual patients.

Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment.

PubMed

Singh, Dadabhai T; Trehan, Rahul; Schmidt, Bertil; Bretschneider, Timo

2008-01-01

Preparedness for a possible global pandemic caused by viruses such as the highly pathogenic influenza A subtype H5N1 has become a global priority. In particular, it is critical to monitor the appearance of any new emerging subtypes. Comparative phyloinformatics can be used to monitor, analyze, and possibly predict the evolution of viruses. However, in order to utilize the full functionality of available analysis packages for large-scale phyloinformatics studies, a team of computer scientists, biostatisticians and virologists is needed--a requirement which cannot be fulfilled in many cases. Furthermore, the time complexities of many algorithms involved leads to prohibitive runtimes on sequential computer platforms. This has so far hindered the use of comparative phyloinformatics as a commonly applied tool in this area. In this paper the graphical-oriented workflow design system called Quascade and its efficient usage for comparative phyloinformatics are presented. In particular, we focus on how this task can be effectively performed in a distributed computing environment. As a proof of concept, the designed workflows are used for the phylogenetic analysis of neuraminidase of H5N1 isolates (micro level) and influenza viruses (macro level). The results of this paper are hence twofold. Firstly, this paper demonstrates the usefulness of a graphical user interface system to design and execute complex distributed workflows for large-scale phyloinformatics studies of virus genes. Secondly, the analysis of neuraminidase on different levels of complexity provides valuable insights of this virus's tendency for geographical based clustering in the phylogenetic tree and also shows the importance of glycan sites in its molecular evolution. The current study demonstrates the efficiency and utility of workflow systems providing a biologist friendly approach to complex biological dataset analysis using high performance computing. In particular, the utility of the platform Quascade for deploying distributed and parallelized versions of a variety of computationally intensive phylogenetic algorithms has been shown. Secondly, the analysis of the utilized H5N1 neuraminidase datasets at macro and micro levels has clearly indicated a pattern of spatial clustering of the H5N1 viral isolates based on geographical distribution rather than temporal or host range based clustering.

Web-GIS-based SARS epidemic situation visualization

NASA Astrophysics Data System (ADS)

Lu, Xiaolin

2004-03-01

In order to research, perform statistical analysis and broadcast the information of SARS epidemic situation according to the relevant spatial position, this paper proposed a unified global visualization information platform for SARS epidemic situation based on Web-GIS and scientific virtualization technology. To setup the unified global visual information platform, the architecture of Web-GIS based interoperable information system is adopted to enable public report SARS virus information to health cure center visually by using the web visualization technology. A GIS java applet is used to visualize the relationship between spatial graphical data and virus distribution, and other web based graphics figures such as curves, bars, maps and multi-dimensional figures are used to visualize the relationship between SARS virus tendency with time, patient number or locations. The platform is designed to display the SARS information in real time, simulate visually for real epidemic situation and offer an analyzing tools for health department and the policy-making government department to support the decision-making for preventing against the SARS epidemic virus. It could be used to analyze the virus condition through visualized graphics interface, isolate the areas of virus source, and control the virus condition within shortest time. It could be applied to the visualization field of SARS preventing systems for SARS information broadcasting, data management, statistical analysis, and decision supporting.

Automatic detection and measurement of viral replication compartments by ellipse adjustment

PubMed Central

Garcés, Yasel; Guerrero, Adán; Hidalgo, Paloma; López, Raul Eduardo; Wood, Christopher D.; Gonzalez, Ramón A.; Rendón-Mancha, Juan Manuel

2016-01-01

Viruses employ a variety of strategies to hijack cellular activities through the orchestrated recruitment of macromolecules to specific virus-induced cellular micro-environments. Adenoviruses (Ad) and other DNA viruses induce extensive reorganization of the cell nucleus and formation of nuclear Replication Compartments (RCs), where the viral genome is replicated and expressed. In this work an automatic algorithm designed for detection and segmentation of RCs using ellipses is presented. Unlike algorithms available in the literature, this approach is deterministic, automatic, and can adjust multiple RCs using ellipses. The proposed algorithm is non iterative, computationally efficient and is invariant to affine transformations. The method was validated over both synthetic images and more than 400 real images of Ad-infected cells at various timepoints of the viral replication cycle obtaining relevant information about the biogenesis of adenoviral RCs. As proof of concept the algorithm was then used to quantitatively compare RCs in cells infected with the adenovirus wild type or an adenovirus mutant that is null for expression of a viral protein that is known to affect activities associated with RCs that result in deficient viral progeny production. PMID:27819325

Automatic detection and measurement of viral replication compartments by ellipse adjustment

NASA Astrophysics Data System (ADS)

Garcés, Yasel; Guerrero, Adán; Hidalgo, Paloma; López, Raul Eduardo; Wood, Christopher D.; Gonzalez, Ramón A.; Rendón-Mancha, Juan Manuel

2016-11-01

Viruses employ a variety of strategies to hijack cellular activities through the orchestrated recruitment of macromolecules to specific virus-induced cellular micro-environments. Adenoviruses (Ad) and other DNA viruses induce extensive reorganization of the cell nucleus and formation of nuclear Replication Compartments (RCs), where the viral genome is replicated and expressed. In this work an automatic algorithm designed for detection and segmentation of RCs using ellipses is presented. Unlike algorithms available in the literature, this approach is deterministic, automatic, and can adjust multiple RCs using ellipses. The proposed algorithm is non iterative, computationally efficient and is invariant to affine transformations. The method was validated over both synthetic images and more than 400 real images of Ad-infected cells at various timepoints of the viral replication cycle obtaining relevant information about the biogenesis of adenoviral RCs. As proof of concept the algorithm was then used to quantitatively compare RCs in cells infected with the adenovirus wild type or an adenovirus mutant that is null for expression of a viral protein that is known to affect activities associated with RCs that result in deficient viral progeny production.

A Combined NMR-Computational Study of the Interaction between Influenza Virus Hemagglutinin and Sialic Derivatives from Human and Avian Receptors on the Surface of Transfected Cells.

PubMed

Vasile, Francesca; Panigada, Maddalena; Siccardi, Antonio; Potenza, Donatella; Tiana, Guido

2018-04-24

The development of small-molecule inhibitors of influenza virus Hemagglutinin could be relevant to the opposition of the diffusion of new pandemic viruses. In this work, we made use of Nuclear Magnetic Resonance (NMR) spectroscopy to study the interaction between two derivatives of sialic acid, Neu5Ac-α-(2,6)-Gal-β-(1⁻4)-GlcNAc and Neu5Ac-α-(2,3)-Gal-β-(1⁻4)-GlcNAc, and hemagglutinin directly expressed on the surface of recombinant human cells. We analyzed the interaction of these trisaccharides with 293T cells transfected with the H5 and H1 variants of hemagglutinin, which thus retain their native trimeric conformation in such a realistic environment. By exploiting the magnetization transfer between the protein and the ligand, we obtained evidence of the binding event, and identified the epitope. We analyzed the conformational features of the glycans with an approach combining NMR spectroscopy and data-driven molecular dynamics simulations, thus obtaining useful information for an efficient drug design.

Computational Prediction of Neutralization Epitopes Targeted by Human Anti-V3 HIV Monoclonal Antibodies

PubMed Central

Shmelkov, Evgeny; Krachmarov, Chavdar; Grigoryan, Arsen V.; Pinter, Abraham; Statnikov, Alexander; Cardozo, Timothy

2014-01-01

The extreme diversity of HIV-1 strains presents a formidable challenge for HIV-1 vaccine design. Although antibodies (Abs) can neutralize HIV-1 and potentially protect against infection, antibodies that target the immunogenic viral surface protein gp120 have widely variable and poorly predictable cross-strain reactivity. Here, we developed a novel computational approach, the Method of Dynamic Epitopes, for identification of neutralization epitopes targeted by anti-HIV-1 monoclonal antibodies (mAbs). Our data demonstrate that this approach, based purely on calculated energetics and 3D structural information, accurately predicts the presence of neutralization epitopes targeted by V3-specific mAbs 2219 and 447-52D in any HIV-1 strain. The method was used to calculate the range of conservation of these specific epitopes across all circulating HIV-1 viruses. Accurately identifying an Ab-targeted neutralization epitope in a virus by computational means enables easy prediction of the breadth of reactivity of specific mAbs across the diversity of thousands of different circulating HIV-1 variants and facilitates rational design and selection of immunogens mimicking specific mAb-targeted epitopes in a multivalent HIV-1 vaccine. The defined epitopes can also be used for the purpose of epitope-specific analyses of breakthrough sequences recorded in vaccine clinical trials. Thus, our study is a prototype for a valuable tool for rational HIV-1 vaccine design. PMID:24587168

Prevalence of human T-cell lymphotropic virus types 1 and 2 in blood donors of the Caruaru Blood Center (Hemope).

PubMed

de Lima, Waleska Mayara Gomes; Esteves, Fabrício Andrade Martins; Torres, Maria do Carmo Morais Rodrigues; Pires, Edna Suely Feitosa

2013-01-01

There is difficulty in gathering data on the prevalence of human T-cell lymphotropic virus in blood donors as confirmatory testing is not mandatory in Brazil. This suggests there may be an underreporting of the prevalence. To estimate the prevalence of human T-cell lymphotropic virus types 1 and 2 in donors of a blood bank in Caruaru, Brazil. This was an observational, epidemiological, descriptive, longitudinal and retrospective study with information about the serology of donors of the Caruaru Blood Center, Fundação de Hematologia e Hemoterapia de Pernambuco (Hemope) from May 2006 to December 2010. The data were analyzed using the Excel 2010 computer program (Microsoft Office(®)). Of 61,881 donors, 60 (0.096%) individuals were identified as potential carriers of human T-cell lymphotropic virus types 1 and 2. Of these, 28 (0.045%) were positive and 32 (0.051%) had inconclusive results in the serological screening. Forty-five (0.072%) were retested; 17 were positive (0.027%) and 3 inconclusive (0.005%). After confirmatory tests, 8 were positive (0.013%). Six (75%) of the confirmed cases were women. Epidemiological surveys like this are very important in order to create campaigns to attract donors and reduce the costs of laboratory tests.

Radiomic analysis in prediction of Human Papilloma Virus status.

PubMed

Yu, Kaixian; Zhang, Youyi; Yu, Yang; Huang, Chao; Liu, Rongjie; Li, Tengfei; Yang, Liuqing; Morris, Jeffrey S; Baladandayuthapani, Veerabhadran; Zhu, Hongtu

2017-12-01

Human Papilloma Virus (HPV) has been associated with oropharyngeal cancer prognosis. Traditionally the HPV status is tested through invasive lab test. Recently, the rapid development of statistical image analysis techniques has enabled precise quantitative analysis of medical images. The quantitative analysis of Computed Tomography (CT) provides a non-invasive way to assess HPV status for oropharynx cancer patients. We designed a statistical radiomics approach analyzing CT images to predict HPV status. Various radiomics features were extracted from CT scans, and analyzed using statistical feature selection and prediction methods. Our approach ranked the highest in the 2016 Medical Image Computing and Computer Assisted Intervention (MICCAI) grand challenge: Oropharynx Cancer (OPC) Radiomics Challenge, Human Papilloma Virus (HPV) Status Prediction. Further analysis on the most relevant radiomic features distinguishing HPV positive and negative subjects suggested that HPV positive patients usually have smaller and simpler tumors.

Analysis of YouTube as a Source of Information for West Nile Virus Infection

PubMed Central

Dubey, Divyanshu; Amritphale, Amod; Sawhney, Anshudha; Dubey, Devashish; Srivastav, Nupur

2014-01-01

Introduction A major outbreak of West Nile Virus was seen last year in different parts of the United States. Adequate dissemination of correct information about the disease would have helped decrease its spread and the associated panic in the general population. In this study, we looked into the use of YouTube as a resource for providing information about West Nile Virus infection. Objective This study aims to identify and evaluate YouTube as resource for providing information on West Nile Virus infection to the general public. Methods YouTube was searched on November 25, 2012, using the keywords West Nile Virus epidemic, West Nile Virus infection, and West Nile Virus prevention for videos uploaded in the past 6 months containing relevant information about the disease. The videos were classified as useful, misleading, or as news updates based on the type of information contained. Total viewership, number of days since upload, total duration of videos, and source of upload were noted. Results A total of 106 videos with information on West Nile Virus infection were included in the study, with 79.24% having useful information about the disease. Among the useful videos, 51/84 (60.71%) had information on disease prevention, and 29/84 (34.52%) contained information on news and research updates. The majority of these videos were uploaded by individuals (54.6%) or news agencies (41.8 %). Healthcare agencies contributed only 3.4 % of the total videos. Even though the useful videos represented 72% of all videos, there was significantly higher total viewership and viewership per day for the non-useful videos (P<0.05). Conclusions YouTube may be a significant resource for dissemination of information on public health issues like West Nile virus infection and should be targeted by healthcare agencies for this use. The major drawback of this medium is lack of verification by authorized healthcare professionals before these videos are made available for viewing by the community. Hence, a strict caution should be exercised in obtaining the information from unauthorized videos posted on YouTube. PMID:24573700

Analysis of YouTube as a source of information for West Nile Virus infection.

PubMed

Dubey, Divyanshu; Amritphale, Amod; Sawhney, Anshudha; Dubey, Devashish; Srivastav, Nupur

2014-12-01

A major outbreak of West Nile Virus was seen last year in different parts of the United States. Adequate dissemination of correct information about the disease would have helped decrease its spread and the associated panic in the general population. In this study, we looked into the use of YouTube as a resource for providing information about West Nile Virus infection. This study aims to identify and evaluate YouTube as resource for providing information on West Nile Virus infection to the general public. YouTube was searched on November 25, 2012, using the keywords West Nile Virus epidemic, West Nile Virus infection, and West Nile Virus prevention for videos uploaded in the past 6 months containing relevant information about the disease. The videos were classified as useful, misleading, or as news updates based on the type of information contained. Total viewership, number of days since upload, total duration of videos, and source of upload were noted. A total of 106 videos with information on West Nile Virus infection were included in the study, with 79.24% having useful information about the disease. Among the useful videos, 51/84 (60.71%) had information on disease prevention, and 29/84 (34.52%) contained information on news and research updates. The majority of these videos were uploaded by individuals (54.6%) or news agencies (41.8 %). Healthcare agencies contributed only 3.4 % of the total videos. Even though the useful videos represented 72% of all videos, there was significantly higher total viewership and viewership per day for the non-useful videos (P<0.05). YouTube may be a significant resource for dissemination of information on public health issues like West Nile virus infection and should be targeted by healthcare agencies for this use. The major drawback of this medium is lack of verification by authorized healthcare professionals before these videos are made available for viewing by the community. Hence, a strict caution should be exercised in obtaining the information from unauthorized videos posted on YouTube. © 2013 Marshfield Clinic.

An intelligent and secure system for predicting and preventing Zika virus outbreak using Fog computing

NASA Astrophysics Data System (ADS)

Sareen, Sanjay; Gupta, Sunil Kumar; Sood, Sandeep K.

2017-10-01

Zika virus is a mosquito-borne disease that spreads very quickly in different parts of the world. In this article, we proposed a system to prevent and control the spread of Zika virus disease using integration of Fog computing, cloud computing, mobile phones and the Internet of things (IoT)-based sensor devices. Fog computing is used as an intermediary layer between the cloud and end users to reduce the latency time and extra communication cost that is usually found high in cloud-based systems. A fuzzy k-nearest neighbour is used to diagnose the possibly infected users, and Google map web service is used to provide the geographic positioning system (GPS)-based risk assessment to prevent the outbreak. It is used to represent each Zika virus (ZikaV)-infected user, mosquito-dense sites and breeding sites on the Google map that help the government healthcare authorities to control such risk-prone areas effectively and efficiently. The proposed system is deployed on Amazon EC2 cloud to evaluate its performance and accuracy using data set for 2 million users. Our system provides high accuracy of 94.5% for initial diagnosis of different users according to their symptoms and appropriate GPS-based risk assessment.

75 FR 25185 - Broadband Initiatives Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

..., excluding desktop or laptop computers, computer hardware and software (including anti-virus, anti-spyware, and other security software), audio or video equipment, computer network components... 10 desktop or laptop computers and individual workstations to be located within the rural library...

A comprehensive map of the influenza A virus replication cycle

PubMed Central

2013-01-01

Background Influenza is a common infectious disease caused by influenza viruses. Annual epidemics cause severe illnesses, deaths, and economic loss around the world. To better defend against influenza viral infection, it is essential to understand its mechanisms and associated host responses. Many studies have been conducted to elucidate these mechanisms, however, the overall picture remains incompletely understood. A systematic understanding of influenza viral infection in host cells is needed to facilitate the identification of influential host response mechanisms and potential drug targets. Description We constructed a comprehensive map of the influenza A virus (‘IAV’) life cycle (‘FluMap’) by undertaking a literature-based, manual curation approach. Based on information obtained from publicly available pathway databases, updated with literature-based information and input from expert virologists and immunologists, FluMap is currently composed of 960 factors (i.e., proteins, mRNAs etc.) and 456 reactions, and is annotated with ~500 papers and curation comments. In addition to detailing the type of molecular interactions, isolate/strain specific data are also available. The FluMap was built with the pathway editor CellDesigner in standard SBML (Systems Biology Markup Language) format and visualized as an SBGN (Systems Biology Graphical Notation) diagram. It is also available as a web service (online map) based on the iPathways+ system to enable community discussion by influenza researchers. We also demonstrate computational network analyses to identify targets using the FluMap. Conclusion The FluMap is a comprehensive pathway map that can serve as a graphically presented knowledge-base and as a platform to analyze functional interactions between IAV and host factors. Publicly available webtools will allow continuous updating to ensure the most reliable representation of the host-virus interaction network. The FluMap is available at http://www.influenza-x.org/flumap/. PMID:24088197

Ontological knowledge structure of intuitive biology

NASA Astrophysics Data System (ADS)

Martin, Suzanne Michele

It has become increasingly important for individuals to understand infections disease, as there has been a tremendous rise in viral and bacterial disease. This research examines systematic misconceptions regarding the characteristics of viruses and bacteria present in individuals previously educated in biological sciences at a college level. 90 pre-nursing students were administered the Knowledge Acquisition Device (KAD) which consists of 100 True/False items that included statements about the possible attributes of four entities: bacteria, virus, amoeba, and protein. Thirty pre-nursing students, who incorrectly stated that viruses were alive, were randomly assigned to three conditions. (1) exposed to information about the ontological nature of viruses, (2) Information about viruses, (3) control. In the condition that addressed the ontological nature of a virus, all of those participants were able to classify viruses correctly as not alive; however any items that required inferences, such as viruses come in male and female forms or viruses breed with each other to make baby viruses were still incorrectly answered by all conditions in the posttest. It appears that functional knowledge, ex. If a virus is alive or dead, or how it is structured, is not enough for an individual to have a full and accurate understanding of viruses. Ontological knowledge information may alter the functional knowledge but underlying inferences remain systematically incorrect.

Why Do Computer Viruses Survive In The Internet?

NASA Astrophysics Data System (ADS)

Ifti, Margarita; Neumann, Paul

2010-01-01

We use the three-species cyclic competition model (Rock-Paper-Scissors), described by reactions A+B→2B, B+C→2C, C+A→2A, for emulating a computer network with e-mail viruses. Different topologies of the network bring about different dynamics of the epidemics. When the parameters of the network are varied, it is observed that very high clustering coefficients are necessary for a pandemics to happen. The differences between the networks of computer users, e-mail networks, and social networks, as well as their role in determining the nature of epidemics are also discussed.

Online social networks—Paradise of computer viruses

NASA Astrophysics Data System (ADS)

Fan, W.; Yeung, K. H.

2011-01-01

Online social network services have attracted more and more users in recent years. So the security of social networks becomes a critical problem. In this paper, we propose a virus propagation model based on the application network of Facebook, which is the most popular among these social network service providers. We also study the virus propagation with an email virus model and compare the behaviors of a virus spreading on Facebook with the original email network. It is found that Facebook provides the same chance for a virus spreading while it gives a platform for application developers. And a virus will spread faster in the Facebook network if users of Facebook spend more time on it.

A new approach for detecting adventitious viruses shows Sf-rhabdovirus-negative Sf-RVN cells are suitable for safe biologicals production.

PubMed

Geisler, Christoph

2018-02-07

Adventitious viral contamination in cell substrates used for biologicals production is a major safety concern. A powerful new approach that can be used to identify adventitious viruses is a combination of bioinformatics tools with massively parallel sequencing technology. Typically, this involves mapping or BLASTN searching individual reads against viral nucleotide databases. Although extremely sensitive for known viruses, this approach can easily miss viruses that are too dissimilar to viruses in the database. Moreover, it is computationally intensive and requires reference cell genome databases. To avoid these drawbacks, we set out to develop an alternative approach. We reasoned that searching genome and transcriptome assemblies for adventitious viral contaminants using TBLASTN with a compact viral protein database covering extant viral diversity as the query could be fast and sensitive without a requirement for high performance computing hardware. We tested our approach on Spodoptera frugiperda Sf-RVN, a recently isolated insect cell line, to determine if it was contaminated with one or more adventitious viruses. We used Illumina reads to assemble the Sf-RVN genome and transcriptome and searched them for adventitious viral contaminants using TBLASTN with our viral protein database. We found no evidence of viral contamination, which was substantiated by the fact that our searches otherwise identified diverse sequences encoding virus-like proteins. These sequences included Maverick, R1 LINE, and errantivirus transposons, all of which are common in insect genomes. We also identified previously described as well as novel endogenous viral elements similar to ORFs encoded by diverse insect viruses. Our results demonstrate TBLASTN searching massively parallel sequencing (MPS) assemblies with a compact, manually curated viral protein database is more sensitive for adventitious virus detection than BLASTN, as we identified various sequences that encoded virus-like proteins, but had no similarity to viral sequences at the nucleotide level. Moreover, searches were fast without requiring high performance computing hardware. Our study also documents the enhanced biosafety profile of Sf-RVN as compared to other Sf cell lines, and supports the notion that Sf-RVN is highly suitable for the production of safe biologicals.

Atypical manifestations of Epstein-Barr virus in children: a diagnostic challenge.

PubMed

Bolis, Vasileios; Karadedos, Christos; Chiotis, Ioannis; Chaliasos, Nikolaos; Tsabouri, Sophia

2016-01-01

Clarify the frequency and the pathophysiological mechanisms of the rare manifestations of Epstein-Barr virus infection. Original research studies published in English between 1985 and 2015 were selected through a computer-assisted literature search (PubMed and Scopus). Computer searches used combinations of key words relating to "EBV infections" and "atypical manifestation." Epstein-Barr virus is a herpes virus responsible for a lifelong latent infection in almost every adult. The primary infection concerns mostly children and presents with the clinical syndrome of infectious mononucleosis. However, Epstein-Barr virus infection may exhibit numerous rare, atypical and threatening manifestations. It may cause secondary infections and various complications of the respiratory, cardiovascular, genitourinary, gastrointestinal, and nervous systems. Epstein-Barr virus also plays a significant role in pathogenesis of autoimmune diseases, allergies, and neoplasms, with Burkitt lymphoma as the main representative of the latter. The mechanisms of these manifestations are still unresolved. Therefore, the main suggestions are direct viral invasion and chronic immune response due to the reactivation of the latent state of the virus, or even various DNA mutations. Physicians should be cautious about uncommon presentations of the viral infection and consider EBV as a causative agent when they encounter similar clinical pictures. Copyright © 2016 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Multiscale Simulation of Microbe Structure and Dynamics

PubMed Central

Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V.; Cheluvaraja, Srinath C.; Ortoleva, Peter J.

2012-01-01

A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin. PMID:21802438

A Computer Security Course in the Undergraduate Computer Science Curriculum.

ERIC Educational Resources Information Center

Spillman, Richard

1992-01-01

Discusses the importance of computer security and considers criminal, national security, and personal privacy threats posed by security breakdown. Several examples are given, including incidents involving computer viruses. Objectives, content, instructional strategies, resources, and a sample examination for an experimental undergraduate computer…

Development of a culturally appropriate computer-delivered tailored Internet-based health literacy intervention for Spanish-dominant Hispanics living with HIV.

PubMed

Jacobs, Robin J; Caballero, Joshua; Ownby, Raymond L; Kane, Michael N

2014-11-30

Low health literacy is associated with poor medication adherence in persons with human immunodeficiency virus (HIV), which can lead to poor health outcomes. As linguistic minorities, Spanish-dominant Hispanics (SDH) face challenges such as difficulties in obtaining and understanding accurate information about HIV and its treatment. Traditional health educational methods (e.g., pamphlets, talking) may not be as effective as delivering through alternate venues. Technology-based health information interventions have the potential for being readily available on desktop computers or over the Internet. The purpose of this research was to adapt a theoretically-based computer application (initially developed for English-speaking HIV-positive persons) that will provide linguistically and culturally appropriate tailored health education to Spanish-dominant Hispanics with HIV (HIV + SDH). A mixed methods approach using quantitative and qualitative interviews with 25 HIV + SDH and 5 key informants guided by the Information-Motivation-Behavioral (IMB) Skills model was used to investigate cultural factors influencing medication adherence in HIV + SDH. We used a triangulation approach to identify major themes within cultural contexts relevant to understanding factors related to motivation to adhere to treatment. From this data we adapted an automated computer-based health literacy intervention to be delivered in Spanish. Culture-specific motivational factors for treatment adherence in HIV + SDH persons that emerged from the data were stigma, familismo (family), mood, and social support. Using this data, we developed a culturally and linguistically adapted a tailored intervention that provides information about HIV infection, treatment, and medication related problem solving skills (proven effective in English-speaking populations) that can be delivered using touch-screen computers, tablets, and smartphones to be tested in a future study. Using a theoretically-grounded Internet-based eHealth education intervention that builds on knowledge and also targets core cultural determinants of adherence may prove a highly effective approach to improve health literacy and medication decision-making in this group.

Use of Obstetric Practice Web Sites to Distribute Zika Virus Information to Pregnant Women During a Zika Virus Outbreak.

PubMed

Lehnert, Jonathan D; Ellingson, Mallory K; Goryoka, Grace W; Kasturi, Raghuraj; Maier, Emily; Chamberlain, Allison T

To describe the current use of obstetric practice Web sites to disseminate Zika virus information to patients. Review of 913 randomly selected practice Web sites and associated social media accounts in January and August 2016. Obstetric practice Web sites and associated social media accounts, United States of America. N/A. Proportion of obstetric practice Web sites and linked social media accounts providing Zika virus information. Twenty-five percent and 35% of obstetric practice Web sites had information posted about Zika virus in January 2016 and August 2016, respectively. Between the 2 time points, the proportion of practices posting Zika virus content on Facebook and Twitter declined (Facebook: 15% in January, 9% in August; Twitter: 12% in January, 8% in August). In August, the most frequently observed Zika virus-related content themes were the use of insect repellent (14%) and travel advisories (14%). At both time points, practices affiliated with large university hospitals were more likely to have posted information on Zika virus than independent OB/GYN-only practices: January: odds ratio (OR) (95% confidence interval [CI]) = 5.68 (3.50-9.20); August: OR (95% CI) = 8.37 (5.31-13.17). Similarly, practices associated with nonuniversity hospitals were more likely to have posted information than independent OB/GYN-only practices: January: OR (95% CI) = 2.71 (1.88-3.92); August: OR (95% CI) = 6.75 (4.75-9.60). Obstetric care practices are not fully utilizing their practice Web sites to relay Zika virus information to their patients. Since practitioner-sponsored Web sites have the capacity to directly reach the populations at greatest risk for Zika virus complications, public health professionals should consider adapting their materials and provider outreach campaigns to more easily accommodate Web site-based information dissemination during this type of public health emergency. There must be greater recognition of the value information gains in the eyes of the patient when it is validated by their own provider, especially when that patient is part of the highest-risk population for a given emergency. Public health organizations should strive to minimize the burden it takes for providers to relay useful resources to patients in order to maximize the impact that those resources can have.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

DOE PAGES

Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna; ...

2016-10-30

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs aremore » grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.« less

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs aremore » grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.« less

From Turing machines to computer viruses.

PubMed

Marion, Jean-Yves

2012-07-28

Self-replication is one of the fundamental aspects of computing where a program or a system may duplicate, evolve and mutate. Our point of view is that Kleene's (second) recursion theorem is essential to understand self-replication mechanisms. An interesting example of self-replication codes is given by computer viruses. This was initially explained in the seminal works of Cohen and of Adleman in the 1980s. In fact, the different variants of recursion theorems provide and explain constructions of self-replicating codes and, as a result, of various classes of malware. None of the results are new from the point of view of computability theory. We now propose a self-modifying register machine as a model of computation in which we can effectively deal with the self-reproduction and in which new offsprings can be activated as independent organisms.

Prevalence of human T-cell lymphotropic virus types 1 and 2 in blood donors of the Caruaru Blood Center (Hemope)

PubMed Central

de Lima, Waleska Mayara Gomes; Esteves, Fabrício Andrade Martins; Torres, Maria do Carmo Morais Rodrigues; Pires, Edna Suely Feitosa

2013-01-01

Background There is difficulty in gathering data on the prevalence of human T-cell lymphotropic virus in blood donors as confirmatory testing is not mandatory in Brazil. This suggests there may be an underreporting of the prevalence. Objective To estimate the prevalence of human T-cell lymphotropic virus types 1 and 2 in donors of a blood bank in Caruaru, Brazil. Methods This was an observational, epidemiological, descriptive, longitudinal and retrospective study with information about the serology of donors of the Caruaru Blood Center, Fundação de Hematologia e Hemoterapia de Pernambuco (Hemope) from May 2006 to December 2010. The data were analyzed using the Excel 2010 computer program (Microsoft Office®). Results Of 61,881 donors, 60 (0.096%) individuals were identified as potential carriers of human T-cell lymphotropic virus types 1 and 2. Of these, 28 (0.045%) were positive and 32 (0.051%) had inconclusive results in the serological screening. Forty-five (0.072%) were retested; 17 were positive (0.027%) and 3 inconclusive (0.005%). After confirmatory tests, 8 were positive (0.013%). Six (75%) of the confirmed cases were women. Conclusion Epidemiological surveys like this are very important in order to create campaigns to attract donors and reduce the costs of laboratory tests. PMID:24106445

77 FR 58997 - Agency Information Collection Activities; Proposed Collection; Comment Request; Guidance on...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-25

... Detection of Specific Novel Influenza A Viruses AGENCY: Food and Drug Administration, HHS. ACTION: Notice... reagents for detection of specific novel influenza A viruses. DATES: Submit either electronic or written... of information technology. Guidance on Reagents for Detection of Specific Novel Influenza A Viruses...

HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1*

PubMed Central

Hernandez, Anna; Buch, Anna; Sodeik, Beate; Cristea, Ileana Mihaela

2016-01-01

Human herpesviruses are widespread human pathogens with a remarkable impact on worldwide public health. Despite intense decades of research, the molecular details in many aspects of their function remain to be fully characterized. To unravel the details of how these viruses operate, a thorough understanding of the relationships between the involved components is key. Here, we present HVint, a novel protein-protein intraviral interaction resource for herpes simplex virus type 1 (HSV-1) integrating data from five external sources. To assess each interaction, we used a scoring scheme that takes into consideration aspects such as the type of detection method and the number of lines of evidence. The coverage of the initial interactome was further increased using evolutionary information, by importing interactions reported for other human herpesviruses. These latter interactions constitute, therefore, computational predictions for potential novel interactions in HSV-1. An independent experimental analysis was performed to confirm a subset of our predicted interactions. This subset covers proteins that contribute to nuclear egress and primary envelopment events, including VP26, pUL31, pUL40, and the recently characterized pUL32 and pUL21. Our findings support a coordinated crosstalk between VP26 and proteins such as pUL31, pUS9, and the CSVC complex, contributing to the development of a model describing the nuclear egress and primary envelopment pathways of newly synthesized HSV-1 capsids. The results are also consistent with recent findings on the involvement of pUL32 in capsid maturation and early tegumentation events. Further, they open the door to new hypotheses on virus-specific regulators of pUS9-dependent transport. To make this repository of interactions readily accessible for the scientific community, we also developed a user-friendly and interactive web interface. Our approach demonstrates the power of computational predictions to assist in the design of targeted experiments for the discovery of novel protein-protein interactions. PMID:27384951

Social Media Messages in an Emerging Health Crisis: Tweeting Bird Flu.

PubMed

Vos, Sarah C; Buckner, Marjorie M

2016-01-01

Limited research has examined the messages produced about health-related crises on social media platforms and whether these messages contain content that would allow individuals to make sense of a crisis and respond effectively. This study uses the crisis and emergency risk communication (CERC) framework to evaluate the content of messages sent via Twitter during an emerging crisis. Using manual and computer-driven content analysis methods, the study analyzed 25,598 tweets about the H7N9 virus that were produced in April 2013. The study found that a large proportion of messages contained sensemaking information. However, few tweets contained efficacy information that would help individuals respond to the crisis appropriately. Implications and recommendations for practice and future study are discussed.

The Impact of the Network Topology on the Viral Prevalence: A Node-Based Approach

PubMed Central

Yang, Lu-Xing; Draief, Moez; Yang, Xiaofan

2015-01-01

This paper addresses the impact of the structure of the viral propagation network on the viral prevalence. For that purpose, a new epidemic model of computer virus, known as the node-based SLBS model, is proposed. Our analysis shows that the maximum eigenvalue of the underlying network is a key factor determining the viral prevalence. Specifically, the value range of the maximum eigenvalue is partitioned into three subintervals: viruses tend to extinction very quickly or approach extinction or persist depending on into which subinterval the maximum eigenvalue of the propagation network falls. Consequently, computer virus can be contained by adjusting the propagation network so that its maximum eigenvalue falls into the desired subinterval. PMID:26222539

Online Hand Holding in Fixing Computer Glitches

ERIC Educational Resources Information Center

Goldsborough, Reid

2005-01-01

According to most surveys, computer manufacturers such as HP puts out reliable products, and computers in general are less troublesome than in the past. But personal computers are still prone to bugs, conflicts, viruses, spyware infestations, hacker and phishing attacks, and--most of all--user error. Unfortunately, technical support from computer…

Novel Nipah virus immune-antagonism strategy revealed by experimental and computational study.

PubMed

Seto, Jeremy; Qiao, Liang; Guenzel, Carolin A; Xiao, Sa; Shaw, Megan L; Hayot, Fernand; Sealfon, Stuart C

2010-11-01

Nipah virus is an emerging pathogen that causes severe disease in humans. It expresses several antagonist proteins that subvert the immune response and that may contribute to its pathogenicity. Studies of its biology are difficult due to its high pathogenicity and requirement for biosafety level 4 containment. We integrated experimental and computational methods to elucidate the effects of Nipah virus immune antagonists. Individual Nipah virus immune antagonists (phosphoprotein and V and W proteins) were expressed from recombinant Newcastle disease viruses, and the responses of infected human monocyte-derived dendritic cells were determined. We developed an ordinary differential equation model of the infectious process that that produced results with a high degree of correlation with these experimental results. In order to simulate the effects of wild-type virus, the model was extended to incorporate published experimental data on the time trajectories of immune-antagonist production. These data showed that the RNA-editing mechanism utilized by the wild-type Nipah virus to produce immune antagonists leads to a delay in the production of the most effective immune antagonists, V and W. Model simulations indicated that this delay caused a disconnection between attenuation of the antiviral response and suppression of inflammation. While the antiviral cytokines were efficiently suppressed at early time points, some early inflammatory cytokine production occurred, which would be expected to increase vascular permeability and promote virus spread and pathogenesis. These results suggest that Nipah virus has evolved a unique immune-antagonist strategy that benefits from controlled expression of multiple antagonist proteins with various potencies.

SAMPLING VIRUSES FROM SOIL

EPA Science Inventory

This chapter describes in detail methods for detecting viruses of bacteria and humans in soil. Methods also are presented for the assay of these viruses. Reference sources are provided for information on viruses of plants.

Computational analysis of Ebolavirus data: prospects, promises and challenges.

PubMed

Michaelis, Martin; Rossman, Jeremy S; Wass, Mark N

2016-08-15

The ongoing Ebola virus (also known as Zaire ebolavirus, a member of the Ebolavirus family) outbreak in West Africa has so far resulted in >28000 confirmed cases compared with previous Ebolavirus outbreaks that affected a maximum of a few hundred individuals. Hence, Ebolaviruses impose a much greater threat than we may have expected (or hoped). An improved understanding of the virus biology is essential to develop therapeutic and preventive measures and to be better prepared for future outbreaks by members of the Ebolavirus family. Computational investigations can complement wet laboratory research for biosafety level 4 pathogens such as Ebolaviruses for which the wet experimental capacities are limited due to a small number of appropriate containment laboratories. During the current West Africa outbreak, sequence data from many Ebola virus genomes became available providing a rich resource for computational analysis. Here, we consider the studies that have already reported on the computational analysis of these data. A range of properties have been investigated including Ebolavirus evolution and pathogenicity, prediction of micro RNAs and identification of Ebolavirus specific signatures. However, the accuracy of the results remains to be confirmed by wet laboratory experiments. Therefore, communication and exchange between computational and wet laboratory researchers is necessary to make maximum use of computational analyses and to iteratively improve these approaches. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Compensating for cross-reactions using avidity and computation in a suspension multiplex immunoassay for serotyping of Zika versus other flavivirus infections.

PubMed

Rönnberg, Bengt; Gustafsson, Åke; Vapalahti, Olli; Emmerich, Petra; Lundkvist, Åke; Schmidt-Chanasit, Jonas; Blomberg, Jonas

2017-10-01

The recent spread of Zika virus (ZIKV) in the Americas and Asia necessitates an increased preparedness for improved maternal and perinatal health and blood safety. However, serological cross-reactions, especially to Dengue virus (DENV), complicate ZIKV antibody serodiagnosis. A novel "pan-Flavi" suspension multiplex immunoassay (PFSMIA) using 25 antigens, whole virus (WV), non-structural protein 1 (NS1), and envelope (E) proteins, from 7 zoonotic flaviviruses for specific detection of ZIKV and DENV IgM and IgG was developed. Patterns of antibody cross-reactivity, avidity, and kinetics were established in 104 sera from returning travelers with known ZIKV and DENV infections. PFSMIA gave IgM- and IgG-sensitivities for both viruses of 96-100%, compared to an immunofluorescence assay. Main IgM cross-reactions were to NS1, for IgG to the E and WV antigens. Infecting virus yielded reactivity to several antigens of the homologous virus, while cross-reactions tended to occur only to a single antigen from heterologous virus(es). A specificity-enhancing computer procedure took into account antibody isotype, number of antibody-reactive antigens per virus, avidity, average degree of cross-reactivity to heterologous flavivirus antigens, and reactivity changes in serial sera. It classified all 50 cases correctly. Applied to sera from 200 pregnant women and 173 blood donors from Sweden, one blood donor was found ZIKV NS1 IgM positive, and another as ZIKV NS1 IgG positive. These samples did not react with other ZIKV antigens and were thereby judged as false-positives. PFSMIA provided sensitive and specific ZIKV and DENV serology, warranting high-throughput serological surveillance and a minimized need for laborious and expensive virus neutralization assays.

Physician use of updated anti-virus software in a tertiary Nigerian hospital.

PubMed

Laabes, E P; Nyango, D D; Ayedima, M M; Ladep, N G

2010-01-01

While physicians are becoming increasingly dependent on computers and the internet, highly lethal malware continue to be loaded into cyberspace. We sought to assess the proportion of physicians with updated anti-virus software in Jos University Teaching Hospital Nigeria and to determine perceived barriers to getting updates. We used a pre-tested semi-structured self-administered questionnaire to conduct a cross-sectional survey among 118 physicians. The mean age (+/- SD) of subjects was 34 (+/- 4) years, with 94 male and 24 female physicians. Forty-two (36.5%) of 115 physicians with anti-virus software used an updated program (95% Cl: 27, 45). The top-three antivirus software were: McAfee 40 (33.9%), AVG 37 (31.4%) and Norton 17 (14.4%). Common infections were: Trojan horse 22 (29.7%), Brontok worm 8 (10.8%), and Ravmonlog.exe 5 (6.8%). Internet browsing with a firewall was an independent determinant for use of updated anti-virus software [OR 4.3, 95% CI, 1.86, 10.02; P < 0.001]. Busy schedule, 40 (33.9%) and lack of credit card 39 (33.1%) were perceived barriers to updating antivirus software. The use of regularly updated anti-virus software is sub-optimal among physicians implying vulnerability to computer viruses. Physicians should be careful with flash drives and should avoid being victims of the raging arms race between malware producers and anti-virus software developers.

78 FR 45929 - Agency Information Collection Activities; Announcement of Office of Management and Budget...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-30

...; Guidance on Reagents for Detection of Specific Novel Influenza A Viruses AGENCY: Food and Drug... Influenza A Viruses'' has been approved by the Office of Management and Budget (OMB) under the Paperwork... collection of information entitled ``Guidance on Reagents for Detection of Specific Novel Influenza A Viruses...

Information Security and Integrity Systems

NASA Technical Reports Server (NTRS)

1990-01-01

Viewgraphs from the Information Security and Integrity Systems seminar held at the University of Houston-Clear Lake on May 15-16, 1990 are presented. A tutorial on computer security is presented. The goals of this tutorial are the following: to review security requirements imposed by government and by common sense; to examine risk analysis methods to help keep sight of forest while in trees; to discuss the current hot topic of viruses (which will stay hot); to examine network security, now and in the next year to 30 years; to give a brief overview of encryption; to review protection methods in operating systems; to review database security problems; to review the Trusted Computer System Evaluation Criteria (Orange Book); to comment on formal verification methods; to consider new approaches (like intrusion detection and biometrics); to review the old, low tech, and still good solutions; and to give pointers to the literature and to where to get help. Other topics covered include security in software applications and development; risk management; trust: formal methods and associated techniques; secure distributed operating system and verification; trusted Ada; a conceptual model for supporting a B3+ dynamic multilevel security and integrity in the Ada runtime environment; and information intelligence sciences.

21 CFR 866.3900 - Varicella-zoster virus serological reagents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Varicella-zoster virus serological reagents. 866... Varicella-zoster virus serological reagents. (a) Identification. Varicella-zoster virus serological reagents... viruses and provides epidemiological information on these diseases. Varicella (chicken pox) is a mild...

21 CFR 866.3900 - Varicella-zoster virus serological reagents.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Varicella-zoster virus serological reagents. 866... Varicella-zoster virus serological reagents. (a) Identification. Varicella-zoster virus serological reagents... viruses and provides epidemiological information on these diseases. Varicella (chicken pox) is a mild...

21 CFR 866.3900 - Varicella-zoster virus serological reagents.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Varicella-zoster virus serological reagents. 866... Varicella-zoster virus serological reagents. (a) Identification. Varicella-zoster virus serological reagents... viruses and provides epidemiological information on these diseases. Varicella (chicken pox) is a mild...

21 CFR 866.3900 - Varicella-zoster virus serological reagents.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Varicella-zoster virus serological reagents. 866... Varicella-zoster virus serological reagents. (a) Identification. Varicella-zoster virus serological reagents... viruses and provides epidemiological information on these diseases. Varicella (chicken pox) is a mild...

21 CFR 866.3900 - Varicella-zoster virus serological reagents.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Varicella-zoster virus serological reagents. 866... Varicella-zoster virus serological reagents. (a) Identification. Varicella-zoster virus serological reagents... viruses and provides epidemiological information on these diseases. Varicella (chicken pox) is a mild...

IT Security Support for the Spaceport Command Control System Development

NASA Technical Reports Server (NTRS)

Varise, Brian

2014-01-01

My job title is IT Security support for the Spaceport Command & Control System Development. As a cyber-security analyst it is my job to ensure NASA's information stays safe from cyber threats, such as, viruses, malware and denial-of-service attacks by establishing and enforcing system access controls. Security is very important in the world of technology and it is used everywhere from personal computers to giant networks ran by Government agencies worldwide. Without constant monitoring analysis, businesses, public organizations and government agencies are vulnerable to potential harmful infiltration of their computer information system. It is my responsibility to ensure authorized access by examining improper access, reporting violations, revoke access, monitor information request by new programming and recommend improvements. My department oversees the Launch Control System and networks. An audit will be conducted for the LCS based on compliance with the Federal Information Security Management Act (FISMA) and The National Institute of Standards and Technology (NIST). I recently finished analyzing the SANS top 20 critical controls to give cost effective recommendations on various software and hardware products for compliance. Upon my completion of this internship, I will have successfully completed my duties as well as gain knowledge that will be helpful to my career in the future as a Cyber Security Analyst.

Prevalence of human influenza virus in Iran: Evidence from a systematic review and meta-analysis.

PubMed

Mozhgani, Sayed-Hamidreza; Zarei Ghobadi, Mohadeseh; Moeini, Sina; Pakzad, Reza; Kananizadeh, Pegah; Behzadian, Farida

2018-02-01

This systematic review and meta-analysis was conducted to consolidate the information on the prevalence of the human influenza virus, including H1N1 and H3N2 as well as B-type influenza across Iran from 2000 to December 2016. The literature search was based on keywords including "influenza and Iran", "human influenza", "prevalence", "relative frequency", "incidence", and "drug" in MEDLINE (PubMed), Web of Science, Scopus, ScienceDirect, the Iranian Research Institute for Information Science and Technology (IranDoc), the Regional Information Centre for Science & Technology (RICeST), and the Scientific Information Database (SID). The literature search revealed 25 prevalence and seven drug resistance studies. In order to investigate the publication bias among studies, funnel plots and Egger's test were used. Additionally, the statistical tests of I 2 , Chi 2 , and Tau 2 were computed, and the results were visualized with forest plots. A high level of I 2 and Chi 2 were obtained among studies, which are representative of the high variation and remarkable heterogeneity between studies. This may be because of various methodologies applied in the studies such as study design, age groups, and different populations. The prevalence of influenza H1N1, H3N2, and B in Iran have not yet been well evaluated. The heterogeneity among studies reveals that more attention should be paid to considering various factors, including gender, population size, and underlying conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Utility of Social Media in Providing Information on Zika Virus.

PubMed

Chandrasekaran, Neeraja; Gressick, Kimberly; Singh, Vivek; Kwal, Jaclyn; Cap, Natalia; Koru-Sengul, Tulay; Curry, Christine L

2017-10-23

Introduction In 2015, there was an outbreak of Zika virus in Brazil that spread throughout the Americas. The association of Zika virus with birth defects in infants born to infected pregnant women created concern for women of childbearing age. Social media is an important platform for health promotion, communication, and education on preventative methods during Zika virus outbreaks. Methods We evaluated the utility of social media on providing information regarding Zika virus. Facebook, Instagram, Twitter, and YouTube were utilized for our study. A search of the term "#Zikavirus" on Twitter and Instagram, and "Zika virus" on Facebook and YouTube was performed. The first 50 search results were analyzed from each source. Only English, Spanish, or Portuguese results were included. Results were categorized into three groups: "Useful", "Not Useful", or "Misleading". Results Search was conducted on December 17th, 2016, with 185 results. Forty (21.6%) were from Facebook, 50 (27%) from Twitter, 48 (25.9%) from YouTube, and 47 (25.4%) from Instagram. A total of 104 (56.22%) results were "Useful", 67 (36.2%) "Not Useful", and 14 (7.5%) were "Misleading". There were significantly more "Useful" results compared to "Not Useful" and "Misleading" results (Fisher's exact: p < 0.0001). Conclusion Social media is a useful resource for providing relevant information on Zika virus. Young women can utilize social media for Zika virus information. The role of social media in public health should be further investigated and established. Patient education interventions should focus on social media impact on behavior modification and education of public to recognize useful information.

Mathematical analysis of dengue virus antibody dynamics

NASA Astrophysics Data System (ADS)

Perera, Sulanie; Perera, SSN

2018-03-01

Dengue is a mosquito borne viral disease causing over 390 million infections worldwide per annum. Even though information on how infection is controlled and eradicated from the body is lacking, antibodies are thought to play a major role in clearing the virus. In this paper, a non-linear conceptual dynamical model with humoral immune response and absorption effect has been proposed for primary dengue infection. We have included the absorption of pathogens into uninfected cells since this effect causes the virus density in the blood to decrease. The time delay that arises in the production of antibodies was accounted and is introduced through a continuous function. The basic reproduction number R0 is computed and a detailed stability analysis is done. Three equilibrium states, namely the infection free equilibrium, no immune equilibrium and the endemic equilibrium were identified and the existence and the stability conditions of these steady states were obtained. Numerical simulations proved the results that were obtained. By establishing the characteristic equation of the model at infection free equilibrium, it was observed that the infection free equilibrium is locally asymptotically stable if R0 < 1. A threshold value for the antibody production rate was identified for which the infection gets completely cured even if R0 > 1. Stability regions are identified for infection free equilibrium state with respect to the external variables and it is observed as the virus burst rate increases, the stability regions would decrease. These results implied that for higher virus burst rates, other conditions in the body must be strong enough to eliminate the disease completely from the host. The effect of time delay of antibody production on virus dynamics is discussed. It was seen that as the time delay in production of antibodies increases, the time for viral decline also increased. Also it was observed that the virus count goes to negligible levels within 7 - 14 days after the onset of symptoms as seen in dengue infections.

How people react to Zika virus outbreaks on Twitter? A computational content analysis.

PubMed

Fu, King-Wa; Liang, Hai; Saroha, Nitin; Tse, Zion Tsz Ho; Ip, Patrick; Fung, Isaac Chun-Hai

2016-12-01

Zika-related Twitter incidence peaked after the World Health Organization declared an emergency. Five themes were identified from Zika-related Twitter content: (1) societal impact of the outbreak; (2) government, public and private sector, and general public responses to the outbreak; (3) pregnancy and microcephaly: negative health consequences related to pregnant women and babies; (4) transmission routes; and (5) case reports. User-generated contents sites were preferred direct information channels rather than those of the government authorities. Copyright © 2016 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Information Entropy Analysis of the H1N1 Genetic Code

NASA Astrophysics Data System (ADS)

Martwick, Andy

2010-03-01

During the current H1N1 pandemic, viral samples are being obtained from large numbers of infected people world-wide and are being sequenced on the NCBI Influenza Virus Resource Database. The information entropy of the sequences was computed from the probability of occurrence of each nucleotide base at every position of each set of sequences using Shannon's definition of information entropy, [ H=∑bpb,2( 1pb ) ] where H is the observed information entropy at each nucleotide position and pb is the probability of the base pair of the nucleotides A, C, G, U. Information entropy of the current H1N1 pandemic is compared to reference human and swine H1N1 entropy. As expected, the current H1N1 entropy is in a low entropy state and has a very large mutation potential. Using the entropy method in mature genes we can identify low entropy regions of nucleotides that generally correlate to critical protein function.

Real-Time Evolution of Zika Virus Disease Outbreak, Roatán, Honduras.

PubMed

Brooks, Trevor; Roy-Burman, Arup; Tuholske, Cascade; Busch, Michael P; Bakkour, Sonia; Stone, Mars; Linnen, Jeffrey M; Gao, Kui; Coleman, Jayleen; Bloch, Evan M

2017-08-01

A Zika virus disease outbreak occurred in Roatán, Honduras, during September 2015-July 2016. Blood samples and clinical information were obtained from 183 patients given a clinical diagnosis of suspected dengue virus infection. A total of 79 patients were positive for Zika virus, 13 for chikungunya virus, and 6 for dengue virus.

vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments

PubMed Central

2010-01-01

Background The replication rate (or fitness) between viral variants has been investigated in vivo and in vitro for human immunodeficiency virus (HIV). HIV fitness plays an important role in the development and persistence of drug resistance. The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness. Results Based on a mathematical model and several statistical methods (least-squares approach and measurement error models), a Web-based computing tool has been developed for improving estimation of virus fitness in growth competition assays of human immunodeficiency virus type 1 (HIV-1). Conclusions Unlike the two-point calculation used in previous studies, the estimation here uses linear regression methods with all observed data in the competition experiment to more accurately estimate relative viral fitness parameters. The dilution factor is introduced for making the computational tool more flexible to accommodate various experimental conditions. This Web-based tool is implemented in C# language with Microsoft ASP.NET, and is publicly available on the Web at http://bis.urmc.rochester.edu/vFitness/. PMID:20482791

vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments.

PubMed

Ma, Jingming; Dykes, Carrie; Wu, Tao; Huang, Yangxin; Demeter, Lisa; Wu, Hulin

2010-05-18

The replication rate (or fitness) between viral variants has been investigated in vivo and in vitro for human immunodeficiency virus (HIV). HIV fitness plays an important role in the development and persistence of drug resistance. The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness. Based on a mathematical model and several statistical methods (least-squares approach and measurement error models), a Web-based computing tool has been developed for improving estimation of virus fitness in growth competition assays of human immunodeficiency virus type 1 (HIV-1). Unlike the two-point calculation used in previous studies, the estimation here uses linear regression methods with all observed data in the competition experiment to more accurately estimate relative viral fitness parameters. The dilution factor is introduced for making the computational tool more flexible to accommodate various experimental conditions. This Web-based tool is implemented in C# language with Microsoft ASP.NET, and is publicly available on the Web at http://bis.urmc.rochester.edu/vFitness/.

38 CFR 1.486 - Disclosure of information related to infection with the human immunodeficiency virus to public...

Code of Federal Regulations, 2014 CFR

2014-07-01

... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false Disclosure of information related to infection with the human immunodeficiency virus to public health authorities. 1.486 Section 1... immunodeficiency virus to public health authorities. (a) In the case of any record which is maintained in...

38 CFR 1.486 - Disclosure of information related to infection with the human immunodeficiency virus to public...

Code of Federal Regulations, 2012 CFR

2012-07-01

... 38 Pensions, Bonuses, and Veterans' Relief 1 2012-07-01 2012-07-01 false Disclosure of information related to infection with the human immunodeficiency virus to public health authorities. 1.486 Section 1... immunodeficiency virus to public health authorities. (a) In the case of any record which is maintained in...

38 CFR 1.486 - Disclosure of information related to infection with the human immunodeficiency virus to public...

Code of Federal Regulations, 2013 CFR

2013-07-01

... 38 Pensions, Bonuses, and Veterans' Relief 1 2013-07-01 2013-07-01 false Disclosure of information related to infection with the human immunodeficiency virus to public health authorities. 1.486 Section 1... immunodeficiency virus to public health authorities. (a) In the case of any record which is maintained in...

Crispen's Five Antivirus Rules.

ERIC Educational Resources Information Center

Crispen, Patrick Douglas

2000-01-01

Explains five rules to protect computers from viruses. Highlights include commercial antivirus software programs and the need to upgrade them periodically (every year to 18 months); updating virus definitions at least weekly; scanning attached files from email with antivirus software before opening them; Microsoft Word macro protection; and the…

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

PubMed

Paez-Espino, David; Chen, I-Min A; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Huang, Jinghua; Markowitz, Victor M; Nielsen, Torben; Huntemann, Marcel; K Reddy, T B; Pavlopoulos, Georgios A; Sullivan, Matthew B; Campbell, Barbara J; Chen, Feng; McMahon, Katherine; Hallam, Steve J; Denef, Vincent; Cavicchioli, Ricardo; Caffrey, Sean M; Streit, Wolfgang R; Webster, John; Handley, Kim M; Salekdeh, Ghasem H; Tsesmetzis, Nicolas; Setubal, Joao C; Pope, Phillip B; Liu, Wen-Tso; Rivers, Adam R; Ivanova, Natalia N; Kyrpides, Nikos C

2017-01-04

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genomic Characterization of the Genus Nairovirus (Family Bunyaviridae).

PubMed

Kuhn, Jens H; Wiley, Michael R; Rodriguez, Sergio E; Bào, Yīmíng; Prieto, Karla; Travassos da Rosa, Amelia P A; Guzman, Hilda; Savji, Nazir; Ladner, Jason T; Tesh, Robert B; Wada, Jiro; Jahrling, Peter B; Bente, Dennis A; Palacios, Gustavo

2016-06-10

Nairovirus, one of five bunyaviral genera, includes seven species. Genomic sequence information is limited for members of the Dera Ghazi Khan, Hughes, Qalyub, Sakhalin, and Thiafora nairovirus species. We used next-generation sequencing and historical virus-culture samples to determine 14 complete and nine coding-complete nairoviral genome sequences to further characterize these species. Previously unsequenced viruses include Abu Mina, Clo Mor, Great Saltee, Hughes, Raza, Sakhalin, Soldado, and Tillamook viruses. In addition, we present genomic sequence information on additional isolates of previously sequenced Avalon, Dugbe, Sapphire II, and Zirqa viruses. Finally, we identify Tunis virus, previously thought to be a phlebovirus, as an isolate of Abu Hammad virus. Phylogenetic analyses indicate the need for reassignment of Sapphire II virus to Dera Ghazi Khan nairovirus and reassignment of Hazara, Tofla, and Nairobi sheep disease viruses to novel species. We also propose new species for the Kasokero group (Kasokero, Leopards Hill, Yogue viruses), the Ketarah group (Gossas, Issyk-kul, Keterah/soft tick viruses) and the Burana group (Wēnzhōu tick virus, Huángpí tick virus 1, Tǎchéng tick virus 1). Our analyses emphasize the sister relationship of nairoviruses and arenaviruses, and indicate that several nairo-like viruses (Shāyáng spider virus 1, Xīnzhōu spider virus, Sānxiá water strider virus 1, South Bay virus, Wǔhàn millipede virus 2) require establishment of novel genera in a larger nairovirus-arenavirus supergroup.

GeneChip Resequencing of the Smallpox Virus Genome Can Identify Novel Strains: a Biodefense Application▿

PubMed Central

Sulaiman, Irshad M.; Tang, Kevin; Osborne, John; Sammons, Scott; Wohlhueter, Robert M.

2007-01-01

We developed a set of seven resequencing GeneChips, based on the complete genome sequences of 24 strains of smallpox virus (variola virus), for rapid characterization of this human-pathogenic virus. Each GeneChip was designed to analyze a divergent segment of approximately 30,000 bases of the smallpox virus genome. This study includes the hybridization results of 14 smallpox virus strains. Of the 14 smallpox virus strains hybridized, only 7 had sequence information included in the design of the smallpox virus resequencing GeneChips; similar information for the remaining strains was not tiled as a reference in these GeneChips. By use of variola virus-specific primers and long-range PCR, 22 overlapping amplicons were amplified to cover nearly the complete genome and hybridized with the smallpox virus resequencing GeneChip set. These GeneChips were successful in generating nucleotide sequences for all 14 of the smallpox virus strains hybridized. Analysis of the data indicated that the GeneChip resequencing by hybridization was fast and reproducible and that the smallpox virus resequencing GeneChips could differentiate the 14 smallpox virus strains characterized. This study also suggests that high-density resequencing GeneChips have potential biodefense applications and may be used as an alternate tool for rapid identification of smallpox virus in the future. PMID:17182757

Viral ancestors of antiviral systems.

PubMed

Villarreal, Luis P

2011-10-01

All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the 'Big Bang' theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.

Viral Ancestors of Antiviral Systems

PubMed Central

Villarreal, Luis P.

2011-01-01

All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the ‘Big Bang’ theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features. PMID:22069523

Real-Time Evolution of Zika Virus Disease Outbreak, Roatán, Honduras

PubMed Central

Roy-Burman, Arup; Tuholske, Cascade; Busch, Michael P.; Bakkour, Sonia; Stone, Mars; Linnen, Jeffrey M.; Gao, Kui; Coleman, Jayleen; Bloch, Evan M.

2017-01-01

A Zika virus disease outbreak occurred in Roatán, Honduras, during September 2015–July 2016. Blood samples and clinical information were obtained from 183 patients given a clinical diagnosis of suspected dengue virus infection. A total of 79 patients were positive for Zika virus, 13 for chikungunya virus, and 6 for dengue virus. PMID:28514227

Among the New Worlds.

ERIC Educational Resources Information Center

Algeo, John; Algeo, Adele

1989-01-01

Presents definitions and examples of usage of late-twentieth century American words and terms, including: bite, dramedy, photo op, photo opportunist, safe computer practice, sound bite, teflon, trapdoor, vaccination program, computer virus, and wait state. (CB)

Zika Virus and Pregnancy.

PubMed

Stagg, Denise; Hurst, Helen M

2016-01-01

Recent outbreaks of Zika virus and reports linking infection in pregnant women with microcephaly in newborns have caused concern worldwide. Information has been evolving rapidly. Nurses and other clinicians, especially those who work with women of childbearing age, play a pivotal role in disseminating accurate information and identifying potential cases of Zika virus infection. © 2016 AWHONN, the Association of Women’s Health, Obstetric and Neonatal Nurses.

Microcephaly: computational and organotypic modeling of a ...

EPA Pesticide Factsheets

lecture discusses computational and organotypic models of microcephaly in an AOP Framework and ToxCast assays. Lecture slide presentation at UNC Chapel Hill for Advanced Toxicology course lecture on Computational Approaches to Developmental and Reproductive Toxicology with presentation on computational and organotypic modeling of a complex human birth defect microcephaly with is associated with the recent Zika virus outbreak.

Top 10 Threats to Computer Systems Include Professors and Students

ERIC Educational Resources Information Center

Young, Jeffrey R.

2008-01-01

User awareness is growing in importance when it comes to computer security. Not long ago, keeping college networks safe from cyberattackers mainly involved making sure computers around campus had the latest software patches. New computer worms or viruses would pop up, taking advantage of some digital hole in the Windows operating system or in…

Grapevine fleck virus-like viruses in Vitis.

PubMed

Sabanadzovic, S; Abou-Ghanem, N; Castellano, M A; Digiaro, M; Martelli, G P

2000-01-01

Two sets of degenerate primers for the specific amplification of 572-575 nt and 386 nt segments of the methyltransferase and RNA- dependent RNA polymerase cistrons of members of the genera Tymovirus and Marafivirus and of the unassigned virus Grapevine fleck virus (GFkV) were designed on the basis of available sequences. These primers were used for amplifying and subsequent cloning and sequencing part of the open reading frame 1 of the genome of GFkV, Grapevine asteroid mosaic-associated virus (GAMaV) and of another previously unreported virus, for which the name Grapevine red globe virus (GRGV) is proposed. Computer-assisted analysis of the amplified genome portions showed that the three grapevine viruses are phylogenetically related with one another and with sequenced tymoviruses and marafiviruses. The relationships with tymoviruses was confirmed by the type of ultrastructural modifications induced in the host cells. RdRp-specific degenerate primers were successfully used for the aspecific detection of the three viruses in crude grapevine sap extracts. Specific virus identification was obtained with RT-PCR using antisense virus-specific primers.

Monitoring the antigenic evolution of human influenza A viruses to understand how and when viruses escape from existing immunity.

PubMed

Liao, Yu-Chieh; Lin, Hsin-Hung; Lin, Chieh-Hua

2013-06-11

The World Health Organization (WHO) organizes consultations in February and September of each year, spearheaded by an advisory group of experts to analyze influenza surveillance data generated by the WHO Global Influenza Surveillance and Response System (GISRS). The purpose of these consultations is to recommend the composition on influenza virus vaccines for the northern and southern hemispheres, respectively. The latest news of influenza viruses is made available to the public and updated on the WHO website. Although WHO discloses the manner in which it has made the recommendation, usually by considering epidemiological and clinical information to analyze the antigenic and genetic characteristics of seasonal influenza viruses, most individuals do not possess an understanding of antigenic drift and when it occurs. We have constructed a web server, named Fluctrl, and implemented a pipeline whereby HA sequence data is downloaded from the Influenza Virus Resource at NCBI along with their isolation information including isolation year and location, which are parsed and managed in MySQL database. By analyzing the frequency of each amino acid residue of the HA1 domain expressed by the viruses on annual basis, users are able to obtain evolutionary dynamics of human influenza viruses corresponding with epidemics. Users are able to upload and analyze their HA1 sequences for generating evolutionary dynamics. In addition, a distribution of amino acid residues at a particular site is represented geographically to trace the location where antigenic variants are seeded. Fluctrl is constructed for monitoring the antigenic evolution of human influenza A viruses. This tool is intended to inform the general public how and when influenza viruses evade the human body's immunity. Furthermore, leveraging the geographic information, the original locations of emerging influenza viruses can be traced. Fluctrl is freely accessible at http://sb.nhri.org.tw/fluctrl.

Animal Viruses Probe dataset (AVPDS) for microarray-based diagnosis and identification of viruses.

PubMed

Yadav, Brijesh S; Pokhriyal, Mayank; Vasishtha, Dinesh P; Sharma, Bhaskar

2014-03-01

AVPDS (Animal Viruses Probe dataset) is a dataset of virus-specific and conserve oligonucleotides for identification and diagnosis of viruses infecting animals. The current dataset contain 20,619 virus specific probes for 833 viruses and their subtypes and 3,988 conserved probes for 146 viral genera. Dataset of virus specific probe has been divided into two fields namely virus name and probe sequence. Similarly conserved probes for virus genera table have genus, and subgroup within genus name and probe sequence. The subgroup within genus is artificially divided subgroups with no taxonomic significance and contains probes which identifies viruses in that specific subgroup of the genus. Using this dataset we have successfully diagnosed the first case of Newcastle disease virus in sheep and reported a mixed infection of Bovine viral diarrhea and Bovine herpesvirus in cattle. These dataset also contains probes which cross reacts across species experimentally though computationally they meet specifications. These probes have been marked. We hope that this dataset will be useful in microarray-based detection of viruses. The dataset can be accessed through the link https://dl.dropboxusercontent.com/u/94060831/avpds/HOME.html.

Comparison of the structures of three circoviruses: chicken anemia virus, porcine circovirus type 2, and beak and feather disease virus.

PubMed

Crowther, R A; Berriman, J A; Curran, W L; Allan, G M; Todd, D

2003-12-01

Circoviruses are small, nonenveloped icosahedral animal viruses characterized by circular single-stranded DNA genomes. Their genomes are the smallest possessed by animal viruses. Infections with circoviruses, which can lead to economically important diseases, frequently result in virus-induced damage to lymphoid tissue and immunosuppression. Within the family Circoviridae, different genera are distinguished by differences in genomic organization. Thus, Chicken anemia virus is in the genus Gyrovirus, while porcine circoviruses and Beak and feather disease virus belong to the genus CIRCOVIRUS: Little is known about the structures of circoviruses. Accordingly, we investigated the structures of these three viruses with a view to determining whether they are related. Three-dimensional maps computed from electron micrographs showed that all three viruses have a T=1 organization with capsids formed from 60 subunits. Porcine circovirus type 2 and beak and feather disease virus show similar capsid structures with flat pentameric morphological units, whereas chicken anemia virus has stikingly different protruding pentagonal trumpet-shaped units. It thus appears that the structures of viruses in the same genus are related but that those of viruses in different genera are unrelated.

Feline leukemia virus and feline immunodeficiency virus in Canada: recommendations for testing and management.

PubMed

Little, Susan; Bienzle, Dorothee; Carioto, Lisa; Chisholm, Hugh; O'Brien, Elizabeth; Scherk, Margie

2011-08-01

Feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) are common and important infectious disease agents of cats in Canada. Seroprevalence data for FeLV and FIV in various populations of Canadian cats are reviewed and recommendations for testing and management of infections by these viruses in cats in Canada are presented. Retrovirus testing in Canada is infrequent in comparison with the United States, and efforts should be focused on reducing physical and other barriers to testing, and on education of veterinarians, veterinary team members, and cat owners regarding the importance of testing. New test methodologies for FeLV and FIV are emerging, and should be independently evaluated in order to provide practitioners with information on test reliability. Finally, more information is needed on FIV subtypes in Canada to improve diagnostics and vaccines, and to provide information on disease outcomes.

A mixed SIR-SIS model to contain a virus spreading through networks with two degrees

NASA Astrophysics Data System (ADS)

Essouifi, Mohamed; Achahbar, Abdelfattah

Due to the fact that the “nodes” and “links” of real networks are heterogeneous, to model computer viruses prevalence throughout the Internet, we borrow the idea of the reduced scale free network which was introduced recently. The purpose of this paper is to extend the previous deterministic two subchains of Susceptible-Infected-Susceptible (SIS) model into a mixed Susceptible-Infected-Recovered and Susceptible-Infected-Susceptible (SIR-SIS) model to contain the computer virus spreading over networks with two degrees. Moreover, we develop its stochastic counterpart. Due to the high protection and security taken for hubs class, we suggest to treat it by using SIR epidemic model rather than the SIS one. The analytical study reveals that the proposed model admits a stable viral equilibrium. Thus, it is shown numerically that the mean dynamic behavior of the stochastic model is in agreement with the deterministic one. Unlike the infection densities i2 and i which both tend to a viral equilibrium for both approaches as in the previous study, i1 tends to the virus-free equilibrium. Furthermore, since a proportion of infectives are recovered, the global infection density i is minimized. Therefore, the permanent presence of viruses in the network due to the lower-degree nodes class. Many suggestions are put forward for containing viruses propagation and minimizing their damages.

Identification of dual-tropic HIV-1 using evolved neural networks.

PubMed

Fogel, Gary B; Lamers, Susanna L; Liu, Enoch S; Salemi, Marco; McGrath, Michael S

2015-11-01

Blocking the binding of the envelope HIV-1 protein to immune cells is a popular concept for development of anti-HIV therapeutics. R5 HIV-1 binds CCR5, X4 HIV-1 binds CXCR4, and dual-tropic HIV-1 can bind either coreceptor for cellular entry. R5 viruses are associated with early infection and over time can evolve to X4 viruses that are associated with immune failure. Dual-tropic HIV-1 is less studied; however, it represents functional antigenic intermediates during the transition of R5 to X4 viruses. Viral tropism is linked partly to the HIV-1 envelope V3 domain, where the amino acid sequence helps dictate the receptor a particular virus will target; however, using V3 sequence information to identify dual-tropic HIV-1 isolates has remained difficult. Our goal in this study was to elucidate features of dual-tropic HIV-1 isolates that assist in the biological understanding of dual-tropism and develop an approach for their detection. Over 1559 HIV-1 subtype B sequences with known tropisms were analyzed. Each sequence was represented by 73 structural, biochemical and regional features. These features were provided to an evolved neural network classifier and evaluated using balanced and unbalanced data sets. The study resolved R5X4 viruses from R5 with an accuracy of 81.8% and from X4 with an accuracy of 78.8%. The approach also identified a set of V3 features (hydrophobicity, structural and polarity) that are associated with tropism transitions. The ability to distinguish R5X4 isolates will improve computational tropism decisions for R5 vs. X4 and assist in HIV-1 research and drug development efforts. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Finding and identifying the viral needle in the metagenomic haystack: trends and challenges

PubMed Central

Soueidan, Hayssam; Schmitt, Louise-Amélie; Candresse, Thierry; Nikolski, Macha

2015-01-01

Collectively, viruses have the greatest genetic diversity on Earth, occupy extremely varied niches and are likely able to infect all living organisms. Viral infections are an important issue for human health and cause considerable economic losses when agriculturally important crops or husbandry animals are infected. The advent of metagenomics has provided a precious tool to study viruses by sampling them in natural environments and identifying the genomic composition of a sample. However, reaching a clear recognition and taxonomic assignment of the identified viruses has been hampered by the computational difficulty of these problems. In this perspective paper we examine the trends in current research for the identification of viral sequences in a metagenomic sample, pinpoint the intrinsic computational difficulties for the identification of novel viral sequences within metagenomic samples, and suggest possible avenues to overcome them. PMID:25610431

OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery

PubMed Central

Perryman, Alexander L.; Horta Andrade, Carolina

2016-01-01

The Zika virus outbreak in the Americas has caused global concern. To help accelerate this fight against Zika, we launched the OpenZika project. OpenZika is an IBM World Community Grid Project that uses distributed computing on millions of computers and Android devices to run docking experiments, in order to dock tens of millions of drug-like compounds against crystal structures and homology models of Zika proteins (and other related flavivirus targets). This will enable the identification of new candidates that can then be tested in vitro, to advance the discovery and development of new antiviral drugs against the Zika virus. The docking data is being made openly accessible so that all members of the global research community can use it to further advance drug discovery studies against Zika and other related flaviviruses. PMID:27764115

OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery.

PubMed

Ekins, Sean; Perryman, Alexander L; Horta Andrade, Carolina

2016-10-01

The Zika virus outbreak in the Americas has caused global concern. To help accelerate this fight against Zika, we launched the OpenZika project. OpenZika is an IBM World Community Grid Project that uses distributed computing on millions of computers and Android devices to run docking experiments, in order to dock tens of millions of drug-like compounds against crystal structures and homology models of Zika proteins (and other related flavivirus targets). This will enable the identification of new candidates that can then be tested in vitro, to advance the discovery and development of new antiviral drugs against the Zika virus. The docking data is being made openly accessible so that all members of the global research community can use it to further advance drug discovery studies against Zika and other related flaviviruses.

Adoption of preventive measures during and after the 2009 influenza A (H1N1) virus pandemic peak in Spain.

PubMed

Agüero, Fernando; Adell, Manel Nebot; Pérez Giménez, Anna; López Medina, María José; Garcia Continente, Xavier

2011-09-01

This study describes the preventive measures adopted by the Spanish population towards 2009 influenza A (H1N1) virus and their associated factors. An anonymous computer-assisted telephone interview survey was conducted in Spain in December 2009 and February 2010. Respondents were asked about their perceptions of influenza A (H1N1) virus and the preventive measures adopted. Factors associated with the adoption of preventive measures were assessed by logistic regression analyses. Out of 4892 households approached, 1627 valid responses were obtained (response rate of 33.3%). The most commonly adopted preventive measures were respiratory hygiene and hand washing. Factors independently associated with the adoption of the preventive measures recommended by the Spanish Ministry of Health were female gender, higher educational level, size of municipality of residence >50,000 inhabitants, high perceived susceptibility to infection, high perceived effectiveness of the measures and high perceived usefulness of the information provided by the government. The presence of school-aged children in household was associated with purchasing masks and hand sanitizer. In addition to demographic factors, modifiable factors such as personal beliefs and expectations play a role in the adoption of preventive measures. Copyright © 2011 Elsevier Inc. All rights reserved.

Simulation models examining the effect of Brugian filariasis on dengue epidemics.

PubMed

Vaughan, Jefferson A; Focks, Dana A; Turell, Michael J

2009-01-01

Concurrent ingestion of microfilariae (mf) and arboviruses by mosquitoes can enhance the transmission of virus compared with when virus is ingested alone. We studied the effect of mf enhancement on the extrinsic incubation period (EIP) of dengue 1 virus within Aedes aegypti mosquitoes by feeding mosquitoes on blood that either contained virus plus Brugia malayi mf or virus only. Mosquitoes were sampled over time to determine viral dissemination rates. Co-ingestion of mf and virus reduced viral EIP by over half. We used the computer simulation program, DENSiM, to compare the predicted patterns of dengue incidence that would result from such a shortened EIP versus the EIP derived from the control (i.e., virus only) group of mosquitoes. Results indicated that, over the 14-year simulation period, mf-induced acceleration of the EIP would generate more frequent (but not necessarily more severe) epidemics. Potential interactions between arboviruses and hematozoans deserve closer scrutiny.

Iterative projection algorithms for ab initio phasing in virus crystallography.

PubMed

Lo, Victor L; Kingston, Richard L; Millane, Rick P

2016-12-01

Iterative projection algorithms are proposed as a tool for ab initio phasing in virus crystallography. The good global convergence properties of these algorithms, coupled with the spherical shape and high structural redundancy of icosahedral viruses, allows high resolution phases to be determined with no initial phase information. This approach is demonstrated by determining the electron density of a virus crystal with 5-fold non-crystallographic symmetry, starting with only a spherical shell envelope. The electron density obtained is sufficiently accurate for model building. The results indicate that iterative projection algorithms should be routinely applicable in virus crystallography, without the need for ancillary phase information. Copyright © 2016 Elsevier Inc. All rights reserved.

A review of feline leukemia virus and feline immunodeficiency virus seroprevalence in cats in Canada.

PubMed

Little, Susan

2011-10-15

Feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) are common and important infectious diseases of cats in Canada. Prevalence data are necessary to define prophylactic, management, and therapeutic measures for stray, feral and owned cats. Recently, comprehensive data on the seroprevalence of retrovirus infections of cats in Canada have become available and are reviewed. Further investigation into geographic variations in retrovirus seroprevalence within Canada is warranted, and may provide information to improve recommendations for testing and prevention. As well, more information is needed on FIV subtypes in Canada to improve diagnostics and vaccines, as well as to provide information on disease outcomes. Copyright © 2011 Elsevier B.V. All rights reserved.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

PubMed Central

Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-01

Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. PMID:29040670

Development of the Large-Scale Oligonucleotide Chip for the Diagnosis of Plant Viruses and its Practical Use

PubMed Central

Nam, Moon; Kim, Jeong-Seon; Lim, Seungmo; Park, Chung Youl; Kim, Jeong-Gyu; Choi, Hong-Soo; Lim, Hyoun-Sub; Moon, Jae Sun; Lee, Su-Heon

2014-01-01

A large-scale oligonucleotide (LSON) chip was developed for the detection of the plant viruses with known genetic information. The LSON chip contains two sets of 3,978 probes for 538 species of targets including plant viruses, satellite RNAs and viroids. A hundred forty thousand probes, consisting of isolate-, species- and genus-specific probes respectively, are designed from 20,000 of independent nucleotide sequence of plant viruses. Based on the economic importance, the amount of genome information, and the number of strains and/or isolates, one to fifty-one probes for each target virus are selected and spotted on the chip. The standard and field samples for the analysis of the LSON chip have been prepared and tested by RT-PCR. The probe’s specific and/or nonspecific reaction patterns by LSON chip allow us to diagnose the unidentified viruses. Thus, the LSON chip in this study could be highly useful for the detection of unexpected plant viruses, the monitoring of emerging viruses and the fluctuation of the population of major viruses in each plant. PMID:25288985

a Discrete Mathematical Model to Simulate Malware Spreading

NASA Astrophysics Data System (ADS)

Del Rey, A. Martin; Sánchez, G. Rodriguez

2012-10-01

With the advent and worldwide development of Internet, the study and control of malware spreading has become very important. In this sense, some mathematical models to simulate malware propagation have been proposed in the scientific literature, and usually they are based on differential equations exploiting the similarities with mathematical epidemiology. The great majority of these models study the behavior of a particular type of malware called computer worms; indeed, to the best of our knowledge, no model has been proposed to simulate the spreading of a computer virus (the traditional type of malware which differs from computer worms in several aspects). In this sense, the purpose of this work is to introduce a new mathematical model not based on continuous mathematics tools but on discrete ones, to analyze and study the epidemic behavior of computer virus. Specifically, cellular automata are used in order to design such model.

Inferences from the Chronology of Dengue and Zika Outbreaks in Human Populations

NASA Astrophysics Data System (ADS)

McDonald, C.; Usmani, M.; Colwell, R. R.; Jutla, A.

2017-12-01

Dengue and Zika virus are becoming global health threats. With a recent resurgence of Zika virus in the Americas, there is a renewed interest to understand the physical pathways on interactions of vectors with human population. However, the challenge is in the availability of the vectors and viruses in regions that have suffered from outbreaks of these infections. Aedes spp. mosquitoes are the primary vectors of both Zika and Dengue viruses. The critical question is how one species of mosquito is able to transmit two different infections. Therefore, there is a need to understand the coherence and co-emergence behavior of Dengue and Zika infections. Our dominant hypothesis is that Dengue precedes Zika viruses. Here, we will show a global chronological trend of Dengue and Zika virus, or how an outbreak of dengue may lead to an outbreak of Zika virus, as regions with Zika virus outbreaks had demonstrated peak dengue incidences in prior months. We will also present global trends on key climatological and weather processes as a function of the emergence of these two viruses. We anticipate that this information can be used concurrently with geographical and meteorological information to more accurately predict the spread of Zika virus.

Genome-Wide Survey of Host Responses: Use of Computational Analysis to Classify Exposures and Extract Signatures of Unconventional Versus Common Viral Exposures

DTIC Science & Technology

2006-11-01

alpha viruses, among which was Venezuelan equine encephalitis (VEE). The “training sets” were constructed from in vitro exposures to purified...virus and 4 serotypes of Dengue), and the forth group include 2 alpha viruses, among which was Venezuelan equine encephalitis (VEE). We have used...We examined our hypothesis that in vitro exposures can predict exposures in vivo. We have used data from PBMC exposed to Venezuelan equine

Stochastic acidification, activation of hemagglutinin and escape of influenza viruses from an endosome

NASA Astrophysics Data System (ADS)

Lagache, Thibault; Sieben, Christian; Meyer, Tim; Herrmann, Andreas; Holcman, David

2017-06-01

Influenza viruses enter the cell inside an endosome. During the endosomal journey, acidification triggers a conformational change of the virus spike protein hemagglutinin (HA) that results in escape of the viral genome from the endosome into the cytoplasm. It is still unclear how the interplay between acidification and HA conformation changes affects the kinetics of the viral endosomal escape. We develop here a stochastic model to estimate the change of conformation of HAs inside the endosome nanodomain. Using a Markov process, we model the arrival of protons to HA binding sites and compute the kinetics of their accumulation. We compute the Mean First Passage Time (MFPT) of the number of HA bound sites to a threshold, which is used to estimate the HA activation rate for a given pH concentration. The present analysis reveals that HA proton binding sites possess a high chemical barrier, ensuring a stability of the spike protein at sub-acidic pH. We predict that activating more than 3 adjacent HAs is necessary to trigger endosomal fusion and this configuration prevents premature release of viruses from early endosomes

Application of viromics: a new approach to the understanding of viral infections in humans.

PubMed

Ramamurthy, Mageshbabu; Sankar, Sathish; Kannangai, Rajesh; Nandagopal, Balaji; Sridharan, Gopalan

2017-12-01

This review is focused at exploring the strengths of modern technology driven data compiled in the areas of virus gene sequencing, virus protein structures and their implication to viral diagnosis and therapy. The information for virome analysis (viromics) is generated by the study of viral genomes (entire nucleotide sequence) and viral genes (coding for protein). Presently, the study of viral infectious diseases in terms of etiopathogenesis and development of newer therapeutics is undergoing rapid changes. Currently, viromics relies on deep sequencing, next generation sequencing (NGS) data and public domain databases like GenBank and unique virus specific databases. Two commonly used NGS platforms: Illumina and Ion Torrent, recommend maximum fragment lengths of about 300 and 400 nucleotides for analysis respectively. Direct detection of viruses in clinical samples is now evolving using these methods. Presently, there are a considerable number of good treatment options for HBV/HIV/HCV. These viruses however show development of drug resistance. The drug susceptibility regions of the genomes are sequenced and the prediction of drug resistance is now possible from 3 public domains available on the web. This has been made possible through advances in the technology with the advent of high throughput sequencing and meta-analysis through sophisticated and easy to use software and the use of high speed computers for bioinformatics. More recently NGS technology has been improved with single-molecule real-time sequencing. Here complete long reads can be obtained with less error overcoming a limitation of the NGS which is inherently prone to software anomalies that arise in the hands of personnel without adequate training. The development in understanding the viruses in terms of their genome, pathobiology, transcriptomics and molecular epidemiology constitutes viromics. It could be stated that these developments will bring about radical changes and advancement especially in the field of antiviral therapy and diagnostic virology.

Identification and integration of Picorna-like viruses in multiple insect taxa

USDA-ARS?s Scientific Manuscript database

Virus infection often leads to incorporation of a piece of the virus genetic code into the genome of the host organism, referred to as integration. Determining if the virus has integrated into the host genome provides valuable information needed to monitor disease spread. Detection of integrated vir...

75 FR 81087 - Plum Pox Virus; Update of Quarantined Areas

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-27

.... APHIS-2010-0089] Plum Pox Virus; Update of Quarantined Areas AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Interim rule and request for comments. SUMMARY: We are amending the plum pox virus.... SUPPLEMENTARY INFORMATION: Background The plum pox virus (PPV) is an extremely serious viral disease of plants...

Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

PubMed

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y F; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick

2014-02-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.

Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

PubMed Central

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y. F.; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie

2014-01-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here. PMID:24284329

Investigation of type-I interferon dysregulation by arenaviruses : a multidisciplinary approach.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozina, Carol L.; Moorman, Matthew Wallace; Branda, Catherine

2011-09-01

This report provides a detailed overview of the work performed for project number 130781, 'A Systems Biology Approach to Understanding Viral Hemorrhagic Fever Pathogenesis.' We report progress in five key areas: single cell isolation devices and control systems, fluorescent cytokine and transcription factor reporters, on-chip viral infection assays, molecular virology analysis of Arenavirus nucleoprotein structure-function, and development of computational tools to predict virus-host protein interactions. Although a great deal of work remains from that begun here, we have developed several novel single cell analysis tools and knowledge of Arenavirus biology that will facilitate and inform future publications and funding proposals.

[Monitoring respiratory syncytial virus through the Spanish influenza surveillance system, 2006-2014].

PubMed

Jiménez-Jorge, Silvia; Delgado-Sanz, Concepción; de Mateo, Salvador; Pozo, Francisco; Casas, Inmaculada; Larrauri, Amparo

2016-02-01

The aim of the study is to analyze the information on respiratory syncytial virus (RSV) obtained through the Spanish Influenza Surveillance System (SISS) and to study its usefulness as supplementary information for the characterization of influenza epidemics. The temporal patterns of both RSV and influenza viruses were analyzed by patterns comparing the weekly viral detection rates from 2006 to 2014. In general, the RSV circulation was characterized by showing a peak between 52-1 weeks, and circulated from 2 to 8 weeks before/prior to influenza viruses. RSV information obtained from the SISS is useful for the characterization of influenza epidemics in Spain. Copyright © 2015 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Influenza Gain-of-Function Experiments: Their Role in Vaccine Virus Recommendation and Pandemic Preparedness

PubMed Central

Webby, R. J.; Webster, R. G.; Kelso, A.; Barr, I. G.; McCauley, J. W.; Daniels, R. S.; Wang, D.; Shu, Y.; Nobusawa, E.; Itamura, S.; Tashiro, M.; Harada, Y.; Watanabe, S.; Odagiri, T.; Ye, Z.; Grohmann, G.; Harvey, R.; Engelhardt, O.; Smith, D.; Hamilton, K.; Claes, F.; Dauphin, G.

2014-01-01

Abstract In recent years, controversy has arisen regarding the risks and benefits of certain types of gain-of-function (GOF) studies involving avian influenza viruses. In this article, we provide specific examples of how different types of data, including information garnered from GOF studies, have helped to shape the influenza vaccine production process—from selection of candidate vaccine viruses (CVVs) to the manufacture and stockpiling of safe, high-yield prepandemic vaccines for the global community. The article is not written to support a specific pro- or anti-GOF stance but rather to inform the scientific community about factors involved in vaccine virus selection and the preparation of prepandemic influenza vaccines and the impact that some GOF information has had on this process. PMID:25505124

The Utility of Social Media in Providing Information on Zika Virus

PubMed Central

Gressick, Kimberly; Singh, Vivek; Kwal, Jaclyn; Cap, Natalia; Koru-Sengul, Tulay; Curry, Christine L

2017-01-01

Introduction In 2015, there was an outbreak of Zika virus in Brazil that spread throughout the Americas. The association of Zika virus with birth defects in infants born to infected pregnant women created concern for women of childbearing age. Social media is an important platform for health promotion, communication, and education on preventative methods during Zika virus outbreaks. Methods We evaluated the utility of social media on providing information regarding Zika virus. Facebook, Instagram, Twitter, and YouTube were utilized for our study. A search of the term “#Zikavirus” on Twitter and Instagram, and “Zika virus” on Facebook and YouTube was performed. The first 50 search results were analyzed from each source. Only English, Spanish, or Portuguese results were included. Results were categorized into three groups: “Useful”, “Not Useful”, or “Misleading”. Results Search was conducted on December 17th, 2016, with 185 results. Forty (21.6%) were from Facebook, 50 (27%) from Twitter, 48 (25.9%) from YouTube, and 47 (25.4%) from Instagram. A total of 104 (56.22%) results were "Useful", 67 (36.2%) "Not Useful", and 14 (7.5%) were "Misleading”. There were significantly more “Useful” results compared to “Not Useful” and “Misleading” results (Fisher’s exact: p < 0.0001). Conclusion Social media is a useful resource for providing relevant information on Zika virus. Young women can utilize social media for Zika virus information. The role of social media in public health should be further investigated and established. Patient education interventions should focus on social media impact on behavior modification and education of public to recognize useful information. PMID:29282437

Block the Buzzing, Bites, and Bumps: Preventing Mosquito-Borne Illnesses

MedlinePlus

... Ten Mosquito Facts West Nile Virus Dengue Fever Malaria Zika Virus Infection Zika Virus Information and Resources References The live attenuated dengue vaccine TV003 elicits complete protection against dengue in a ...

Predicted secondary structure similarity in the absence of primary amino acid sequence homology: hepatitis B virus open reading frames.

PubMed Central

Schaeffer, E; Sninsky, J J

1984-01-01

Proteins that are related evolutionarily may have diverged at the level of primary amino acid sequence while maintaining similar secondary structures. Computer analysis has been used to compare the open reading frames of the hepatitis B virus to those of the woodchuck hepatitis virus at the level of amino acid sequence, and to predict the relative hydrophilic character and the secondary structure of putative polypeptides. Similarity is seen at the levels of relative hydrophilicity and secondary structure, in the absence of sequence homology. These data reinforce the proposal that these open reading frames encode viral proteins. Computer analysis of this type can be more generally used to establish structural similarities between proteins that do not share obvious sequence homology as well as to assess whether an open reading frame is fortuitous or codes for a protein. PMID:6585835

HIV-1 Strategies of Immune Evasion

NASA Astrophysics Data System (ADS)

Castiglione, F.; Bernaschi, M.

We simulate the progression of the HIV-1 infection in untreated host organisms. The phenotype features of the virus are represented by the replication rate, the probability of activating the transcription, the mutation rate and the capacity to stimulate an immune response (the so-called immunogenicity). It is very difficult to study in-vivo or in-vitro how these characteristics of the virus influence the evolution of the disease. Therefore we resorted to simulations based on a computer model validated in previous studies. We observe, by means of computer experiments, that the virus continuously evolves under the selective pressure of an immune response whose effectiveness downgrades along with the disease progression. The results of the simulations show that immunogenicity is the most important factor in determining the rate of disease progression but, by itself, it is not sufficient to drive the disease to a conclusion in all cases.

Paleovirology of bornaviruses: What can be learned from molecular fossils of bornaviruses.

PubMed

Horie, Masayuki; Tomonaga, Keizo

2018-04-06

Endogenous viral elements (EVEs) are virus-derived sequences embedded in eukaryotic genomes formed by germline integration of viral sequences. As many EVEs were integrated into eukaryotic genomes millions of years ago, EVEs are considered molecular fossils of viruses. EVEs can be valuable informational sources about ancient viruses, including their time scale, geographical distribution, genetic information, and hosts. Although integration of viral sequences is not required for replications of viruses other than retroviruses, many non-retroviral EVEs have been reported to exist in eukaryotes. Investigation of these EVEs has expanded our knowledge regarding virus-host interactions, as well as provided information on ancient viruses. Among them, EVEs derived from bornaviruses, non-retroviral RNA viruses, have been relatively well studied. Bornavirus-derived EVEs are widely distributed in animal genomes, including the human genome, and the history of bornaviruses can be dated back to more than 65 million years. Although there are several reports focusing on the biological significance of bornavirus-derived sequences in mammals, paleovirology of bornaviruses has not yet been well described and summarized. In this paper, we describe what can be learned about bornaviruses from endogenous bornavirus-like elements from the view of paleovirology using published results and our novel data. Copyright © 2018 Elsevier B.V. All rights reserved.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

PubMed

Lefkowitz, Elliot J; Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-04

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Analysis of full-length sequences of two Citrus yellow mosaic badnavirus isolates infecting Citrus jambhiri (Rough Lemon) and Citrus sinensis L. Osbeck (Sweet Orange) from a nursery in India.

PubMed

Anthony Johnson, A M; Borah, B K; Sai Gopal, D V R; Dasgupta, I

2012-12-01

Citrus yellow mosaic badna virus (CMBV), a member of the Family Caulimoviridae, Genus Badnavirus is the causative agent of mosaic disease among Citrus species in southern India. Despite its reported prevalence in several citrus species, complete information on clear functional genomics or functional information of full-length genomes from all the CMBV isolates infecting citrus species are not available in publicly accessible databases. CMBV isolates from Rough Lemon and Sweet Orange collected from a nursery were cloned and sequenced. The analysis revealed high sequence homology of the two CMBV isolates with previously reported CMBV sequences implying that they represent new variants. Based on computational analysis of the predicted secondary structures, the possible functions of some CMBV proteins have been analyzed.

Estimated Incubation Period for Zika Virus Disease.

PubMed

Krow-Lucal, Elisabeth R; Biggerstaff, Brad J; Staples, J Erin

2017-05-01

Information about the Zika virus disease incubation period can help identify risk periods and local virus transmission. In 2015-2016, data from 197 symptomatic travelers with recent Zika virus infection indicated an estimated incubation period of 3-14 days. For symptomatic persons with symptoms >2 weeks after travel, transmission might be not travel associated.

Biological and historical overview of Zika virus

PubMed Central

Armstrong, Najealicka; Hou, Wangheng; Tang, Qiyi

2017-01-01

The recent outbreak of the Zika virus attracts worldwide attention probably because the most recently affected country (Brazil) will host the 2016 Olympic Game. Zika virus infected cases are now spreading to many other countries and its infection might be linked to some severe medical sequelae. Since its first isolation from the infected monkey in 1947 in Uganda, only a few studies had been taken until recent outbreak. According to the history of referenced publications, there is a 19-year gap from 1989 to 2007. This might be because only mild diseases were diagnosed from Zika virus infected populations. Obviously, the recent reports that Zika virus infection is probably associated with microcephaly of the neonates makes us reevaluate the medical significance of the viral pathogen. It can be transmitted sexually or by mosquito biting. Sexual transmission of the Zika virus distinguishes it from other members of the Genus Flavivirus. Detailed information of the Zika virus is needed through a thorough investigation covering basic, epidemical, subclinical and clinical studies. Here, we reviewed the published information of Zika virus. PMID:28239566

A Constructive Induction Approach to Computer Immunology

DTIC Science & Technology

1999-03-01

LVM98] Lamont, Gary B., David A. Van Veldhuizen , and Robert E Marmelstein, A Distributed Architecture for a Self-Adaptive Computer Virus...Artificial Intelligence, Herndon, VA, 1995. [MVL98] Marmelstein, Robert E., David A. Van Veldhuizen , and Gary B. Lamont. Modeling & Analysis

Respiratory Syncytial Virus (RSV) Test: MedlinePlus Lab Test Information

MedlinePlus

... this page: https://medlineplus.gov/labtests/respiratorysyncytialvirusrsvtest.html Respiratory Syncytial Virus (RSV) Test To use the sharing ... is an RSV test? RSV , which stands for respiratory syncytial virus, is an infection that affects the ...

Ebola Virus Disease: A Review of Its Past and Present.

PubMed

Murray, Michael J

2015-09-01

Ebola virus, the virus responsible for Ebola virus disease, has spawned several epidemics during the past 38 years. In 2014, an Ebola epidemic spread from Africa to other continents, becoming a pandemic. The virus's relatively unique structure, its infectivity and lethality, the difficulty in stopping its spread, and the lack of an effective treatment captured the world's attention. This article provides a brief review of the known history of Ebola virus disease, its etiology, epidemiology, and pathophysiology and a review of the limited information on managing patients with Ebola virus disease.

Computational approach for predicting the conserved B-cell epitopes of hemagglutinin H7 subtype influenza virus.

PubMed

Wang, Xiangyu; Sun, Qi; Ye, Zhonghua; Hua, Ying; Shao, Na; Du, Yanli; Zhang, Qiwei; Wan, Chengsong

2016-10-01

An avian-origin influenza H7N9 virus epidemic occurred in China in 2013-2014, in which >422 infected people suffered from pneumonia, respiratory distress syndrome and septic shock. H7N9 viruses belong to the H7 subtype of avian-origin influenza viruses (AIV-H7). Hemagglutinin (HA) is a vital membrane protein of AIV that has an important role in host recognition and infection. The epitopes of HA are significant determinants of the regularity of epidemic and viral mutation and recombination mechanisms. The present study aimed to predict the conserved B-cell epitopes of AIV-H7 HA using a bioinformatics approach, including the three most effective epitope prediction softwares available online: Artificial Neural Network based B-cell Epitope Prediction (ABCpred), B-cell Epitope Prediction (BepiPred) and Linear B-cell Epitope Prediction (LBtope). A total of 24 strains of Euro-Asiatic AIV-H7 that had been associated with a serious poultry pandemic or had infected humans in the past 30 years were selected to identify the conserved regions of HA. Sequences were obtained from the National Center for Biotechnology Information and Global Initiative on Sharing Avian Influenza Data databases. Using a combination of software prediction and sequence comparisons, the conserved epitopes of AIV-H7 were predicted and clarified. A total of five conserved epitopes [amino acids (aa) 37-52, 131-142, 215-234, 465-484 and 487-505] with a suitable length, high antigenicity and minimal variation were predicted and confirmed. Each obtained a score of >0.80 in ABCpred, 60% in LBtope and a level of 0.35 in Bepipred. In addition, a representative amino acid change (glutamine 235 -to-leucine 235 ) in the HA protein of the 2013 AIV-H7N9 was discovered. The strategy adopted in the present study may have profound implications on the rapid diagnosis and control of infectious disease caused by H7N9 viruses, as well as by other virulent viruses, such as the Ebola virus.

Analytical and computational modeling of early penetration of non-enveloped icosahedral viruses into cells.

PubMed

Katzengold, Rona; Zaharov, Evgeniya; Gefen, Amit

2016-07-27

As obligate intracellular parasites, all viruses penetrate target cells to initiate replication and infection. This study introduces two approaches for evaluating the contact loads applied to a cell during early penetration of non-enveloped icosahedral viruses. The first approach is analytical modeling which is based on Hertz's theory for the contact of two elastic bodies; here we model the virus capsid as a triangle and the cell as an order-of-magnitude larger sphere. The second approach is finite element modeling, where we simulate three types of viruses: adeno-, papilloma- and polio- viruses, each interacting with a cell section. We find that the peak contact pressures and forces generated at the initial virus-cell contact depend on the virus geometry - that is both size and shape. With respect to shape, we show that the icosahedral virus shape induces greater peak pressures compared to a spherical virus shape. With respect to size, it is shown that the larger the virus is the greater are the contact loads in the attacked cell. Utilization of our modeling can be substantially useful not only for basic science studies, but also in other, more applied fields, such as in the field of gene therapy, or in `phage' virus studies.

Characteristics of a Widespread Community Cluster of H275Y Oseltamivir-Resistant A(H1N1)pdm09 Influenza in Australia

PubMed Central

Hurt, A. C.; Hardie, K.; Wilson, N. J.; Deng, Y. M.; Osbourn, M.; Leang, S. K.; Lee, R. T. C.; Iannello, P.; Gehrig, N.; Shaw, R.; Wark, P.; Caldwell, N.; Givney, R. C.; Xue, L.; Maurer-Stroh, S.; Dwyer, D. E.; Wang, B.; Smith, D. W.; Levy, A.; Booy, R.; Dixit, R.; Merritt, T.; Kelso, A.; Dalton, C.; Durrheim, D.; Barr, I. G.

2012-01-01

Background. Oseltamivir resistance in A(H1N1)pdm09 influenza is rare, particularly in untreated community cases. Sustained community transmission has not previously been reported. Methods. Influenza specimens from the Asia–Pacific region were collected through sentinel surveillance, hospital, and general practitioner networks. Clinical and epidemiological information was collected on patients infected with oseltamivir-resistant viruses. Results. Twenty-nine (15%) of 191 A(H1N1)pdm09 viruses collected between May and September 2011 from Hunter New England (HNE), Australia, contained the H275Y neuraminidase substitution responsible for oseltamivir resistance. Only 1 patient had received oseltamivir before specimen collection. The resistant strains were genetically very closely related, suggesting the spread of a single variant. Ninety percent of cases lived within 50 kilometers. Three genetically similar oseltamivir-resistant variants were detected outside of HNE, including 1 strain from Perth, approximately 4000 kilometers away. Computational analysis predicted that neuraminidase substitutions V241I, N369K, and N386S in these viruses may offset the destabilizing effect of the H275Y substitution. Conclusions This cluster represents the first widespread community transmission of H275Y oseltamivir-resistant A(H1N1)pdm09 influenza. These cases and data on potential permissive mutations suggest that currently circulating A(H1N1)pdm09 viruses retain viral fitness in the presence of the H275Y mutation and that widespread emergence of oseltamivir-resistant strains may now be more likely. PMID:22561367

Scalable metagenomic taxonomy classification using a reference genome database

PubMed Central

Ames, Sasha K.; Hysom, David A.; Gardner, Shea N.; Lloyd, G. Scott; Gokhale, Maya B.; Allen, Jonathan E.

2013-01-01

Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. Results: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. Availability: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat Contact: allen99@llnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23828782

CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens.

PubMed

Qiu, Tianyi; Yang, Yiyan; Qiu, Jingxuan; Huang, Yang; Xu, Tianlei; Xiao, Han; Wu, Dingfeng; Zhang, Qingchen; Zhou, Chen; Zhang, Xiaoyan; Tang, Kailin; Xu, Jianqing; Cao, Zhiwei

2018-05-02

Major challenges in vaccine development include rapidly selecting or designing immunogens for raising cross-protective immunity against different intra- or inter-subtypic pathogens, especially for the newly emerging varieties. Here we propose a computational method, Conformational Epitope (CE)-BLAST, for calculating the antigenic similarity among different pathogens with stable and high performance, which is independent of the prior binding-assay information, unlike the currently available models that heavily rely on the historical experimental data. Tool validation incorporates influenza-related experimental data sufficient for stability and reliability determination. Application to dengue-related data demonstrates high harmonization between the computed clusters and the experimental serological data, undetectable by classical grouping. CE-BLAST identifies the potential cross-reactive epitope between the recent zika pathogen and the dengue virus, precisely corroborated by experimental data. The high performance of the pathogens without the experimental binding data suggests the potential utility of CE-BLAST to rapidly design cross-protective vaccines or promptly determine the efficacy of the currently marketed vaccine against emerging pathogens, which are the critical factors for containing emerging disease outbreaks.

Zika Virus: Critical Information for Emergency Providers.

PubMed

Shastry, Siri; Koenig, Kristi L; Hirshon, Jon Mark

2016-08-01

Zika virus is an arbovirus of the Flaviviridae family. It is primarily a minimally symptomatic mosquito-borne infection. However, with Zika's 2015 to 2016 introduction into the Western Hemisphere and its dramatic and rapid spread, it has become a public health concern, in large part due to congenital abnormalities associated with infection in pregnant women. In early 2016, the World Health Organization declared the microcephaly and other neurologic conditions associated with Zika virus infection a public health emergency of international concern. This article discusses the current epidemiologic and clinical understanding of Zika virus, focusing on critical information needed by emergency providers. Copyright © 2016 Elsevier Inc. All rights reserved.

Cyber War: The Next Frontier for NATO

DTIC Science & Technology

2015-03-01

cyber-attacks as a way to advance their agenda. Common examples of cyber- attacks include computer viruses, worms , malware, and distributed denial of...take advantage of security holes and cause damage to computer systems, steal financial data, or acquire sensitive secrets. As technology becomes

Safeguarding Databases Basic Concepts Revisited.

ERIC Educational Resources Information Center

Cardinali, Richard

1995-01-01

Discusses issues of database security and integrity, including computer crime and vandalism, human error, computer viruses, employee and user access, and personnel policies. Suggests some precautions to minimize system vulnerability such as careful personnel screening, audit systems, passwords, and building and software security systems. (JKP)

Oncogenic Viruses and Breast Cancer: Mouse Mammary Tumor Virus (MMTV), Bovine Leukemia Virus (BLV), Human Papilloma Virus (HPV), and Epstein-Barr Virus (EBV).

PubMed

Lawson, James S; Salmons, Brian; Glenn, Wendy K

2018-01-01

Although the risk factors for breast cancer are well established, namely female gender, early menarche and late menopause plus the protective influence of early pregnancy, the underlying causes of breast cancer remain unknown. The development of substantial recent evidence indicates that a handful of viruses may have a role in breast cancer. These viruses are mouse mammary tumor virus (MMTV), bovine leukemia virus (BLV), human papilloma viruses (HPVs), and Epstein-Barr virus (EBV-also known as human herpes virus type 4). Each of these viruses has documented oncogenic potential. The aim of this review is to inform the scientific and general community about this recent evidence. MMTV and human breast cancer-the evidence is detailed and comprehensive but cannot be regarded as conclusive. BLV and human breast cancer-the evidence is limited. However, in view of the emerging information about BLV in human breast cancer, it is prudent to encourage the elimination of BLV in cattle, particularly in the dairy industry. HPVs and breast cancer-the evidence is substantial but not conclusive. The availability of effective preventive vaccines is a major advantage and their use should be encouraged. EBV and breast cancer-the evidence is also substantial but not conclusive. Currently, there are no practical means of either prevention or treatment. Although there is evidence of genetic predisposition, and cancer in general is a culmination of events, there is no evidence that inherited genetic traits are causal. The influence of oncogenic viruses is currently the major plausible hypothesis for a direct cause of human breast cancer.

Epidemics in Complex Networks: The Diversity of Hubs

NASA Astrophysics Data System (ADS)

Kitsak, Maksim; Gallos, Lazaros K.; Havlin, Shlomo; Stanley, H. Eugene; Makse, Hernan A.

2009-03-01

Many complex systems are believed to be vulnerable to spread of viruses and information owing to their high level of interconnectivity. Even viruses of low contagiousness easily proliferate the Internet. Rumors, fads, and innovation ideas are prone to efficient spreading in various social systems. Another commonly accepted standpoint is the importance of the most connected elements (hubs) in the spreading processes. We address following questions. Do all hubs conduct epidemics in the same manner? How does the epidemics spread depend on the structure of the network? What is the most efficient way to spread information over the system? We analyze several large-scale systems in the framework of of the susceptible/infective/removed (SIR) disease spread model which can also be mapped to the problem of rumor or fad spreading. We show that hubs are often ineffective in the transmission of virus or information owing to the highly heterogeneous topology of most networks. We also propose a new tool to evaluate the efficiency of nodes in spreading virus or information.

Mitigating Cybersecurity Risks.

PubMed

Rose, Rachel V; Kass, Joseph S

2017-04-01

Cybersecurity issues and their impact on compliance with the Health Insurance Portability and Accountability Act (HIPAA) and the Health Information Technology for Economic and Clinical Health (HITECH) Act are becoming more of an enforcement focus for a variety of government agencies, including the US Department of Health and Human Services, the Federal Trade Commission, and the Department of Justice. In the case presented in this article, a nurse in a neurology practice opted to speak with a patient about human immunodeficiency virus testing procedures in a manner audible to others in the waiting room. Computer screens with patient information were visible to anyone approaching a desk, the staff had not been trained on cybersecurity issues, and malware infected the computers used in the practice. In light of these circumstances and the launch of Phase 2 of the HIPAA Audit Program by the US Department of Health and Human Services Office for Civil Rights, the neurology practice must consider the following questions. First, could the gaps in the technical, administrative, and physical requirements of HIPAA and the HITECH Act result in an adverse audit and penalties? Second, what course of action does the law mandate in response to a ransomware attack?

Viral hepatitis and primates: historical and molecular analysis of human and nonhuman primate hepatitis A, B, and the GB-related viruses.

PubMed

Robertson, B H

2001-07-01

The hepatitis viruses have long been assumed to be highly host-specific, with infection of other nonhuman primates occurring due to inoculation with, or exposure to, human viruses. This paradigm has slowly changed over the last 10 years, as mounting data has revealed nonhuman primate equivalents of hepatitis A virus, hepatitis B virus, and the hepatitis C-related viruses GBV-C and GBV-A. This review summarizes the historical and molecular information for each of these groups and highlights the impact of these nonhuman primate hepatitis viruses on our understanding of the evolution of each of these viruses.

Avian influenza virus and free-ranging wild birds

USGS Publications Warehouse

Dierauf, Leslie A.; Karesh, W.B.; Ip, Hon S.; Gilardi, K.V.; Fischer, John R.

2006-01-01

Recent media and news reports and other information implicate wild birds in the spread of highly pathogenic avian influenza in Asia and Eastern Europe. Although there is little information concerning highly pathogenic avian influenza viruses in wild birds, scientists have amassed a large amount of data on low-pathogenicity avian influenza viruses during decades of research with wild birds. This knowledge can provide sound guidance to veterinarians, public health professionals, the general public, government agencies, and other entities with concerns about avian influenza.

Evaluation of Placental and Fetal Tissue Specimens for Zika Virus Infection - 50 States and District of Columbia, January-December, 2016.

PubMed

Reagan-Steiner, Sarah; Simeone, Regina; Simon, Elizabeth; Bhatnagar, Julu; Oduyebo, Titilope; Free, Rebecca; Denison, Amy M; Rabeneck, Demi B; Ellington, Sascha; Petersen, Emily; Gary, Joy; Hale, Gillian; Keating, M Kelly; Martines, Roosecelis B; Muehlenbachs, Atis; Ritter, Jana; Lee, Ellen; Davidson, Alexander; Conners, Erin; Scotland, Sarah; Sandhu, Kayleigh; Bingham, Andrea; Kassens, Elizabeth; Smith, Lou; St George, Kirsten; Ahmad, Nina; Tanner, Mary; Beavers, Suzanne; Miers, Brooke; VanMaldeghem, Kelley; Khan, Sumaiya; Rabe, Ingrid; Gould, Carolyn; Meaney-Delman, Dana; Honein, Margaret A; Shieh, Wun-Ju; Jamieson, Denise J; Fischer, Marc; Zaki, Sherif R

2017-06-23

Zika virus infection during pregnancy can cause congenital microcephaly and brain abnormalities (1), and detection of Zika virus RNA in clinical and tissue specimens can provide definitive laboratory evidence of recent Zika virus infection. Whereas duration of viremia is typically short, prolonged detection of Zika virus RNA in placental, fetal, and neonatal brain tissue has been reported and can provide key diagnostic information by confirming recent Zika virus infection (2). In accordance with recent guidance (3,4), CDC provides Zika virus testing of placental and fetal tissues in clinical situations where this information could add diagnostic value. This report describes the evaluation of formalin-fixed paraffin-embedded (FFPE) tissue specimens tested for Zika virus infection in 2016 and the contribution of this testing to the public health response. Among 546 live births with possible maternal Zika virus exposure, for which placental tissues were submitted by the 50 states and District of Columbia (DC), 60 (11%) were positive by Zika virus reverse transcription-polymerase chain reaction (RT-PCR). Among 81 pregnancy losses for which placental and/or fetal tissues were submitted, 18 (22%) were positive by Zika virus RT-PCR. Zika virus RT-PCR was positive on placental tissues from 38/363 (10%) live births with maternal serologic evidence of recent unspecified flavivirus infection and from 9/86 (10%) with negative maternal Zika virus immunoglobulin M (IgM) where possible maternal exposure occurred >12 weeks before serum collection. These results demonstrate that Zika virus RT-PCR testing of tissue specimens can provide a confirmed diagnosis of recent maternal Zika virus infection.

Primary angiocentric/angioinvasive T-cell lymphoma of the tympanic bulla in a feline leukaemia virus-positive cat.

PubMed

Santagostino, Sara F; Mortellaro, Carlo M; Buchholz, Julia; Lugli, Margherita; Forlani, Annalisa; Ghisleni, Gabriele; Roccabianca, Paola

2015-01-01

Case summary A 5-year-old neutered female feline leukaemia virus (FeLV)-positive domestic shorthair cat with a 5 month history of otitis media was referred for head tilt, stertor and dyspnoea. Computed tomography scan revealed soft tissue opacities inside the right tympanic bulla, with bone remodelling, and concurrent nasopharyngeal and intracranial invasion. Endoscopically guided bioptic samples were collected from the nasopharynx and middle ear. Histology revealed dense sheets of round, large, neoplastic cells, often surrounding or invading vascular walls. Neoplastic cells expressed CD3, FeLV p27 and gp70 antigens. A middle ear angiocentric/angioinvasive T-cell lymphoma was diagnosed. After improvement of clinical conditions following radiation therapy, the cat died unexpectedly. At necropsy, hepatic and splenic spread was detected. Relevance and novel information Primary middle ear tumours are rare and their diagnosis is often delayed as clinical signs mimic more common otological conditions. Multiple bioptic specimens are pivotal for a definitive diagnosis. The young age of the cat, serology and immunohistochemistry revealed a possible transforming role of FeLV.

A web-based resource for designing therapeutics against Ebola Virus.

PubMed

Dhanda, Sandeep Kumar; Chaudhary, Kumardeep; Gupta, Sudheer; Brahmachari, Samir Kumar; Raghava, Gajendra P S

2016-04-26

In this study, we describe a web-based resource, developed for assisting the scientific community in designing an effective therapeutics against the Ebola virus. Firstly, we predicted and identified experimentally validated epitopes in each of the antigens/proteins of the five known ebolaviruses. Secondly, we generated all the possible overlapping 9mer peptides from the proteins of ebolaviruses. Thirdly, conserved peptides across all the five ebolaviruses (four human pathogenic species) with no identical sequence in the human proteome, based on 1000 Genomes project, were identified. Finally, we identified peptide or epitope-based vaccine candidates that could activate both the B- and T-cell arms of the immune system. In addition, we also identified efficacious siRNAs against the mRNA transcriptome (absent in human transcriptome) of all the five ebolaviruses. It was observed that three species can potentially be targeted by a single siRNA (19mer) and 75 siRNAs can potentially target at least two species. A web server, EbolaVCR, has been developed that incorporates all the above information and useful computational tools (http://crdd.osdd.net/oscadd/ebola/).

A web-based resource for designing therapeutics against Ebola Virus

NASA Astrophysics Data System (ADS)

Dhanda, Sandeep Kumar; Chaudhary, Kumardeep; Gupta, Sudheer; Brahmachari, Samir Kumar; Raghava, Gajendra P. S.

2016-04-01

In this study, we describe a web-based resource, developed for assisting the scientific community in designing an effective therapeutics against the Ebola virus. Firstly, we predicted and identified experimentally validated epitopes in each of the antigens/proteins of the five known ebolaviruses. Secondly, we generated all the possible overlapping 9mer peptides from the proteins of ebolaviruses. Thirdly, conserved peptides across all the five ebolaviruses (four human pathogenic species) with no identical sequence in the human proteome, based on 1000 Genomes project, were identified. Finally, we identified peptide or epitope-based vaccine candidates that could activate both the B- and T-cell arms of the immune system. In addition, we also identified efficacious siRNAs against the mRNA transcriptome (absent in human transcriptome) of all the five ebolaviruses. It was observed that three species can potentially be targeted by a single siRNA (19mer) and 75 siRNAs can potentially target at least two species. A web server, EbolaVCR, has been developed that incorporates all the above information and useful computational tools (http://crdd.osdd.net/oscadd/ebola/).

Chains of transmission and control of Ebola virus disease in Conakry, Guinea, in 2014: an observational study.

PubMed

Faye, Ousmane; Boëlle, Pierre-Yves; Heleze, Emmanuel; Faye, Oumar; Loucoubar, Cheikh; Magassouba, N'Faly; Soropogui, Barré; Keita, Sakoba; Gakou, Tata; Bah, El Hadji Ibrahima; Koivogui, Lamine; Sall, Amadou Alpha; Cauchemez, Simon

2015-03-01

An epidemic of Ebola virus disease of unprecedented size continues in parts of west Africa. For the first time, large urban centres such as Conakry, the capital of Guinea, are affected. We did an observational study of patients with Ebola virus disease in three regions of Guinea, including Conakry, aiming to map the routes of transmission and assess the effect of interventions. Between Feb 10, 2014, and Aug 25, 2014, we obtained data from the linelist of all confirmed and probable cases in Guinea (as of Sept 16, 2014), a laboratory database of information about patients, and interviews with patients and their families and neighbours. With this information, we mapped chains of transmission, identified which setting infections most probably originated from (community, hospitals, or funerals), and computed the context-specific and overall reproduction numbers. Of 193 confirmed and probable cases of Ebola virus disease reported in Conakry, Boffa, and Télimélé, 152 (79%) were positioned in chains of transmission. Health-care workers contributed little to transmission. In March, 2014, individuals with Ebola virus disease who were not health-care workers infected a mean of 2·3 people (95% CI 1·6-3·2): 1·4 (0·9-2·2) in the community, 0·4 (0·1-0·9) in hospitals, and 0·5 (0·2-1·0) at funerals. After the implementation of infection control in April, the reproduction number in hospitals and at funerals reduced to lower than 0·1. In the community, the reproduction number dropped by 50% for patients that were admitted to hospital, but remained unchanged for those that were not. In March, hospital transmissions constituted 35% (seven of 20) of all transmissions and funeral transmissions constituted 15% (three); but from April to the end of the study period, they constituted only 9% (11 of 128) and 4% (five), respectively. 82% (119 of 145) of transmission occurred in the community and 72% (105) between family members. Our simulations show that a 10% increase in hospital admissions could have reduced the length of chains by 26% (95% CI 4-45). In Conakry, interventions had the potential to stop the epidemic, but reintroductions of the disease and poor cooperation of a few families led to prolonged low-level spread, showing the challenges of Ebola virus disease control in large urban centres. Monitoring of chains of transmission is crucial to assess and optimise local control strategies for Ebola virus disease. Labex IBEID, Reacting, PREDEMICS, NIGMS MIDAS initiative, Institut Pasteur de Dakar. Copyright © 2015 Elsevier Ltd. All rights reserved.

How to Keep Your Campus Safe from Infection

ERIC Educational Resources Information Center

Brown, Scott

2005-01-01

In this article, the author explains how antivirus programs work. He also explains how performances of various antivirus programs vary from one to another. He also takes a look at 13 antivirus programs and explains which of these will keep computers protected. These programs include: (1) Sophos Anti-Virus Version 3.86.2; (2) McAfee VirusScan 9.0;…

Computer Security-Risks, Threats, and Safeguards.

ERIC Educational Resources Information Center

Ekhaml, Leticia

2001-01-01

Describes a variety of Internet threats to computers and networks used in schools. Discusses electronic trashing; clearing hard drives; cyber spying on Web sites visited; protection against cyber spying, including disposable email accounts; password sniffers; privacy policies; email snooping; email attachments that carry viruses; and hoaxes. (LRW)

A survey-based study of Zika virus communication preferences among pregnant women in Georgia, United States.

PubMed

Ellingson, Mallory K; Bonk, Catherine M; Chamberlain, Allison T

2017-09-26

Because of the particularly severe perinatal outcomes associated with antenatal Zika virus infection, it is important for prenatal care providers to communicate Zika virus risks and strategies for prevention to their patients. Although face-to-face communication is ideal, clinic visits may not allow for in-depth discussion of all concerns. While previous studies have shown prenatal providers to be pregnant women's most trusted sources of health information, there is little knowledge on what secondary communication modalities pregnant women prefer for receiving information from their providers about an evolving public health emergency. A cross-sectional, descriptive anonymous 27-item survey was distributed to pregnant women at four clinics around Atlanta, Georgia from May 5th to June 20th, 2016. The survey assessed women's interest in and communication preferences about prenatal topics, including Zika virus. Descriptive statistics were calculated and chi-square tests were used to evaluate associations between the primary outcomes and patient characteristics. Four-hundred and eight women completed the survey. The most popular resource for obtaining Zika virus information was the Centers for Disease Control and Prevention (CDC) website (73.0%). While their prenatal provider's own website for Zika information ranked 5th among sources currently accessed for Zika information, it ranked third behind educational brochures and emails for ways in which women wanted to receive information. The characteristics of Zika virus information deemed most important were: evidence-based (87.5%), endorsed by the CDC (74.1%), and endorsed by their own provider (67.9%). In any public health emergency affecting pregnant women, women are going to seek advice from their obstetric providers. Because providers may lack sufficient time to discuss concerns with every patient, they may consider providing patient education in other ways. For the women included in this study, educational brochures, emails and providers' own practice websites were preferred. Providers should consider taking greater advantage of these modalities to supplement in-person exchanges, particularly during a public health emergency.

Designing and Testing Broadly-Protective Filoviral Vaccines Optimized for Cytotoxic T-Lymphocyte Epitope Coverage

PubMed Central

Fenimore, Paul W.; Foley, Brian T.; Bakken, Russell R.; Thurmond, James R.; Yusim, Karina; Yoon, Hyejin; Parker, Michael; Hart, Mary Kate; Dye, John M.; Korber, Bette; Kuiken, Carla

2012-01-01

We report the rational design and in vivo testing of mosaic proteins for a polyvalent pan-filoviral vaccine using a computational strategy designed for the Human Immunodeficiency Virus type 1 (HIV-1) but also appropriate for Hepatitis C virus (HCV) and potentially other diverse viruses. Mosaics are sets of artificial recombinant proteins that are based on natural proteins. The recombinants are computationally selected using a genetic algorithm to optimize the coverage of potential cytotoxic T lymphocyte (CTL) epitopes. Because evolutionary history differs markedly between HIV-1 and filoviruses, we devised an adapted computational technique that is effective for sparsely sampled taxa; our first significant result is that the mosaic technique is effective in creating high-quality mosaic filovirus proteins. The resulting coverage of potential epitopes across filovirus species is superior to coverage by any natural variants, including current vaccine strains with demonstrated cross-reactivity. The mosaic cocktails are also robust: mosaics substantially outperformed natural strains when computationally tested against poorly sampled species and more variable genes. Furthermore, in a computational comparison of cross-reactive potential a design constructed prior to the Bundibugyo outbreak performed nearly as well against all species as an updated design that included Bundibugyo. These points suggest that the mosaic designs would be more resilient than natural-variant vaccines against future Ebola outbreaks dominated by novel viral variants. We demonstrate in vivo immunogenicity and protection against a heterologous challenge in a mouse model. This design work delineates the likely requirements and limitations on broadly-protective filoviral CTL vaccines. PMID:23056184

Closteroviridae

USDA-ARS?s Scientific Manuscript database

The current ICTV report lists 2284 virus and viroid species distributed amongst 349 genera, 19 subfamilies, 87 families and 6 orders. There is also a chapter of unassigned viruses that provides information on a number of viruses that have not yet been classified but are probably representatives of n...

High risk blueberry viruses by region in the North America; implications for certification, nurseries, and fruit production

USDA-ARS?s Scientific Manuscript database

There is limited information about the distribution of blueberry viruses in the U.S. or around the world other than where the viruses were first discovered and characterized. A survey for blueberry viruses was carried out in the U.S. in 2015-2017. With the lack of a reliable woody indicator, most bl...

Microscopic Characterization of the Brazilian Giant Samba Virus.

PubMed

Schrad, Jason R; Young, Eric J; Abrahão, Jônatas S; Cortines, Juliana R; Parent, Kristin N

2017-02-14

Prior to the discovery of the mimivirus in 2003, viruses were thought to be physically small and genetically simple. Mimivirus, with its ~750-nm particle size and its ~1.2-Mbp genome, shattered these notions and changed what it meant to be a virus. Since this discovery, the isolation and characterization of giant viruses has exploded. One of the more recently discovered giant viruses, Samba virus, is a Mimivirus that was isolated from the Rio Negro in the Brazilian Amazon. Initial characterization of Samba has revealed some structural information, although the preparation techniques used are prone to the generation of structural artifacts. To generate more native-like structural information for Samba, we analyzed the virus through cryo-electron microscopy, cryo-electron tomography, scanning electron microscopy, and fluorescence microscopy. These microscopy techniques demonstrated that Samba particles have a capsid diameter of ~527 nm and a fiber length of ~155 nm, making Samba the largest Mimivirus yet characterized. We also compared Samba to a fiberless mimivirus variant. Samba particles, unlike those of mimivirus, do not appear to be rigid, and quasi-icosahedral, although the two viruses share many common features, including a multi-layered capsid and an asymmetric nucleocapsid, which may be common amongst the Mimiviruses .

Microscopic Characterization of the Brazilian Giant Samba Virus

PubMed Central

Schrad, Jason R.; Young, Eric J.; Abrahão, Jônatas S.; Cortines, Juliana R.; Parent, Kristin N.

2017-01-01

Prior to the discovery of the mimivirus in 2003, viruses were thought to be physically small and genetically simple. Mimivirus, with its ~750-nm particle size and its ~1.2-Mbp genome, shattered these notions and changed what it meant to be a virus. Since this discovery, the isolation and characterization of giant viruses has exploded. One of the more recently discovered giant viruses, Samba virus, is a Mimivirus that was isolated from the Rio Negro in the Brazilian Amazon. Initial characterization of Samba has revealed some structural information, although the preparation techniques used are prone to the generation of structural artifacts. To generate more native-like structural information for Samba, we analyzed the virus through cryo-electron microscopy, cryo-electron tomography, scanning electron microscopy, and fluorescence microscopy. These microscopy techniques demonstrated that Samba particles have a capsid diameter of ~527 nm and a fiber length of ~155 nm, making Samba the largest Mimivirus yet characterized. We also compared Samba to a fiberless mimivirus variant. Samba particles, unlike those of mimivirus, do not appear to be rigid, and quasi-icosahedral, although the two viruses share many common features, including a multi-layered capsid and an asymmetric nucleocapsid, which may be common amongst the Mimiviruses. PMID:28216551

Mutualism, parasitism and competition in the evolution of coviruses.

PubMed Central

Nee, S

2000-01-01

Coviruses are viruses with the property that their genetic information is divided up among two or more different viral particles. I model the evolution of coviruses using information on both viral virulence and the interactions between viruses and molecules that parasitize them: satellite viruses, satellite RNAs and defective interfering viruses. The model ultimately, and inevitably contains within it single-species dynamics as well as mutualistic, parasitic, cooperative and competitive relationships. The model shows that coexistence between coviruses and the self-sufficient viruses that spawned them is unlikely, in the sense that the quantitative conditions for coexistence are not easy to satisfy I also describe an abrupt transition from mutualistic two-species to single-species dynamics, showing a new sense in which questions such as 'Is a lichen one species or two?' can be given a definite answer. PMID:11127906

Evaluation of Nipah Virus as a Human and Animal Biological Terrorism and Warfare Agent

DTIC Science & Technology

2001-09-01

UNCLASSIFIED Defense Technical Information Center Compilation Part Notice ADP013384 TITLE: Evaluation of Nipah Virus as a Human and Animal Biological...following component part numbers comprise the compilation report: ADP013371 thru ADP013468 UNCLASSIFIED 14. EVALUATION OF NIPAH VIRUS AS A HUMAN AND ANIMAL...of BTWC proposed including Nipah virus in the list of animal pathogens. This paper describes an evaluation of Nipah virus as a biological agent for

Use of Lean response to improve pandemic influenza surge in public health laboratories.

PubMed

Isaac-Renton, Judith L; Chang, Yin; Prystajecky, Natalie; Petric, Martin; Mak, Annie; Abbott, Brendan; Paris, Benjamin; Decker, K C; Pittenger, Lauren; Guercio, Steven; Stott, Jeff; Miller, Joseph D

2012-01-01

A novel influenza A (H1N1) virus detected in April 2009 rapidly spread around the world. North American provincial and state laboratories have well-defined roles and responsibilities, including providing accurate, timely test results for patients and information for regional public health and other decision makers. We used the multidisciplinary response and rapid implementation of process changes based on Lean methods at the provincial public health laboratory in British Columbia, Canada, to improve laboratory surge capacity in the 2009 influenza pandemic. Observed and computer simulating evaluation results from rapid processes changes showed that use of Lean tools successfully expanded surge capacity, which enabled response to the 10-fold increase in testing demands.

Modeling Virus Coinfection to Inform Management of Maize Lethal Necrosis in Kenya

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hilker, Frank M.; Allen, Linda J. S.; Bokil, Vrushali A.

Maize lethal necrosis (MLN) has emerged as a serious threat to food security in sub-Saharan Africa. MLN is caused by coinfection with two viruses, Maize chlorotic mottle virus and a potyvirus, often Sugarcane mosaic virus. To better understand the dynamics of MLN and to provide insight into disease management, we modeled the spread of the viruses causing MLN within and between growing seasons. The model allows for transmission via vectors, soil, and seed, as well as exogenous sources of infection. Following model parameterization, we predict how management affects disease prevalence and crop performance over multiple seasons. Resource-rich farmers with largemore » holdings can achieve good control by combining clean seed and insect control. However, crop rotation is often required to effect full control. Resource-poor farmers with smaller holdings must rely on rotation and roguing, and achieve more limited control. For both types of farmer, unless management is synchronized over large areas, exogenous sources of infection can thwart control. As well as providing practical guidance, our modeling framework is potentially informative for other cropping systems in which coinfection has devastating effects. Finally, our work also emphasizes how mathematical modeling can inform management of an emerging disease even when epidemiological information remains scanty.« less

Modeling Virus Coinfection to Inform Management of Maize Lethal Necrosis in Kenya

DOE PAGES

Hilker, Frank M.; Allen, Linda J. S.; Bokil, Vrushali A.; ...

2017-08-01

Maize lethal necrosis (MLN) has emerged as a serious threat to food security in sub-Saharan Africa. MLN is caused by coinfection with two viruses, Maize chlorotic mottle virus and a potyvirus, often Sugarcane mosaic virus. To better understand the dynamics of MLN and to provide insight into disease management, we modeled the spread of the viruses causing MLN within and between growing seasons. The model allows for transmission via vectors, soil, and seed, as well as exogenous sources of infection. Following model parameterization, we predict how management affects disease prevalence and crop performance over multiple seasons. Resource-rich farmers with largemore » holdings can achieve good control by combining clean seed and insect control. However, crop rotation is often required to effect full control. Resource-poor farmers with smaller holdings must rely on rotation and roguing, and achieve more limited control. For both types of farmer, unless management is synchronized over large areas, exogenous sources of infection can thwart control. As well as providing practical guidance, our modeling framework is potentially informative for other cropping systems in which coinfection has devastating effects. Finally, our work also emphasizes how mathematical modeling can inform management of an emerging disease even when epidemiological information remains scanty.« less

Zika virus pandemic-analysis of Facebook as a social media health information platform.

PubMed

Sharma, Megha; Yadav, Kapil; Yadav, Nitika; Ferdinand, Keith C

2017-03-01

The arrival of Zika virus in the United States has generated a lot of activity on social media focusing on the algorithmic increase in the spread of the disease and its concerning complications. Accurate and credible dissemination of correct information about the arbovirus could help in decreasing the pandemic spread and associated apprehension in the population. Our study examined the effective use of the social media site Facebook (Facebook Inc, Menlo Park, CA) as an information source for the Zika virus pandemic. We found that the misleading posts were far more popular than the posts dispersing accurate, relevant public health information about the disease. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Network Penetration Testing and Research

NASA Technical Reports Server (NTRS)

Murphy, Brandon F.

2013-01-01

This paper will focus the on research and testing done on penetrating a network for security purposes. This research will provide the IT security office new methods of attacks across and against a company's network as well as introduce them to new platforms and software that can be used to better assist with protecting against such attacks. Throughout this paper testing and research has been done on two different Linux based operating systems, for attacking and compromising a Windows based host computer. Backtrack 5 and BlackBuntu (Linux based penetration testing operating systems) are two different "attacker'' computers that will attempt to plant viruses and or NASA USRP - Internship Final Report exploits on a host Windows 7 operating system, as well as try to retrieve information from the host. On each Linux OS (Backtrack 5 and BlackBuntu) there is penetration testing software which provides the necessary tools to create exploits that can compromise a windows system as well as other operating systems. This paper will focus on two main methods of deploying exploits 1 onto a host computer in order to retrieve information from a compromised system. One method of deployment for an exploit that was tested is known as a "social engineering" exploit. This type of method requires interaction from unsuspecting user. With this user interaction, a deployed exploit may allow a malicious user to gain access to the unsuspecting user's computer as well as the network that such computer is connected to. Due to more advance security setting and antivirus protection and detection, this method is easily identified and defended against. The second method of exploit deployment is the method mainly focused upon within this paper. This method required extensive research on the best way to compromise a security enabled protected network. Once a network has been compromised, then any and all devices connected to such network has the potential to be compromised as well. With a compromised network, computers and devices can be penetrated through deployed exploits. This paper will illustrate the research done to test ability to penetrate a network without user interaction, in order to retrieve personal information from a targeted host.

Transcriptome analysis of the whitefly, Bemisia tabaci MEAM1 on tomato infected with the crinivirus, Tomato chlorosis virus, identifies a temporal shift in gene expression and differential regulation of novel orphan genes

USDA-ARS?s Scientific Manuscript database

Whiteflies threaten agricultural crop production worldwide, are polyphagous in nature, and transmit hundreds of plant viruses. Little information exists on how whitefly gene expression is altered due to feeding on plants infected with a semipersistently transmitted virus. Tomato chlorosis virus (T...

Reconstruction of viruses from solution x-ray scattering data

NASA Astrophysics Data System (ADS)

Zheng, Yibin; Doerschuk, Peter C.; Johnson, John E.

1995-08-01

A model-based method for reconstructing the 3D structure of icosahedrally-symmetric viruses from solution x-ray scattering is presented. An example of the reconstruction, for data from cowpea mosaic virus, is described. The major opportunity provided by solution x-ray scattering is the ability to study the dynamics of virus particles in solution, information that is not accessible to crystal x-ray diffraction experiments.

Chapter A7. Section 7.2. Fecal Indicator Viruses

USGS Publications Warehouse

Bushon, Rebecca N.

2003-01-01

More than 100 types of human pathogenic viruses may be present in fecal-contaminated waters. Coliphages are used as indicators of virus-related fecal contamination and of the microbiological quality of waters. This report provides information on the equipment, sampling protocols, and laboratory methods that are in standard use by U.S. Geological Survey (USGS) personnel for the collection of data on fecal indicator viruses.

A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells

PubMed Central

Shen, Betty W.; Song, Yifan; Frayo, Shani; Convertine, Anthony J.; Margineantu, Daciana; Booth, Garrett; Correia, Bruno E.; Cheng, Yuanhua; Schief, William R.; Hockenbery, David M.; Press, Oliver W.; Stoddard, Barry L.; Stayton, Patrick S.; Baker, David

2014-01-01

SUMMARY Since apoptosis of infected cells can limit virus production and spread, some viruses have co-opted prosurvival genes from the host. This includes the Epstein-Barr virus (EBV) gene BHRF1, a homologue of human Bcl-2 proteins that block apoptosis and are associated with cancer. Computational design and experimental optimization were used to generate a novel protein called BINDI that binds BHRF1 with picomolar affinity. BINDI recognizes the hydrophobic cleft of BHRF1 in a manner similar to other Bcl-2 protein interactions, but makes many additional contacts to achieve exceptional affinity and specificity. BINDI induces apoptosis in EBV-infected cancer lines, and when delivered with an antibody-targeted intracellular delivery carrier, BINDI suppressed tumor growth and extended survival in a xenograft disease model of EBV-positive human lymphoma. High specificity designed proteins that selectively kill target cells may provide an advantage over the toxic compounds used in current generation antibody-drug conjugates. PMID:24949974

Infectious Agents As Markers of Human Migration toward the Amazon Region of Brazil

PubMed Central

Ishak, Ricardo; Machado, Luiz F. A.; Cayres-Vallinoto, Izaura; Guimarães Ishak, Marluísa de O.; Vallinoto, Antonio C. R.

2017-01-01

Infectious agents are common companions of humans and since ancient times they follow human migration on their search for a better place to live. The study of paleomicrobiology was significantly improved in its accuracy of measurement with the constant development of better methods to detect and analyze nucleic acids. Human tissues are constantly used to trace ancient infections and the association of anthropological evidences are important to confirm the microbiological information. Infectious agents which establish human persistent infections are particularly useful to trace human migrations. In the present article, the evidence of infection by viral agents such as human T-lymphotropic virus 1, human T-lymphotropic virus 2, human herpes virus-8, JC virus, and a bacterium, Chlamydia trachomatis, was described using different methodologies for their detection. Their presence was further used as biomarkers associated with anthropological and other relevant information to trace human migration into the Amazon region of Brazil. The approach also evidenced their microbiological origin, emergence, evolution, and spreading. The information obtained confirms much of the archeological information available tracing ancient and more recent human migration into this particular geographical region. In this article, the paleomicrobiological information on the subject was summarized and reviewed. PMID:28912770

Argonne News Brief: Two Key Zika Proteins Unlocked at Advanced Photon Source

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

The Zika virus is a global health emergency. Now two new studies have revealed the molecular structure of important Zika virus proteins, providing scientists around the globe with new information about how the virus replicates—and potential avenues for antiviral drugs or vaccines.

A computationally optimized broadly reactive H5 hemagglutinin vaccine provides protection against homologous and heterologous H5N1 highly pathogenic avian influenza virus infection in chickens

USDA-ARS?s Scientific Manuscript database

Since its emergence in 1996 in China, H5N1 highly pathogenic avian influenza (HPAI) virus has continuously evolved into different genetic clades that have created challenges to maintaining antigenically relevant H5N1 vaccine seeds. Therefore, a universal (multi-hemagglutinin [HA] subtype) or more c...

Computer Security: Virus Highlights Need for Improved Internet Management

DTIC Science & Technology

1989-06-01

and Finance Committee on Energy and Commerce House of Representatives Dear Mr. Chairman: This report responds to your October 14,1988, request and...virus incident, the Chairman, Subcommittee on Telecommunications and Finance , House Committee on Energy and Commerce, asked GAO to provide an overview...Chairman, Subcom- mittee on Telecommunications and Finance , House Committee on Energy and Commerce, and subsequent agreements with his office, the

Implementation of a study to examine the persistence of Ebola virus in the body fluids of Ebola virus disease survivors in Sierra Leone: Methodology and lessons learned

PubMed Central

Marrinan, Jaclyn E.; Sesay, Foday R.; Ervin, Elizabeth; Thorson, Anna E.; Xu, Wenbo; Ströher, Ute; Ongpin, Patricia; Abad, Neetu; Ariyarajah, Archchun; Malik, Tasneem; Liu, Hongtu; Ross, Christine; Durski, Kara N.; Gaillard, Philippe; Morgan, Oliver; Formenty, Pierre; Knust, Barbara; Broutet, Nathalie; Sahr, Foday

2017-01-01

Background The 2013–2016 West African Ebola virus disease epidemic was unprecedented in terms of the number of cases and survivors. Prior to this epidemic there was limited data available on the persistence of Ebola virus in survivors’ body fluids and the potential risk of transmission, including sexual transmission. Methodology/Principal findings Given the urgent need to determine the persistence of Ebola virus in survivors’ body fluids, an observational cohort study was designed and implemented during the epidemic response operation in Sierra Leone. This publication describes study implementation methodology and the key lessons learned. Challenges encountered during implementation included unforeseen duration of follow-up, complexity of interpreting and communicating laboratory results to survivors, and the urgency of translating research findings into public health practice. Strong community engagement helped rapidly implement the study during the epidemic. The study was conducted in two phases. The first phase was initiated within five months of initial protocol discussions and assessed persistence of Ebola virus in semen of 100 adult men. The second phase assessed the persistence of virus in multiple body fluids (semen or vaginal fluid, menstrual blood, breast milk, and urine, rectal fluid, sweat, saliva, tears), of 120 men and 120 women. Conclusion/Significance Data from this study informed national and global guidelines in real time and demonstrated the need to implement semen testing programs among Ebola virus disease survivors. The lessons learned and study tools developed accelerated the implementation of such programs in Ebola virus disease affected countries, and also informed studies examining persistence of Zika virus. Research is a vital component of the public health response to an epidemic of a poorly characterized disease. Adequate resources should be rapidly made available to answer critical research questions, in order to better inform response efforts. PMID:28892501

Implementation of a study to examine the persistence of Ebola virus in the body fluids of Ebola virus disease survivors in Sierra Leone: Methodology and lessons learned.

PubMed

Deen, Gibrilla Fadlu; McDonald, Suzanna L R; Marrinan, Jaclyn E; Sesay, Foday R; Ervin, Elizabeth; Thorson, Anna E; Xu, Wenbo; Ströher, Ute; Ongpin, Patricia; Abad, Neetu; Ariyarajah, Archchun; Malik, Tasneem; Liu, Hongtu; Ross, Christine; Durski, Kara N; Gaillard, Philippe; Morgan, Oliver; Formenty, Pierre; Knust, Barbara; Broutet, Nathalie; Sahr, Foday

2017-09-01

The 2013-2016 West African Ebola virus disease epidemic was unprecedented in terms of the number of cases and survivors. Prior to this epidemic there was limited data available on the persistence of Ebola virus in survivors' body fluids and the potential risk of transmission, including sexual transmission. Given the urgent need to determine the persistence of Ebola virus in survivors' body fluids, an observational cohort study was designed and implemented during the epidemic response operation in Sierra Leone. This publication describes study implementation methodology and the key lessons learned. Challenges encountered during implementation included unforeseen duration of follow-up, complexity of interpreting and communicating laboratory results to survivors, and the urgency of translating research findings into public health practice. Strong community engagement helped rapidly implement the study during the epidemic. The study was conducted in two phases. The first phase was initiated within five months of initial protocol discussions and assessed persistence of Ebola virus in semen of 100 adult men. The second phase assessed the persistence of virus in multiple body fluids (semen or vaginal fluid, menstrual blood, breast milk, and urine, rectal fluid, sweat, saliva, tears), of 120 men and 120 women. Data from this study informed national and global guidelines in real time and demonstrated the need to implement semen testing programs among Ebola virus disease survivors. The lessons learned and study tools developed accelerated the implementation of such programs in Ebola virus disease affected countries, and also informed studies examining persistence of Zika virus. Research is a vital component of the public health response to an epidemic of a poorly characterized disease. Adequate resources should be rapidly made available to answer critical research questions, in order to better inform response efforts.

Space lab system analysis: Advanced Solid Rocket Motor (ASRM) communications networks analysis

NASA Technical Reports Server (NTRS)

Ingels, Frank M.; Moorhead, Robert J., II; Moorhead, Jane N.; Shearin, C. Mark; Thompson, Dale R.

1990-01-01

A synopsis of research on computer viruses and computer security is presented. A review of seven technical meetings attended is compiled. A technical discussion on the communication plans for the ASRM facility is presented, with a brief tutorial on the potential local area network media and protocols.

The Hidden Costs of Wireless Computer Labs

ERIC Educational Resources Information Center

Daly, Una

2005-01-01

Various elementary schools and middle schools across the U.S. have purchased one or more mobile laboratories. Although the wireless labs have provided more classroom computing, teachers and technology aides still have mixed views about their cost-benefit ratio. This is because the proliferation of viruses and spyware has dramatically increased…

Mommy, Daddy--What's AIDS?

ERIC Educational Resources Information Center

National Association of Pediatric Nurse Associates and Practitioners, Cherry Hill, NJ.

This brochure is designed to help parents answer the questions that their children may ask them about Acquired Immune Deficiency Syndrome (AIDS) and the Human Immuno Deficiency Virus (HIV), the virus that causes AIDS. It provides basic information about AIDS and HIV, as well as sources for further information, such as the National AIDS Hotline. It…

Modeling and Analyzing Intrusion Attempts to a Computer Network Operating in a Defense in Depth Posture

DTIC Science & Technology

2004-09-01

protection. Firewalls, Intrusion Detection Systems (IDS’s), Anti-Virus (AV) software , and routers are such tools used. In recent years, computer security...associated with operating systems, application software , and computing hardware. When IDS’s are utilized on a host computer or network, there are two...primary approaches to detecting and / or preventing attacks. Traditional IDS’s, like most AV software , rely on known “signatures” to detect attacks

All-atom molecular dynamics of virus capsids as drug targets

DOE PAGES

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong; ...

2016-04-29

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

All-atom molecular dynamics of virus capsids as drug targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

Culicoides variipennis and bluetongue-virus epidemiology in the United States.

PubMed

Tabachnick, W J

1996-01-01

The bluetongue viruses are transmitted to ruminants in North America by Culicoides variipennis. US annual losses of approximately $125 million are due to restrictions on the movement of livestock and germplasm to bluetongue-free countries. Bluetongue is the most economically important arthropod-borne animal disease in the United States. Bluetongue is absent in the northeastern United States because of the inefficient vector ability there of C. variipennis for bluetongue. The vector of bluetongue virus elsewhere in the United States is C. variipennis sonorensis. The three C. variipennis subspecies differ in vector competence for bluetongue virus in the laboratory. Understanding C. variipennis genetic variation controlling bluetongue transmission will help identify geographic regions at risk for bluetongue and provide opportunities to prevent virus transmission. Information on C. variipennis and bluetongue epidemiology will improve trade and provide information to protect US livestock from domestic and foreign arthropod-borne pathogens.

Virus Particle Detection by Convolutional Neural Network in Transmission Electron Microscopy Images.

PubMed

Ito, Eisuke; Sato, Takaaki; Sano, Daisuke; Utagawa, Etsuko; Kato, Tsuyoshi

2018-06-01

A new computational method for the detection of virus particles in transmission electron microscopy (TEM) images is presented. Our approach is to use a convolutional neural network that transforms a TEM image to a probabilistic map that indicates where virus particles exist in the image. Our proposed approach automatically and simultaneously learns both discriminative features and classifier for virus particle detection by machine learning, in contrast to existing methods that are based on handcrafted features that yield many false positives and require several postprocessing steps. The detection performance of the proposed method was assessed against a dataset of TEM images containing feline calicivirus particles and compared with several existing detection methods, and the state-of-the-art performance of the developed method for detecting virus was demonstrated. Since our method is based on supervised learning that requires both the input images and their corresponding annotations, it is basically used for detection of already-known viruses. However, the method is highly flexible, and the convolutional networks can adapt themselves to any virus particles by learning automatically from an annotated dataset.

Camino Verde (The Green Way): evidence-based community mobilisation for dengue control in Nicaragua and Mexico: feasibility study and study protocol for a randomised controlled trial.

PubMed

Andersson, Neil; Arostegui, Jorge; Nava-Aguilera, Elizabeth; Harris, Eva; Ledogar, Robert J

2017-05-30

Since the Aedes aegypti mosquitoes that transmit dengue virus can breed in clean water, WHO-endorsed vector control strategies place sachets of organophosphate pesticide, temephos (Abate), in household water storage containers. These and other pesticide-dependent approaches have failed to curb the spread of dengue and multiple dengue virus serotypes continue to spread throughout tropical and subtropical regions worldwide. A feasibility study in Managua, Nicaragua, generated instruments, intervention protocols, training schedules and impact assessment tools for a cluster randomised controlled trial of community-based approaches to vector control comprising an alternative strategy for dengue prevention and control in Nicaragua and Mexico. The Camino Verde (Green Way) is a pragmatic parallel group trial of pesticide-free dengue vector control, adding effectiveness to the standard government dengue control. A random sample from the most recent census in three coastal regions of Guerrero state in Mexico will generate 90 study clusters and the equivalent sampling frame in Managua, Nicaragua will generate 60 clusters, making a total of 150 clusters each of 137-140 households. After a baseline study, computer-driven randomisation will allocate to intervention one half of the sites, stratified by country, evidence of recent dengue virus infection in children aged 3-9 years and, in Nicaragua, level of community organisation. Following a common evidence-based education protocol, each cluster will develop and implement its own collective interventions including house-to-house visits, school-based programmes and inter-community visits. After 18 months, a follow-up study will compare dengue history, serological evidence of recent dengue virus infection (via measurement of anti-dengue virus antibodies in saliva samples) and entomological indices between intervention and control sites. Our hypothesis is that informed community mobilisation adds effectiveness in controlling dengue. ISRCTN27581154 .

Zika Virus

MedlinePlus

... Operations Administrative Services Office of Biodefense Research & Surety Communications Government Relations Cyber Infrastructure Computational Biology Equal Employment Opportunity Ethics Global Research Office of Mission Integration and Financial ...

Avian Influenza A (H7N9) Virus

MedlinePlus

... Variant Pandemic Other Asian Lineage Avian Influenza A (H7N9) Virus Language: English (US) Español Recommend on Facebook ... Guidance Laboratorian Guidance H7N9 Images Additional Information Asian H7N9 Outbreak Characterization Asian H7N9 virus infections in poultry ...

Evaluation of porcine epidemic diarrhea virus transmission and the immune response in growing pigs

USDA-ARS?s Scientific Manuscript database

Clinical disease associated with porcine epidemic diarrhea virus (PEDV) infection in naïve pigs is well chronicled; however, information on endemic PEDV infection is limited. To characterize chronic PEDV infection, the duration of infectious virus shedding and development of protective immunity was ...

Mortality associated with hepatitis C and hepatitis B virus infection: A nationwide study on multiple causes of death data.

PubMed

Fedeli, Ugo; Grande, Enrico; Grippo, Francesco; Frova, Luisa

2017-03-14

To analyze mortality associated with hepatitis C virus (HCV) and hepatitis B virus (HBV) infection in Italy. Death certificates mentioning either HBV or HCV infection were retrieved from the Italian National Cause of Death Register for the years 2011-2013. Mortality rates and proportional mortality (percentage of deaths with mention of HCV/HBV among all registered deaths) were computed by gender and age class. The geographical variability in HCV-related mortality rates was investigated by directly age-standardized rates (European standard population). Proportional mortality for HCV and HBV among subjects aged 20-59 years was assessed in the native population and in different immigrant groups. HCV infection was mentioned in 1.6% ( n = 27730) and HBV infection in 0.2% ( n = 3838) of all deaths among subjects aged ≥ 20 years. Mortality rates associated with HCV infection increased exponentially with age in both genders, with a male to female ratio close to unity among the elderly; a further peak was observed in the 50-54 year age group especially among male subjects. HCV-related mortality rates were higher in Southern Italy among elderly people (45/100000 in subjects aged 60-79 and 125/100000 in subjects aged ≥ 80 years), and in North-Western Italy among middle-aged subjects (9/100000 in the 40-59 year age group). Proportional mortality was higher among Italian citizens and North African immigrants for HCV, and among Sub-Saharan African and Asian immigrants for HBV. Population ageing, immigration, and new therapeutic approaches are shaping the epidemiology of virus-related chronic liver disease. In spite of limits due to the incomplete reporting and misclassification of the etiology of liver disease, mortality data represent an additional source of information for surveillance.

High-end Home Firewalls CIAC-2326

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orvis, W

Networking in most large organizations is protected with corporate firewalls and managed by seasoned security professionals. Attempts to break into systems at these organizations are extremely difficult to impossible for an external intruder. With the growth in networking and the options that it makes possible, new avenues of intrusion are opening up. Corporate machines exist that are completely unprotected against intrusions, that are not managed by a security professional, and that are regularly connected to the company network. People have the option of and are encouraged to work at home using a home computer linked to the company network. Managersmore » have home computers linked to internal machines so they can keep an eye on internal processes while not physically at work. Researchers do research or writing at home and connect to the company network to download information and upload results. In most cases, these home computers are completely unprotected, except for any protection that the home user might have installed. Unfortunately, most home users are not security professionals and home computers are often used by other family members, such as children downloading music, who are completely unconcerned about security precautions. When these computers are connected to the company network, they can easily introduce viruses, worms, and other malicious code or open a channel behind the company firewall for an external intruder.« less

Virus Assembly and Maturation

NASA Astrophysics Data System (ADS)

Johnson, John E.

2004-03-01

We use two techniques to look at three-dimensional virus structure: electron cryomicroscopy (cryoEM) and X-ray crystallography. Figure 1 is a gallery of virus particles whose structures Timothy Baker, one of my former colleagues at Purdue University, used cryoEM to determine. It illustrates the variety of sizes of icosahedral virus particles. The largest virus particle on this slide is the Herpes simplex virus, around 1200Å in diameter; the smallest we examined was around 250Å in diameter. Viruses bear their genomic information either as positive-sense DNA and RNA, double-strand DNA, double-strand RNA, or negative-strand RNA. Viruses utilize the various structure and function "tactics" seen throughout cell biology to replicate at high levels. Many of the biological principles that we consider general were in fact discovered in the context of viruses ...

Structure-based energetics of protein interfaces guide Foot-and-Mouth Disease virus vaccine design

PubMed Central

Scott, Katherine; Burman, Alison; Loureiro, Silvia; Ren, Jingshan; Porta, Claudine; Ginn, Helen M.; Jackson, Terry; Perez-Martin, Eva; Siebert, C. Alistair; Paul, Guntram; Huiskonen, Juha T.; Jones, Ian M.; Esnouf, Robert M.; Fry, Elizabeth E.; Maree, Francois F.; Charleston, Bryan; Stuart, David I.

2018-01-01

Summary Virus capsids are primed for disassembly yet capsid integrity is key to generating a protective immune response. Here we devise a computational method to assess relative stability of protein-protein interfaces and use it to design improved candidate vaccines for two of the least stable, but globally important, serotypes of Foot-and-Mouth Disease virus (FMDV), O and SAT2. FMDV capsids comprise identical pentameric protein subunits held together by tenuous non-covalent interactions, and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. We use a novel restrained molecular dynamics strategy, to rank mutations predicted to strengthen the pentamer interfaces to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralising antibody responses to stabilised particles over parental viruses and wild-type capsids. PMID:26389739

Resource Manual for Handling Body Fluids in the School Setting To Prevent the Transmission of Human Immunodeficiency Virus and Hepatitis B Virus.

ERIC Educational Resources Information Center

Maryland State Dept. of Health and Mental Hygiene, Baltimore.

Guidelines to prevent the transmission of blood-borne diseases, especially those caused by the Human Immunodeficiency Virus (HIV) and the Hepatitis B Virus (HBV), in the school setting are provided in this resource manual for school staff. Sections include information on the reasons for the development of this manual; a summary of the means of HIV…

Complete sequence determination of a novel reptile iridovirus isolated from soft-shelled turtle and evolutionary analysis of Iridoviridae

PubMed Central

Huang, Youhua; Huang, Xiaohong; Liu, Hong; Gong, Jie; Ouyang, Zhengliang; Cui, Huachun; Cao, Jianhao; Zhao, Yingtao; Wang, Xiujie; Jiang, Yulin; Qin, Qiwei

2009-01-01

Background Soft-shelled turtle iridovirus (STIV) is the causative agent of severe systemic diseases in cultured soft-shelled turtles (Trionyx sinensis). To our knowledge, the only molecular information available on STIV mainly concerns the highly conserved STIV major capsid protein. The complete sequence of the STIV genome is not yet available. Therefore, determining the genome sequence of STIV and providing a detailed bioinformatic analysis of its genome content and evolution status will facilitate further understanding of the taxonomic elements of STIV and the molecular mechanisms of reptile iridovirus pathogenesis. Results We determined the complete nucleotide sequence of the STIV genome using 454 Life Science sequencing technology. The STIV genome is 105 890 bp in length with a base composition of 55.1% G+C. Computer assisted analysis revealed that the STIV genome contains 105 potential open reading frames (ORFs), which encode polypeptides ranging from 40 to 1,294 amino acids and 20 microRNA candidates. Among the putative proteins, 20 share homology with the ancestral proteins of the nuclear and cytoplasmic large DNA viruses (NCLDVs). Comparative genomic analysis showed that STIV has the highest degree of sequence conservation and a colinear arrangement of genes with frog virus 3 (FV3), followed by Tiger frog virus (TFV), Ambystoma tigrinum virus (ATV), Singapore grouper iridovirus (SGIV), Grouper iridovirus (GIV) and other iridovirus isolates. Phylogenetic analysis based on conserved core genes and complete genome sequence of STIV with other virus genomes was performed. Moreover, analysis of the gene gain-and-loss events in the family Iridoviridae suggested that the genes encoded by iridoviruses have evolved for favoring adaptation to different natural host species. Conclusion This study has provided the complete genome sequence of STIV. Phylogenetic analysis suggested that STIV and FV3 are strains of the same viral species belonging to the Ranavirus genus in the Iridoviridae family. Given virus-host co-evolution and the phylogenetic relationship among vertebrates from fish to reptiles, we propose that iridovirus might transmit between reptiles and amphibians and that STIV and FV3 are strains of the same viral species in the Ranavirus genus. PMID:19439104

Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method

PubMed Central

2014-01-01

Background Recent efforts in HIV-1 vaccine design have focused on immunogens that evoke potent neutralizing antibody responses to a broad spectrum of viruses circulating worldwide. However, the development of effective vaccines will depend on the identification and characterization of the neutralizing antibodies and their epitopes. We developed bioinformatics methods to predict epitope networks and antigenic determinants using structural information, as well as corresponding genotypes and phenotypes generated by a highly sensitive and reproducible neutralization assay. 282 clonal envelope sequences from a multiclade panel of HIV-1 viruses were tested in viral neutralization assays with an array of broadly neutralizing monoclonal antibodies (mAbs: b12, PG9,16, PGT121 - 128, PGT130 - 131, PGT135 - 137, PGT141 - 145, and PGV04). We correlated IC50 titers with the envelope sequences, and used this information to predict antibody epitope networks. Structural patches were defined as amino acid groups based on solvent-accessibility, radius, atomic depth, and interaction networks within 3D envelope models. We applied a boosted algorithm consisting of multiple machine-learning and statistical models to evaluate these patches as possible antibody epitope regions, evidenced by strong correlations with the neutralization response for each antibody. Results We identified patch clusters with significant correlation to IC50 titers as sites that impact neutralization sensitivity and therefore are potentially part of the antibody binding sites. Predicted epitope networks were mostly located within the variable loops of the envelope glycoprotein (gp120), particularly in V1/V2. Site-directed mutagenesis experiments involving residues identified as epitope networks across multiple mAbs confirmed association of these residues with loss or gain of neutralization sensitivity. Conclusions Computational methods were implemented to rapidly survey protein structures and predict epitope networks associated with response to individual monoclonal antibodies, which resulted in the identification and deeper understanding of immunological hotspots targeted by broadly neutralizing HIV-1 antibodies. PMID:24646213

Background review for diagnostic test development for Zika virus infection.

PubMed

Charrel, Rémi N; Leparc-Goffart, Isabelle; Pas, Suzan; de Lamballerie, Xavier; Koopmans, Marion; Reusken, Chantal

2016-08-01

To review the state of knowledge about diagnostic testing for Zika virus infection and identify areas of research needed to address the current gaps in knowledge. We made a non-systematic review of the published literature about Zika virus and supplemented this with information from commercial diagnostic test kits and personal communications with researchers in European preparedness networks. The review covered current knowledge about the geographical spread, pathogen characteristics, life cycle and infection kinetics of the virus. The available molecular and serological tests and biosafety issues are described and discussed in the context of the current outbreak strain. We identified the following areas of research to address current knowledge gaps: (i) an urgent assessment of the laboratory capacity and capability of countries to detect Zika virus; (ii) rapid and extensive field validation of the available molecular and serological tests in areas with and without Zika virus transmission, with a focus on pregnant women; (iii) monitoring the genomic diversity of circulating Zika virus strains; (iv) prospective studies into the virus infection kinetics, focusing on diagnostic sampling (specimen types, combinations and timings); and (v) developing external quality assessments for molecular and serological testing, including differential diagnosis for similar viruses and symptom clusters. The availability of reagents for diagnostic development (virus strains and antigens, quantified viral ribonucleic acid) needs to be facilitated. An international laboratory response is needed, including preparation of protocols for prospective studies to address the most pressing information needs.

Background review for diagnostic test development for Zika virus infection

PubMed Central

Charrel, Rémi N; Leparc-Goffart, Isabelle; Pas, Suzan; de Lamballerie, Xavier; Koopmans, Marion; Reusken, Chantal

2016-01-01

Abstract Objective To review the state of knowledge about diagnostic testing for Zika virus infection and identify areas of research needed to address the current gaps in knowledge. Methods We made a non-systematic review of the published literature about Zika virus and supplemented this with information from commercial diagnostic test kits and personal communications with researchers in European preparedness networks. The review covered current knowledge about the geographical spread, pathogen characteristics, life cycle and infection kinetics of the virus. The available molecular and serological tests and biosafety issues are described and discussed in the context of the current outbreak strain. Findings We identified the following areas of research to address current knowledge gaps: (i) an urgent assessment of the laboratory capacity and capability of countries to detect Zika virus; (ii) rapid and extensive field validation of the available molecular and serological tests in areas with and without Zika virus transmission, with a focus on pregnant women; (iii) monitoring the genomic diversity of circulating Zika virus strains; (iv) prospective studies into the virus infection kinetics, focusing on diagnostic sampling (specimen types, combinations and timings); and (v) developing external quality assessments for molecular and serological testing, including differential diagnosis for similar viruses and symptom clusters. The availability of reagents for diagnostic development (virus strains and antigens, quantified viral ribonucleic acid) needs to be facilitated. Conclusion An international laboratory response is needed, including preparation of protocols for prospective studies to address the most pressing information needs. PMID:27516635

Virus Infections of Honeybees Apis Mellifera

PubMed Central

Tantillo, Giuseppina; Bottaro, Marilisa; Di Pinto, Angela; Martella, Vito; Di Pinto, Pietro

2015-01-01

The health and vigour of honeybee colonies are threatened by numerous parasites (such as Varroa destructor and Nosema spp.) and pathogens, including viruses, bacteria, protozoa. Among honeybee pathogens, viruses are one of the major threats to the health and well-being of honeybees and cause serious concern for researchers and beekeepers. To tone down the threats posed by these invasive organisms, a better understanding of bee viral infections will be of crucial importance in developing effective and environmentally benign disease control strategies. Here we summarize recent progress in the understanding of the morphology, genome organization, transmission, epidemiology and pathogenesis of eight honeybee viruses: Deformed wing virus (DWV) and Kakugo virus (KV); Sacbrood virus (SBV); Black Queen cell virus (BQCV); Acute bee paralysis virus (ABPV); Kashmir bee virus (KBV); Israeli Acute Paralysis Virus (IAPV); Chronic bee paralysis virus (CBPV). The review has been designed to provide researchers in the field with updated information about honeybee viruses and to serve as a starting point for future research. PMID:27800411

Cell-free transmission of human adenovirus by passive mass transfer in cell culture simulated in a computer model.

PubMed

Yakimovich, Artur; Gumpert, Heidi; Burckhardt, Christoph J; Lütschg, Verena A; Jurgeit, Andreas; Sbalzarini, Ivo F; Greber, Urs F

2012-09-01

Viruses spread between cells, tissues, and organisms by cell-free and cell-cell transmissions. Both mechanisms enhance disease development, but it is difficult to distinguish between them. Here, we analyzed the transmission mode of human adenovirus (HAdV) in monolayers of epithelial cells by wet laboratory experimentation and a computer simulation. Using live-cell fluorescence microscopy and replication-competent HAdV2 expressing green fluorescent protein, we found that the spread of infection invariably occurred after cell lysis. It was affected by convection and blocked by neutralizing antibodies but was independent of second-round infections. If cells were overlaid with agarose, convection was blocked and round plaques developed around lytic infected cells. Infected cells that did not lyse did not give rise to plaques, highlighting the importance of cell-free transmission. Key parameters for cell-free virus transmission were the time from infection to lysis, the dose of free viruses determining infection probability, and the diffusion of single HAdV particles in aqueous medium. With these parameters, we developed an in silico model using multiscale hybrid dynamics, cellular automata, and particle strength exchange. This so-called white box model is based on experimentally determined parameters and reproduces viral infection spreading as a function of the local concentration of free viruses. These analyses imply that the extent of lytic infections can be determined by either direct plaque assays or can be predicted by calculations of virus diffusion constants and modeling.

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

PubMed Central

Dolja, Valerian V.

2014-01-01

SUMMARY Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus “self” that defines the identity of deep, ancient viral lineages. However, several other widespread viral “hallmark genes” encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host. PMID:24847023

Sentinel surveillance of influenza-like illness in two hospitals in Maracay, Venezuela: 2006-2010.

PubMed

Comach, Guillermo; Teneza-Mora, Nimfa; Kochel, Tadeusz J; Espino, Carlos; Sierra, Gloria; Camacho, Daria E; Laguna-Torres, V Alberto; Garcia, Josefina; Chauca, Gloria; Gamero, Maria E; Sovero, Merly; Bordones, Slave; Villalobos, Iris; Melchor, Angel; Halsey, Eric S

2012-01-01

Limited information exists on the epidemiology of acute febrile respiratory illnesses in tropical South American countries such as Venezuela. The objective of the present study was to examine the epidemiology of influenza-like illness (ILI) in two hospitals in Maracay, Venezuela. We performed a prospective surveillance study of persons with ILI who presented for care at two hospitals in Maracay, Venezuela, from October 2006 to December 2010. A respiratory specimen and clinical information were obtained from each participant. Viral isolation and identification with immunofluorescent antibodies and molecular methods were employed to detect respiratory viruses such as adenovirus, influenza A and B, parainfluenza, and respiratory sincytial virus, among others. There were 916 participants in the study (median age: 17 years; range: 1 month--86 years). Viruses were identified in 143 (15.6%) subjects, and one participant was found to have a co-infection with more than one virus. Influenza viruses, including pandemic H1N1 2009, were the most frequently detected pathogens, accounting for 67.4% (97/144) of the viruses detected. Adenovirus (15/144), parainfluenza virus (13/144), and respiratory syncytial virus (11/144) were also important causes of ILI in this study. Pandemic H1N1 2009 virus became the most commonly isolated influenza virus during its initial appearance in 2009. Two waves of the pandemic were observed: the first which peaked in August 2009 and the second--higher than the preceding - that peaked in October 2009. In 2010, influenza A/H3N2 re-emerged as the most predominant respiratory virus detected. Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Pandemic H1N1 2009 influenza virus did not completely replace other circulating influenza viruses during its initial appearance in 2009. Seasonal influenza A/H3N2 was the most common influenza virus in the post-pandemic phase.

Virus inactivation studies using ion beams, electron and gamma irradiation

NASA Astrophysics Data System (ADS)

Smolko, Eduardo E.; Lombardo, Jorge H.

2005-07-01

Known methods of virus inactivation are based on the chemical action of some substances such as acetylethylenimine, betapropiolactone, glycidalaldehyde, formaldehyde, etc. In such a process, the viral suspension should be kept at room or higher temperatures for 24-48 h. Under these conditions, physical and chemical agents act to degrade the virus antigenic proteins. On the contrary with ionizing radiations at low temperatures, the treatment does not cause such degradation allowing the study of different viral functions. In this work, particle (α, d and ß) and γ irradiations were used for partial and total inactivation of Foot and Mouth Disease Virus (FMDV), Rauscher Leukemia Virus (RLV) and Herpes Simplex Virus (HSV). Obtention of the D37 dose from survival curves and the application of the target theory, permitted the determination of molecular weight of the nucleic acid genomes, EBR values and useful information for vaccine preparation. For RLV virus, a two target model of the RNA genome was deduced in accordance with biological information while from data from the literature and our own work on the structure of the scrapie prion, considering the molecular weight obtained by application of the theory, a new model for prion replication is presented, based on a trimer molecule.

A Lagrangian particle model to predict the airborne spread of foot-and-mouth disease virus

NASA Astrophysics Data System (ADS)

Mayer, D.; Reiczigel, J.; Rubel, F.

Airborne spread of bioaerosols in the boundary layer over a complex terrain is simulated using a Lagrangian particle model, and applied to modelling the airborne spread of foot-and-mouth disease (FMD) virus. Two case studies are made with study domains located in a hilly region in the northwest of the Styrian capital Graz, the second largest town in Austria. Mountainous terrain as well as inhomogeneous and time varying meteorological conditions prevent from application of so far used Gaussian dispersion models, while the proposed model can handle these realistically. In the model, trajectories of several thousands of particles are computed and the distribution of virus concentration near the ground is calculated. This allows to assess risk of infection areas with respect to animal species of interest, such as cattle, swine or sheep. Meteorological input data like wind field and other variables necessary to compute turbulence were taken from the new pre-operational version of the non-hydrostatic numerical weather prediction model LMK ( Lokal-Modell-Kürzestfrist) running at the German weather service DWD ( Deutscher Wetterdienst). The LMK model provides meteorological parameters with a spatial resolution of about 2.8 km. To account for the spatial resolution of 400 m used by the Lagrangian particle model, the initial wind field is interpolated upon the finer grid by a mass consistent interpolation method. Case studies depict a significant influence of local wind systems on the spread of virus. Higher virus concentrations at the upwind side of the hills and marginal concentrations in the lee are well observable, as well as canalization effects by valleys. The study demonstrates that the Lagrangian particle model is an appropriate tool for risk assessment of airborne spread of virus by taking into account the realistic orographic and meteorological conditions.

Zika Virus Infection Among U.S. Pregnant Travelers - August 2015-February 2016.

PubMed

Meaney-Delman, Dana; Hills, Susan L; Williams, Charnetta; Galang, Romeo R; Iyengar, Preetha; Hennenfent, Andrew K; Rabe, Ingrid B; Panella, Amanda; Oduyebo, Titilope; Honein, Margaret A; Zaki, Sherif; Lindsey, Nicole; Lehman, Jennifer A; Kwit, Natalie; Bertolli, Jeanne; Ellington, Sascha; Igbinosa, Irogue; Minta, Anna A; Petersen, Emily E; Mead, Paul; Rasmussen, Sonja A; Jamieson, Denise J

2016-03-04

After reports of microcephaly and other adverse pregnancy outcomes in infants of mothers infected with Zika virus during pregnancy, CDC issued a travel alert on January 15, 2016, advising pregnant women to consider postponing travel to areas with active transmission of Zika virus. On January 19, CDC released interim guidelines for U.S. health care providers caring for pregnant women with travel to an affected area, and an update was released on February 5. As of February 17, CDC had received reports of nine pregnant travelers with laboratory-confirmed Zika virus disease; 10 additional reports of Zika virus disease among pregnant women are currently under investigation. No Zika virus-related hospitalizations or deaths among pregnant women were reported. Pregnancy outcomes among the nine confirmed cases included two early pregnancy losses, two elective terminations, and three live births (two apparently healthy infants and one infant with severe microcephaly); two pregnancies (approximately 18 weeks' and 34 weeks' gestation) are continuing without known complications. Confirmed cases of Zika virus infection were reported among women who had traveled to one or more of the following nine areas with ongoing local transmission of Zika virus: American Samoa, Brazil, El Salvador, Guatemala, Haiti, Honduras, Mexico, Puerto Rico, and Samoa. This report summarizes findings from the nine women with confirmed Zika virus infection during pregnancy, including case reports for four women with various clinical outcomes. U.S. health care providers caring for pregnant women with possible Zika virus exposure during pregnancy should follow CDC guidelines for patient evaluation and management. Zika virus disease is a nationally notifiable condition. CDC has developed a voluntary registry to collect information about U.S. pregnant women with confirmed Zika virus infection and their infants. Information about the registry is in preparation and will be available on the CDC website.

Modeling Virus Coinfection to Inform Management of Maize Lethal Necrosis in Kenya.

PubMed

Hilker, Frank M; Allen, Linda J S; Bokil, Vrushali A; Briggs, Cheryl J; Feng, Zhilan; Garrett, Karen A; Gross, Louis J; Hamelin, Frédéric M; Jeger, Michael J; Manore, Carrie A; Power, Alison G; Redinbaugh, Margaret G; Rúa, Megan A; Cunniffe, Nik J

2017-10-01

Maize lethal necrosis (MLN) has emerged as a serious threat to food security in sub-Saharan Africa. MLN is caused by coinfection with two viruses, Maize chlorotic mottle virus and a potyvirus, often Sugarcane mosaic virus. To better understand the dynamics of MLN and to provide insight into disease management, we modeled the spread of the viruses causing MLN within and between growing seasons. The model allows for transmission via vectors, soil, and seed, as well as exogenous sources of infection. Following model parameterization, we predict how management affects disease prevalence and crop performance over multiple seasons. Resource-rich farmers with large holdings can achieve good control by combining clean seed and insect control. However, crop rotation is often required to effect full control. Resource-poor farmers with smaller holdings must rely on rotation and roguing, and achieve more limited control. For both types of farmer, unless management is synchronized over large areas, exogenous sources of infection can thwart control. As well as providing practical guidance, our modeling framework is potentially informative for other cropping systems in which coinfection has devastating effects. Our work also emphasizes how mathematical modeling can inform management of an emerging disease even when epidemiological information remains scanty. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Swine Influenza/Variant Influenza Viruses

MedlinePlus

... Address What's this? Submit What's this? Submit Button Influenza Types Seasonal Avian Swine Variant Pandemic Other Information on Swine Influenza/Variant Influenza Virus Language: English (US) Español Recommend ...

Current approaches to the development of vaccines effective against parainfluenza viruses

PubMed Central

Murphy, B. R.

1988-01-01

Infection of infants and children with parainfluenza viruses can lead to serious lower respiratory tract disease. In order to review new information on the genetic organization, epidemiology, and immunobiology of these viruses and of respiratory syncytial virus, WHO, in conjunction with the National Institute of Allergy and Infectious Diseases, held a workshop in Bethesda, MD, USA, 4-5 May 1987. New data on the immunobiology and epidemiology of human parainfluenza 3 virus were presented that should facilitate the development of a vaccine against this pathogen. PMID:2844427

Data mining cDNAs reveals three new single stranded RNA viruses in Nasonia (Hymenopetera:Pteromalidae)

USDA-ARS?s Scientific Manuscript database

Hymenopteran viruses may provide insights into colony collapse disorder in honey bees and other insect species. Three novel small RNA viruses were discovered during the genomics effort for the beneficial parasitoid of flies in the genus Nasonia (Hymenoptera). Genomics provides a great deal of inform...

Transcription factor regulation and cytokine expression following in vitro infection of primary chicken cell culture with low pathogenic avian influenza virus

USDA-ARS?s Scientific Manuscript database

Avian influenza virus (AIV) induced proinflammatory cytokine expression is believed to contribute to the disease pathogenesis following infection. However, there is limited information on the avian immune response to infection with low pathogenic avian influenza virus (LPAIV). To gain a better under...

Isolation of H15N7 influenza virus from wild birds in Eastern Europe and its relationship to viruses from other regions

USDA-ARS?s Scientific Manuscript database

Background: Continuous monitoring of influenza viruses circulating in the natural reservoir in wild birds is important for early warning and forecasting of epizootic and epidemiological situation with influenza. These studies allow getting much valuable information on the environmental features of ...

76 FR 45262 - Agency Information Collection Activities; Proposed Collection; Comment Request; Current Good...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-28

... blood and blood components notify donors who have reactive test results for HIV, Hepatitis B Virus (HBV... who are at increased risk for transmitting human immunodeficiency virus (HIV) or hepatitis C virus... require immediate corrective action. Under the reporting requirements, Sec. 606.170(b), in brief, requires...

Virus Information Update CIAC-2301

DTIC Science & Technology

1998-05-21

a tune through a sound card. Byway is reported to be in the wild internationally, especially in Venezuela, Mexico , Bulgaria, UK and USA. REMOVAL NOTE...1482, Varicella Type: Program. Disk Location: Features: Damage: Size: See Also: Notes: v6-146: This virus was written to hurt users of the TBCLEAN...antivirus package. If you have a file infected with the Varicella virus, and if you tried to clean this virus infected file with tbclean, what would

76 FR 1559 - Guidelines for the Use of Electronic Voting Systems in Union Officer Elections

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-11

... voting. Id. However, there are still concerns regarding on-line computer security, viruses and attacks... casting votes at polling sites; electronic voting from remote site personal computers via the Internet..., Washington, DC 20210. Because of security precautions, the Department continues to experience delays in U.S...

Adapting a computer-delivered brief alcohol intervention for veterans with Hepatitis C.

PubMed

Cucciare, Michael A; Jamison, Andrea L; Combs, Ann S; Joshi, Gauri; Cheung, Ramsey C; Rongey, Catherine; Huggins, Joe; Humphreys, Keith

2017-12-01

This study adapted an existing computer-delivered brief alcohol intervention (cBAI) for use in Veterans with the hepatitis C virus (HCV) and examined its acceptability and feasibility in this patient population. A four-stage model consisting of initial pilot testing, qualitative interviews with key stakeholders, development of a beta version of the cBAI, and usability testing was used to achieve the study objectives. In-depth interviews gathered feedback for modifying the cBAI, including adding HCV-related content such as the health effects of alcohol on liver functioning, immune system functioning, and management of HCV, a preference for concepts to be displayed through "newer looking" graphics, and limiting the use of text to convey key concepts. Results from usability testing indicated that the modified cBAI was acceptable and feasible for use in this patient population. The development model used in this study is effective for gathering actionable feedback that can inform the development of a cBAI and can result in the development of an acceptable and feasible intervention for use in this population. Findings also have implications for developing computer-delivered interventions targeting behavior change more broadly.

Influenza Virus Reassortment Is Enhanced by Semi-infectious Particles but Can Be Suppressed by Defective Interfering Particles

PubMed Central

Tao, Hui; Steel, John; Lowen, Anice C.

2015-01-01

A high particle to infectivity ratio is a feature common to many RNA viruses, with ~90–99% of particles unable to initiate a productive infection under low multiplicity conditions. A recent publication by Brooke et al. revealed that, for influenza A virus (IAV), a proportion of these seemingly non-infectious particles are in fact semi-infectious. Semi-infectious (SI) particles deliver an incomplete set of viral genes to the cell, and therefore cannot support a full cycle of replication unless complemented through co-infection. In addition to SI particles, IAV populations often contain defective-interfering (DI) particles, which actively interfere with production of infectious progeny. With the aim of understanding the significance to viral evolution of these incomplete particles, we tested the hypothesis that SI and DI particles promote diversification through reassortment. Our approach combined computational simulations with experimental determination of infection, co-infection and reassortment levels following co-inoculation of cultured cells with two distinct influenza A/Panama/2007/99 (H3N2)-based viruses. Computational results predicted enhanced reassortment at a given % infection or multiplicity of infection with increasing semi-infectious particle content. Comparison of experimental data to the model indicated that the likelihood that a given segment is missing varies among the segments and that most particles fail to deliver ≥1 segment. To verify the prediction that SI particles augment reassortment, we performed co-infections using viruses exposed to low dose UV. As expected, the introduction of semi-infectious particles with UV-induced lesions enhanced reassortment. In contrast to SI particles, inclusion of DI particles in modeled virus populations could not account for observed reassortment outcomes. DI particles were furthermore found experimentally to suppress detectable reassortment, relative to that seen with standard virus stocks, most likely by interfering with production of infectious progeny from co-infected cells. These data indicate that semi-infectious particles increase the rate of reassortment and may therefore accelerate adaptive evolution of IAV. PMID:26440404

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification.

PubMed

Aiewsakun, Pakorn; Simmonds, Peter

2018-02-20

The International Committee on Taxonomy of Viruses (ICTV) classifies viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of viruses detected in environmental (metagenomic) studies that lack any phenotypic data. The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for viruses of all genome configurations and genome sizes. The analysis pipeline that we have called 'Genome Relationships Applied to Virus Taxonomy' (GRAViTy) was highly effective at reproducing the current assignments of viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned viruses from unassigned viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy. A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.

Trends in plant virus epidemiology: opportunities from new or improved technologies.

PubMed

Jones, R A C

2014-06-24

This review focuses on new or improved technologies currently being applied, or likely to be applied in the future, to worldwide research on plant virus epidemiology. Recent technological advances and innovations provide many opportunities to improve understanding of the way diverse types of plant virus epidemics develop and how to manage them. The review starts at the macro level by considering how recent innovations in remote sensing and precision agriculture can provide valuable information about (i) virus epidemics occurring at continental, regional or district scales (via satellites) and within individual crops (mostly via lightweight unmanned aerial vehicles), and (ii) exactly where to target control measures. It then considers recent improvements in information systems and innovations in modelling that improve (i) understanding of virus epidemics and ability to predict them, and (ii) delivery to end-users of critical advice on control measures, such as Internet-based Decision Support Systems. The review goes on to discuss how advances in analysis of spatiotemporal virus spread patterns within crops can help to enhance understanding of how virus epidemics develop and validate potentially useful virus control measures. At the micro level, the review then considers the many insights that advances in molecular epidemiology can provide about genetic variation within plant virus populations involved in epidemics, and how this variation drives what occurs at the macro level. Next, it describes how recent innovations in virus detection technologies are providing many opportunities to collect and analyse new types, and ever increasing amounts, of data about virus epidemics, and the genetic variability of the virus populations involved. Finally, the implications for plant virus epidemiology of technologies likely to be important in the future are considered. To address looming world food insecurity and threats to plant biodiversity resulting from climate change and rapid population growth, it is important that new and improved technologies that help understand and control epidemics of damaging plant viruses are adopted as smoothly and speedily as possible. Copyright © 2013 Elsevier B.V. All rights reserved.

Primate immunodeficiency virus classification and nomenclature: Review

DOE PAGES

Foley, Brian T.; Leitner, Thomas; Paraskevis, Dimitrios; ...

2016-10-24

The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. As a result, this review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written inmore » 2000.« less

An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery

PubMed Central

Parker, Michael T.

2016-01-01

Recent advances in sequencing technologies have opened the door for the classification of the human virome. While taxonomic classification can be applied to the viruses identified in such studies, this gives no information as to the type of interaction the virus has with the host. As follow-up studies are performed to address these questions, the description of these virus-host interactions would be greatly enriched by applying a standard set of definitions that typify them. This paper describes a framework with which all members of the human virome can be classified based on principles of ecology. The scaffold not only enables categorization of the human virome, but can also inform research aimed at identifying novel virus-host interactions. PMID:27698618

Computer loss experience and predictions

NASA Astrophysics Data System (ADS)

Parker, Donn B.

1996-03-01

The types of losses organizations must anticipate have become more difficult to predict because of the eclectic nature of computers and the data communications and the decrease in news media reporting of computer-related losses as they become commonplace. Total business crime is conjectured to be decreasing in frequency and increasing in loss per case as a result of increasing computer use. Computer crimes are probably increasing, however, as their share of the decreasing business crime rate grows. Ultimately all business crime will involve computers in some way, and we could see a decline of both together. The important information security measures in high-loss business crime generally concern controls over authorized people engaged in unauthorized activities. Such controls include authentication of users, analysis of detailed audit records, unannounced audits, segregation of development and production systems and duties, shielding the viewing of screens, and security awareness and motivation controls in high-value transaction areas. Computer crimes that involve highly publicized intriguing computer misuse methods, such as privacy violations, radio frequency emanations eavesdropping, and computer viruses, have been reported in waves that periodically have saturated the news media during the past 20 years. We must be able to anticipate such highly publicized crimes and reduce the impact and embarrassment they cause. On the basis of our most recent experience, I propose nine new types of computer crime to be aware of: computer larceny (theft and burglary of small computers), automated hacking (use of computer programs to intrude), electronic data interchange fraud (business transaction fraud), Trojan bomb extortion and sabotage (code security inserted into others' systems that can be triggered to cause damage), LANarchy (unknown equipment in use), desktop forgery (computerized forgery and counterfeiting of documents), information anarchy (indiscriminate use of crypto without control), Internet abuse (antisocial use of data communications), and international industrial espionage (governments stealing business secrets). A wide variety of safeguards are necessary to deal with these new crimes. The most powerful controls include (1) carefully controlled use of cryptography and digital signatures with good key management and overriding business and government decryption capability and (2) use of tokens such as smart cards to increase the strength of secret passwords for authentication of computer users. Jewelry-type security for small computers--including registration of serial numbers and security inventorying of equipment, software, and connectivity--will be necessary. Other safeguards include automatic monitoring of computer use and detection of unusual activities, segmentation and filtering of networks, special paper and ink for documents, and reduction of paper documents. Finally, international cooperation of governments to create trusted environments for business is essential.

Introduction

NASA Astrophysics Data System (ADS)

Dum, Ralph

Various types of diverse networks — communication networks, transport networks, global business networks, networks of friends, or the Internet — shape our daily life and the way we think and act. We depend on various social, economic, and technological networks that weave a tissue of businesses, governments, technologies and that contain us as citizens, users, or customers. We only become aware of our dependence if failures occur in these networks: when cities are plunged into darkness because of a breakdown of the power grid like happened recently in New York, when national economies collapse because of a failure of global financial systems like happened in the South-Asian banking crisis, or when computer viruses spread with mind-boggling speed over information networks destroying or, even worse, exposing sensitive data.

Use of Lean Response to Improve Pandemic Influenza Surge in Public Health Laboratories

PubMed Central

Chang, Yin; Prystajecky, Natalie; Petric, Martin; Mak, Annie; Abbott, Brendan; Paris, Benjamin; Decker, K.C.; Pittenger, Lauren; Guercio, Steven; Stott, Jeff; Miller, Joseph D.

2012-01-01

A novel influenza A (H1N1) virus detected in April 2009 rapidly spread around the world. North American provincial and state laboratories have well-defined roles and responsibilities, including providing accurate, timely test results for patients and information for regional public health and other decision makers. We used the multidisciplinary response and rapid implementation of process changes based on Lean methods at the provincial public health laboratory in British Columbia, Canada, to improve laboratory surge capacity in the 2009 influenza pandemic. Observed and computer simulating evaluation results from rapid processes changes showed that use of Lean tools successfully expanded surge capacity, which enabled response to the 10-fold increase in testing demands. PMID:22257385

Are Aquatic Viruses a Biological Archive of Genetic Information from Universe?

NASA Astrophysics Data System (ADS)

Toparceanu, F.; Negoita, Gh. T.; Nita, I. I.; Sava, D.

2009-04-01

After 1990, when the viruses were admited as the most abundant lifeforms from aquatic environments, it became obvious that viral lysis had an essential role on release and recycling of nutrients. Studies on cellular cultures and modeling suggest that this is an important quantitative process. The viruses from oceans represent the widest source of genetic diversity on the Earth, uncharacterized yet. The ancient lifeforms records stretching back a million years are locked in ice caps. The trend of glaciers melting as effect of actual climate change will promote the release of ancient viruses from ice caps. The increasing of the freshwater layer led to the replace of some algae species by others. Law-Racovitza Station (69o23'S 76o23'E) from East Antarctica (Larsemann Hills Oasis) offers opportunities to study the Antarctic marine ecosystem, as well as archaic aquatic ecosystems from this area ( 150 lakes and waterways resulted from ice and snow melting during the austral summer). According to Law-Racovitza Station Scientific Program, we are performing studies regarding the effect of climate changes on virus-algae host relationship in these aquatic ecosystems. Phycodnaviruses, that infect the eukaryote algae, are comprised of ancient genes and they are considered a "peek" of genetic diversity useful in biological studies and exobiology regarding the evolution of genetic sequencing. The latest discoveries of the giant aquatic viruses open the unexpected perspectives for understanding the role of viral infection in global ecosystem; beyond the old concept which considered that the viruses were only etiological agents of human, animals and plants illnesses. The aquatic viruses which infect microalgae contain similar genes of other viruses, bacteria, arhebacteria and eukaryotes, all of them being on the same genome. Which is the signification of enormous abundance of viruses and excessive diversity of genetic information encoded by viruses? There is the possibility that the viruses to be a biological archive which contains all genetic information of the whole Earth? So, there are a lot of questions and we are attempting to find answers in the present work which will be examined in the framework of the project entitled ,,The structure and dynamics of polar ecosystems: interhemispheric comparisons of micro, macroflora and biogeochemical processes in relation to climate change" (PolarCLIMATE programme of ESF PP-039/24.11.2008) coordinated by Romania.

Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses

PubMed Central

Harvey, William T.; Benton, Donald J.; Gregory, Victoria; Hall, James P. J.; Daniels, Rodney S.; Bedford, Trevor; Haydon, Daniel T.; Hay, Alan J.; McCauley, John W.; Reeve, Richard

2016-01-01

Determining phenotype from genetic data is a fundamental challenge. Identification of emerging antigenic variants among circulating influenza viruses is critical to the vaccine virus selection process, with vaccine effectiveness maximized when constituents are antigenically similar to circulating viruses. Hemagglutination inhibition (HI) assay data are commonly used to assess influenza antigenicity. Here, sequence and 3-D structural information of hemagglutinin (HA) glycoproteins were analyzed together with corresponding HI assay data for former seasonal influenza A(H1N1) virus isolates (1997–2009) and reference viruses. The models developed identify and quantify the impact of eighteen amino acid substitutions on the antigenicity of HA, two of which were responsible for major transitions in antigenic phenotype. We used reverse genetics to demonstrate the causal effect on antigenicity for a subset of these substitutions. Information on the impact of substitutions allowed us to predict antigenic phenotypes of emerging viruses directly from HA gene sequence data and accuracy was doubled by including all substitutions causing antigenic changes over a model incorporating only the substitutions with the largest impact. The ability to quantify the phenotypic impact of specific amino acid substitutions should help refine emerging techniques that predict the evolution of virus populations from one year to the next, leading to stronger theoretical foundations for selection of candidate vaccine viruses. These techniques have great potential to be extended to other antigenically variable pathogens. PMID:27057693

Aedes-Borne Virus-Mosquito Interactions: Mass Spectrometry Strategies and Findings.

PubMed

Pando-Robles, Victoria; Batista, Cesar V

2017-06-01

Aedes-borne viruses are responsible for high-impact neglected tropical diseases and unpredictable outbreaks such as the ongoing Zika epidemics. Aedes mosquitoes spread different arboviruses such as Dengue virus (DENV), Chikungunya virus (CHIKV), and Zika virus, among others, and are responsible for the continuous emergence and reemergence of these pathogens. These viruses have complex transmission cycles that include two hosts, namely the Aedes mosquito as a vector and susceptible vertebrate hosts. Human infection with arboviruses causes diseases that range from subclinical or mild to febrile diseases, encephalitis, and hemorrhagic fever. Infected mosquitoes do not show detectable signs of disease, even though the virus maintains a lifelong persistent infection. The infection of the Aedes mosquito by viruses involves a molecular crosstalk between cell and viral proteins. An understanding of how mosquito vectors and viruses interact is of fundamental interest, and it also offers novel perspectives for disease control. In recent years, mass spectrometry (MS)-based strategies in combination with bioinformatics have been successfully applied to identify and quantify global changes in cellular proteins, lipids, peptides, and metabolites in response to viral infection. Although the information about proteomics in the Aedes mosquito is limited, the information that has been reported can set up the basis for future studies. This review reflects how MS-based approaches have extended our understanding of Aedes mosquito biology and the development of DENV and CHIKV infection in the vector. Finally, this review discusses future challenges in the field.

Rapid quantitation of neuraminidase inhibitor drug resistance in influenza virus quasispecies.

PubMed

Lackenby, Angie; Democratis, Jane; Siqueira, Marilda M; Zambon, Maria C

2008-01-01

Emerging resistance of influenza viruses to neuraminidase inhibitors is a concern, both in surveillance of global circulating strains and in treatment of individual patients. Current methodologies to detect resistance rely on the use of cultured virus, thus taking time to complete or lacking the sensitivity to detect mutations in viral quasispecies. Methodology for rapid detection of clinically meaningful resistance is needed to assist individual patient management and to track the transmission of resistant viruses in the community. We have developed a pyrosequencing methodology to detect and quantitate influenza neuraminidase inhibitor resistance mutations in cultured virus and directly in clinical material. Our assays target polymorphisms associated with drug resistance in the neuraminidase genes of human influenza A H1N1 as well as human and avian H5N1 viruses. Quantitation can be achieved using viral RNA extracted directly from respiratory or tissue samples, thus eliminating the need for virus culture and allowing the assay of highly pathogenic viruses such as H5N1 without high containment laboratory facilities. Antiviral-resistant quasispecies are detected and quantitated accurately when present in the total virus population at levels as low as 10%. Pyrosequencing is a real-time assay; therefore, results can be obtained within a clinically relevant timeframe and provide information capable of informing individual patient or outbreak management. Pyrosequencing is ideally suited for early identification of emerging antiviral resistance in human and avian influenza infection and is a useful tool for laboratory surveillance and pandemic preparedness.

Virus world as an evolutionary network of viruses and capsidless selfish elements.

PubMed

Koonin, Eugene V; Dolja, Valerian V

2014-06-01

Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus "self" that defines the identity of deep, ancient viral lineages. However, several other widespread viral "hallmark genes" encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

The use of experimental structures to model protein dynamics.

PubMed

Katebi, Ataur R; Sankar, Kannan; Jia, Kejue; Jernigan, Robert L

2015-01-01

The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very high-for example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methods-Principal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to accomplish each step and show how to use these programs and tools. We also include computer programs to generate movies based on PCs and ENM modes and describe how to visualize them.

The Use of Experimental Structures to Model Protein Dynamics

PubMed Central

Katebi, Ataur R.; Sankar, Kannan; Jia, Kejue; Jernigan, Robert L.

2014-01-01

Summary The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very high – for example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methods – Principal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to accomplish each step and show how to use these programs and tools. We also include computer programs to generate movies based on PCs and ENM modes and describe how to visualize them. PMID:25330965

Parameter and observation importance in modelling virus transport in saturated porous media - Investigations in a homogenous system

USGS Publications Warehouse

Barth, Gilbert R.; Hill, M.C.

2005-01-01

This paper evaluates the importance of seven types of parameters to virus transport: hydraulic conductivity, porosity, dispersivity, sorption rate and distribution coefficient (representing physical-chemical filtration), and in-solution and adsorbed inactivation (representing virus inactivation). The first three parameters relate to subsurface transport in general while the last four, the sorption rate, distribution coefficient, and in-solution and adsorbed inactivation rates, represent the interaction of viruses with the porous medium and their ability to persist. The importance of four types of observations to estimate the virus-transport parameters are evaluated: hydraulic heads, flow, temporal moments of conservative-transport concentrations, and virus concentrations. The evaluations are conducted using one- and two-dimensional homogeneous simulations, designed from published field experiments, and recently developed sensitivity-analysis methods. Sensitivity to the transport-simulation time-step size is used to evaluate the importance of numerical solution difficulties. Results suggest that hydraulic conductivity, porosity, and sorption are most important to virus-transport predictions. Most observation types provide substantial information about hydraulic conductivity and porosity; only virus-concentration observations provide information about sorption and inactivation. The observations are not sufficient to estimate these important parameters uniquely. Even with all observation types, there is extreme parameter correlation between porosity and hydraulic conductivity and between the sorption rate and in-solution inactivation. Parameter estimation was accomplished by fixing values of porosity and in-solution inactivation.

Artificial-life researchers try to create social reality.

PubMed

Flam, F

1994-08-12

Some scientists, among them cosmologist Stephen Hawking, argue that computer viruses are alive. A better case might be made for many of the self-replicating silicon-based creatures featured at the fourth Conference on Artificial Life, held on 5 to 8 July in Boston. Researchers from computer science, biology, and other disciplines presented computer programs that, among other things, evolved cooperative strategies in a selfish world and recreated themselves in ever more complex forms.

38 CFR 1.487 - Disclosure of information related to infection with the human immunodeficiency virus to the...

Code of Federal Regulations, 2011 CFR

2011-07-01

... related to infection with the human immunodeficiency virus to the spouse or sexual partner of the patient... the human immunodeficiency virus to the spouse or sexual partner of the patient. (a) Subject to... to an individual whom the patient has, during the process of professional counseling or of testing to...

38 CFR 1.487 - Disclosure of information related to infection with the human immunodeficiency virus to the...

Code of Federal Regulations, 2014 CFR

2014-07-01

... related to infection with the human immunodeficiency virus to the spouse or sexual partner of the patient... the human immunodeficiency virus to the spouse or sexual partner of the patient. (a) Subject to... to an individual whom the patient has, during the process of professional counseling or of testing to...

38 CFR 1.487 - Disclosure of information related to infection with the human immunodeficiency virus to the...

Code of Federal Regulations, 2012 CFR

2012-07-01

... related to infection with the human immunodeficiency virus to the spouse or sexual partner of the patient... the human immunodeficiency virus to the spouse or sexual partner of the patient. (a) Subject to... to an individual whom the patient has, during the process of professional counseling or of testing to...

38 CFR 1.487 - Disclosure of information related to infection with the human immunodeficiency virus to the...

Code of Federal Regulations, 2013 CFR

2013-07-01

... related to infection with the human immunodeficiency virus to the spouse or sexual partner of the patient... the human immunodeficiency virus to the spouse or sexual partner of the patient. (a) Subject to... to an individual whom the patient has, during the process of professional counseling or of testing to...

38 CFR 1.487 - Disclosure of information related to infection with the human immunodeficiency virus to the...

Code of Federal Regulations, 2010 CFR

2010-07-01

... related to infection with the human immunodeficiency virus to the spouse or sexual partner of the patient... the human immunodeficiency virus to the spouse or sexual partner of the patient. (a) Subject to... to an individual whom the patient has, during the process of professional counseling or of testing to...

38 CFR 1.486 - Disclosure of information related to infection with the human immunodeficiency virus to public...

Code of Federal Regulations, 2010 CFR

2010-07-01

... related to infection with the human immunodeficiency virus to public health authorities. 1.486 Section 1... immunodeficiency virus to public health authorities. (a) In the case of any record which is maintained in... may be disclosed to a Federal, State, or local public health authority, charged under Federal or State...

38 CFR 1.486 - Disclosure of information related to infection with the human immunodeficiency virus to public...

Code of Federal Regulations, 2011 CFR

2011-07-01

... related to infection with the human immunodeficiency virus to public health authorities. 1.486 Section 1... immunodeficiency virus to public health authorities. (a) In the case of any record which is maintained in... may be disclosed to a Federal, State, or local public health authority, charged under Federal or State...

Zika Virus -10 Public Health Achievements in 2016 and Future Priorities.

PubMed

Oussayef, Nadia L; Pillai, Satish K; Honein, Margaret A; Ben Beard, C; Bell, Beth; Boyle, Coleen A; Eisen, Lars M; Kohl, Katrin; Kuehnert, Matthew J; Lathrop, Eva; Martin, Stacey W; Martin, Rebecca; McAllister, Janet C; McClune, Elizabeth Pantino; Mead, Paul; Meaney-Delman, Dana; Petersen, Brett; Petersen, Lyle R; Polen, Kara N D; Powers, Ann M; Redd, Stephen C; Sejvar, James J; Sharp, Tyler; Villanueva, Julie; Jamieson, Denise J

2017-01-06

The introduction of Zika virus into the Region of the Americas (Americas) and the subsequent increase in cases of congenital microcephaly resulted in activation of CDC's Emergency Operations Center on January 22, 2016, to ensure a coordinated response and timely dissemination of information, and led the World Health Organization to declare a Public Health Emergency of International Concern on February 1, 2016. During the past year, public health agencies and researchers worldwide have collaborated to protect pregnant women, inform clinicians and the public, and advance knowledge about Zika virus (Figure 1). This report summarizes 10 important contributions toward addressing the threat posed by Zika virus in 2016. To protect pregnant women and their fetuses and infants from the effects of Zika virus infection during pregnancy, public health activities must focus on preventing mosquito-borne transmission through vector control and personal protective practices, preventing sexual transmission by advising abstention from sex or consistent and correct use of condoms, and preventing unintended pregnancies by reducing barriers to access to highly effective reversible contraception.

Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses

PubMed Central

Zhou, Bin; Barnes, John R.; Sessions, October M.; Chou, Tsui-Wen; Wilson, Malania; Stark, Thomas J.; Volk, Michelle; Spirason, Natalie; Halpin, Rebecca A.; Kamaraj, Uma Sangumathi; Ding, Tao; Stockwell, Timothy B.; Ghedin, Elodie; Barr, Ian G.

2017-01-01

ABSTRACT Influenza A and B viruses are the causative agents of annual influenza epidemics that can be severe, and influenza A viruses intermittently cause pandemics. Sequence information from influenza virus genomes is instrumental in determining mechanisms underpinning antigenic evolution and antiviral resistance. However, due to sequence diversity and the dynamics of influenza virus evolution, rapid and high-throughput sequencing of influenza viruses remains a challenge. We developed a single-reaction influenza A/B virus (FluA/B) multiplex reverse transcription-PCR (RT-PCR) method that amplifies the most critical genomic segments (hemagglutinin [HA], neuraminidase [NA], and matrix [M]) of seasonal influenza A and B viruses for next-generation sequencing, regardless of viral type, subtype, or lineage. Herein, we demonstrate that the strategy is highly sensitive and robust. The strategy was validated on thousands of seasonal influenza A and B virus-positive specimens using multiple next-generation sequencing platforms. PMID:28978683

Infection dynamics of pandemic 2009 H1N1 influenza virus in a two-site swine herd.

PubMed

Allerson, M W; Davies, P R; Gramer, M R; Torremorell, M

2014-12-01

Influenza A viruses are common causes of respiratory disease in pigs and can be transmitted among multiple host species, including humans. The current lack of published information on infection dynamics of influenza viruses within swine herds hinders the ability to make informed animal health, biosecurity and surveillance programme decisions. The objectives of this serial cross-sectional study were to describe the infection dynamics of influenza virus in a two-site swine system by estimating the prevalence of influenza virus in animal subpopulations at the swine breeding herd and describing the temporal pattern of infection in a selected cohort of growing pigs weaned from the breeding herd. Nasal swab and blood samples were collected at approximately 30-day intervals from the swine breeding herd (Site 1) known to be infected with pandemic 2009 H1N1 influenza virus. Sows, gilts and neonatal pigs were sampled at each sampling event, and samples were tested for influenza virus genome using matrix gene RRT-PCR. Influenza virus was detected in neonatal pigs, but was not detected in sow or gilt populations via RRT-PCR. A virus genetically similar to that detected in the neonatal pig population at Site 1 was also detected at the wean-to-finish site (Site 2), presumably following transportation of infected weaned pigs. Longitudinal sampling of nasal swabs and oral fluids revealed that influenza virus persisted in the growing pigs at Site 2 for at least 69 days. The occurrence of influenza virus in neonatal pigs, but not breeding females, at Site 1 emphasizes the potential for virus maintenance in this dynamic subpopulation, the importance of including this subpopulation in surveillance programmes and the potential transport of influenza virus between sites via the movement of weaned pigs. © 2013 Blackwell Verlag GmbH.

PREDAC-H3: a user-friendly platform for antigenic surveillance of human influenza a(H3N2) virus based on hemagglutinin sequences.

PubMed

Peng, Yousong; Yang, Lei; Li, Honglei; Zou, Yuanqiang; Deng, Lizong; Wu, Aiping; Du, Xiangjun; Wang, Dayan; Shu, Yuelong; Jiang, Taijiao

2016-08-15

Timely surveillance of the antigenic dynamics of the influenza virus is critical for accurate selection of vaccine strains, which is important for effective prevention of viral spread and infection. Here, we provide a computational platform, called PREDAC-H3, for antigenic surveillance of human influenza A(H3N2) virus based on the sequence of surface protein hemagglutinin (HA). PREDAC-H3 not only determines the antigenic variants and antigenic cluster (grouped for similar antigenicity) to which the virus belongs, based on HA sequences, but also allows visualization of the spatial distribution and temporal dynamics of antigenic clusters of viruses isolated from around the world, thus assisting in antigenic surveillance of human influenza A(H3N2) virus. It is publicly available from: http://biocloud.hnu.edu.cn/influ411/html/index.php : yshu@cnic.org.cn or taijiao@moon.ibp.ac.cn. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Problems in understanding the structure and assembly of viruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, J.

1997-12-01

Though viruses infect the cells of all groups of animals, plants, and microorganisms, their structures follow a limited number of general themes; spherical or cylindrical shells built of hundreds of repeated protein subunits enclosing a nucleic acid - DNA or RNA - genome. Since the 1960s it has been known that the protein shells of spherical viruses in fact conform to icosahedral symmetry or to subtle deviations from icosahedral symmetry. The construction of the shell lattices and the transformations they go through in the different stages of the viral life cycle are not fully understood. The shells contain the nucleicmore » in a highly condensed state, of unknown coiling/organization. Features of the well studied bacterial viruses will be reviewed, with examples from adenoviruses, herpesviruses, poliovirus, and HIV. The emergence of new viral disease has led to increased interest in the development of agents which interfere with virus reproduction at the level of the assembly or function of the organized particle. Recently computational approaches to the problem of virus assembly have made important contributions to clarifying shell assembly processes. 1 ref.« less

Antiviral agents: structural basis of action and rational design.

PubMed

Menéndez-Arias, Luis; Gago, Federico

2013-01-01

During the last 30 years, significant progress has been made in the development of novel antiviral drugs, mainly crystallizing in the establishment of potent antiretroviral therapies and the approval of drugs inhibiting hepatitis C virus replication. Although major targets of antiviral intervention involve intracellular processes required for the synthesis of viral proteins and nucleic acids, a number of inhibitors blocking virus assembly, budding, maturation, entry or uncoating act on virions or viral capsids. In this review, we focus on the drug discovery process while presenting the currently used methodologies to identify novel antiviral drugs by using a computer-based approach. We provide examples illustrating structure-based antiviral drug development, specifically neuraminidase inhibitors against influenza virus (e.g. oseltamivir and zanamivir) and human immunodeficiency virus type 1 protease inhibitors (i.e. the development of darunavir from early peptidomimetic compounds such as saquinavir). A number of drugs in preclinical development acting against picornaviruses, hepatitis B virus and human immunodeficiency virus and their mechanism of action are presented to show how viral capsids can be exploited as targets of antiviral therapy.

The Binding Interface between Human APOBEC3F and HIV-1 Vif Elucidated by Genetic and Computational Approaches.

PubMed

Richards, Christopher; Albin, John S; Demir, Özlem; Shaban, Nadine M; Luengas, Elizabeth M; Land, Allison M; Anderson, Brett D; Holten, John R; Anderson, John S; Harki, Daniel A; Amaro, Rommie E; Harris, Reuben S

2015-12-01

APOBEC3 family DNA cytosine deaminases provide overlapping defenses against pathogen infections. However, most viruses have elaborate evasion mechanisms such as the HIV-1 Vif protein, which subverts cellular CBF-β and a polyubiquitin ligase complex to neutralize these enzymes. Despite advances in APOBEC3 and Vif biology, a full understanding of this direct host-pathogen conflict has been elusive. We combine virus adaptation and computational studies to interrogate the APOBEC3F-Vif interface and build a robust structural model. A recurring compensatory amino acid substitution from adaptation experiments provided an initial docking constraint, and microsecond molecular dynamic simulations optimized interface contacts. Virus infectivity experiments validated a long-lasting electrostatic interaction between APOBEC3F E289 and HIV-1 Vif R15. Taken together with mutagenesis results, we propose a wobble model to explain how HIV-1 Vif has evolved to bind different APOBEC3 enzymes and, more generally, how pathogens may evolve to escape innate host defenses. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Human papilloma virus vaccination: perceptions of young Korean women.

PubMed

Kang, Hee Sun; Shin, Hyunsook; Hyun, Myung-Sun; Kim, Mi Ja

2010-09-01

This paper is a report of a descriptive study of young Korean women's perceptions of use of the human papilloma virus vaccine. In Korea, cervical cancer is one of the leading cancers in women, and the rate of human papilloma virus infection is increasing. A national media campaign has recently begun to promote human papilloma virus vaccination. However, research addressing the acceptability of this vaccine to women in Korea has been limited. Twenty-five Korean women, 21-30 years of age, participated in seven focus groups. The data were collected in 2007. Participants were concerned about the potential harmful effects of the human papilloma virus vaccine, a possible increase in unsafe sexual behaviours, and the high cost of the vaccine, which is not covered by health insurance. They suggested group vaccination at-cost or free of charge. They discussed ambivalence about the vaccination, the need for more information about the vaccine, and questions about its effectiveness. Most preferred to wait until more people have been vaccinated. There is a need for more aggressive dissemination of information about the safety and efficacy of the human papilloma virus vaccine. More reasonable cost, insurance coverage, or free vaccination using a group approach might increase young Korean women's acceptance and use of the human papilloma virus vaccine.

Diversity, Distribution, and Evolution of Tomato Viruses in China Uncovered by Small RNA Sequencing.

PubMed

Xu, Chenxi; Sun, Xuepeng; Taylor, Angela; Jiao, Chen; Xu, Yimin; Cai, Xiaofeng; Wang, Xiaoli; Ge, Chenhui; Pan, Guanghui; Wang, Quanxi; Fei, Zhangjun; Wang, Quanhua

2017-06-01

Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here, we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified, including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with cold spots and hot spots. Most samples were coinfected by multiple viruses, and the majority of identified viruses are positive-sense single-stranded RNA viruses. Evolutionary analysis of one of the most dominant tomato viruses, Tomato yellow leaf curl virus (TYLCV), predicts its origin and the time back to its most recent common ancestor. The broadly sampled data have enabled us to identify several unreported viruses in tomato, including a completely new virus, which has a genome of ∼13.4 kb and groups with aphid-transmitted viruses in the genus Cytorhabdovirus Although both DNA and RNA viruses can trigger the biogenesis of virus-derived small interfering RNAs (vsiRNAs), we show that features such as length distribution, paired distance, and base selection bias of vsiRNA sequences reflect different plant Dicer-like proteins and Argonautes involved in vsiRNA biogenesis. Collectively, this study offers insights into host-virus interaction in tomato and provides valuable information to facilitate the management of viral diseases. IMPORTANCE Tomato is an important source of micronutrients in the human diet and is extensively consumed around the world. Virus is among the major constraints on tomato production. Categorizing virus species that are capable of infecting tomato and understanding their diversity and evolution are challenging due to difficulties in detecting such fast-evolving biological entities. Here, we report the landscape of the tomato virome in China, the leading country in tomato production. We identified dozens of viruses present in tomato, including both well-documented and completely new viruses. Some newly emerged viruses in tomato were found to spread fast, and therefore, prompt attention is needed to control them. Moreover, we show that the virus genomes exhibit considerable degree of polymorphisms and recombination, and the virus-derived small interfering RNA (vsiRNA) sequences indicate distinct vsiRNA biogenesis mechanisms for different viruses. The Chinese tomato virome that we developed provides valuable information to facilitate the management of tomato viral diseases. Copyright © 2017 American Society for Microbiology.

Diversity, Distribution, and Evolution of Tomato Viruses in China Uncovered by Small RNA Sequencing

PubMed Central

Xu, Chenxi; Taylor, Angela; Jiao, Chen; Xu, Yimin; Cai, Xiaofeng; Wang, Xiaoli; Ge, Chenhui; Pan, Guanghui; Wang, Quanxi

2017-01-01

ABSTRACT Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here, we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified, including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with cold spots and hot spots. Most samples were coinfected by multiple viruses, and the majority of identified viruses are positive-sense single-stranded RNA viruses. Evolutionary analysis of one of the most dominant tomato viruses, Tomato yellow leaf curl virus (TYLCV), predicts its origin and the time back to its most recent common ancestor. The broadly sampled data have enabled us to identify several unreported viruses in tomato, including a completely new virus, which has a genome of ∼13.4 kb and groups with aphid-transmitted viruses in the genus Cytorhabdovirus. Although both DNA and RNA viruses can trigger the biogenesis of virus-derived small interfering RNAs (vsiRNAs), we show that features such as length distribution, paired distance, and base selection bias of vsiRNA sequences reflect different plant Dicer-like proteins and Argonautes involved in vsiRNA biogenesis. Collectively, this study offers insights into host-virus interaction in tomato and provides valuable information to facilitate the management of viral diseases. IMPORTANCE Tomato is an important source of micronutrients in the human diet and is extensively consumed around the world. Virus is among the major constraints on tomato production. Categorizing virus species that are capable of infecting tomato and understanding their diversity and evolution are challenging due to difficulties in detecting such fast-evolving biological entities. Here, we report the landscape of the tomato virome in China, the leading country in tomato production. We identified dozens of viruses present in tomato, including both well-documented and completely new viruses. Some newly emerged viruses in tomato were found to spread fast, and therefore, prompt attention is needed to control them. Moreover, we show that the virus genomes exhibit considerable degree of polymorphisms and recombination, and the virus-derived small interfering RNA (vsiRNA) sequences indicate distinct vsiRNA biogenesis mechanisms for different viruses. The Chinese tomato virome that we developed provides valuable information to facilitate the management of tomato viral diseases. PMID:28331089

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foley, Brian T.; Leitner, Thomas; Paraskevis, Dimitrios

The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. As a result, this review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written inmore » 2000.« less

Transmission of Hepatitis C Virus during Computed Tomography Scanning with Contrast

PubMed Central

Rius, Cristina; Caylà, Joan A.

2008-01-01

Six cases of acute hepatitis C related to computed tomography scanning with contrast were identified in 3 hospitals. A patient with chronic hepatitis C had been subjected to the same procedure immediately before each patient who developed acute infection. Viral molecular analysis showed identity between isolates from cases with acute and chronic hepatitis C. PMID:18258135

The Weekly Fab Five: Things You Should Do Every Week To Keep Your Computer Running in Tip-Top Shape.

ERIC Educational Resources Information Center

Crispen, Patrick

2001-01-01

Describes five steps that school librarians should follow every week to keep their computers running at top efficiency. Explains how to update virus definitions; run Windows update; run ScanDisk to repair errors on the hard drive; run a disk defragmenter; and backup all data. (LRW)

Preventing Catastrophes from Data Loss

ERIC Educational Resources Information Center

Goldsborough, Reid

2004-01-01

What's the worst thing that can happen to your computer? Worse than a hard disk crash, virus infection, spam assault, denial-of-service attack, hacker take-over, fire, flood, or other human, mechanical or natural disaster is a faulty backup when you really need it. If the computer blows up, as long as your data is backed up securely, you can…

A Signature in HIV-1 Envelope Leader Peptide Associated with Transition from Acute to Chronic Infection Impacts Envelope Processing and Infectivity

PubMed Central

Asmal, Mohammed; Hellmann, Ina; Liu, Weimin; Keele, Brandon F.; Perelson, Alan S.; Bhattacharya, Tanmoy; Gnanakaran, S.; Daniels, Marcus; Haynes, Barton F.; Korber, Bette T.; Hahn, Beatrice H.; Shaw, George M.; Letvin, Norman L.

2011-01-01

Mucosal transmission of the human immunodeficiency virus (HIV) results in a bottleneck in viral genetic diversity. Gnanakaran and colleagues used a computational strategy to identify signature amino acids at particular positions in Envelope that were associated either with transmitted sequences sampled very early in infection, or sequences sampled during chronic infection. Among the strongest signatures observed was an enrichment for the stable presence of histidine at position 12 at transmission and in early infection, and a recurrent loss of histidine at position 12 in chronic infection. This amino acid lies within the leader peptide of Envelope, a region of the protein that has been shown to influence envelope glycoprotein expression and virion infectivity. We show a strong association between a positively charged amino acid like histidine at position 12 in transmitted/founder viruses with more efficient trafficking of the nascent envelope polypeptide to the endoplasmic reticulum and higher steady-state glycoprotein expression compared to viruses that have a non-basic position 12 residue, a substitution that was enriched among viruses sampled from chronically infected individuals. When expressed in the context of other viral proteins, transmitted envelopes with a basic amino acid position 12 were incorporated at higher density into the virus and exhibited higher infectious titers than did non-signature envelopes. These results support the potential utility of using a computational approach to examine large viral sequence data sets for functional signatures and indicate the importance of Envelope expression levels for efficient HIV transmission. PMID:21876761

Enzymes and Enzyme Activity Encoded by Nonenveloped Viruses.

PubMed

Azad, Kimi; Banerjee, Manidipa; Johnson, John E

2017-09-29

Viruses are obligate intracellular parasites that rely on host cell machineries for their replication and survival. Although viruses tend to make optimal use of the host cell protein repertoire, they need to encode essential enzymatic or effector functions that may not be available or accessible in the host cellular milieu. The enzymes encoded by nonenveloped viruses-a group of viruses that lack any lipid coating or envelope-play vital roles in all the stages of the viral life cycle. This review summarizes the structural, biochemical, and mechanistic information available for several classes of enzymes and autocatalytic activity encoded by nonenveloped viruses. Advances in research and development of antiviral inhibitors targeting specific viral enzymes are also highlighted.

Crimean-Congo Hemorrhagic Fever (CCHF)

MedlinePlus

... Congo Hemorrhagic Fever (CCHF) [PDF – 2 pages] Virus Ecology Viral Hemorrhagic Fever (VHF) Information for Specific Groups ... Diagnosis Treatment Prevention Outbreak Distribution Map Resources Virus Ecology File Formats Help: How do I view different ...

Avian Influenza (Bird Flu)

MedlinePlus

... Spread Bird Flu to People Interim Guidance on Testing Pandemic Flu Key Information Prevention & Treatment Influenza A Type Viruses & Subtypes Transmission of Avian Influenza A Viruses Between Animals and People Related Links Research Glossary of Influenza ( ...

Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses.

PubMed

Chang, Hsiao-Han; Huber, Roland G; Bond, Peter J; Grad, Yonatan H; Camerini, David; Maurer-Stroh, Sebastian; Lipsitch, Marc

2017-07-01

To analyse the proportions of protein identity between Zika virus and dengue, Japanese encephalitis, yellow fever, West Nile and chikungunya viruses as well as polymorphism between different Zika virus strains. We used published protein sequences for the Zika virus and obtained protein sequences for the other viruses from the National Center for Biotechnology Information (NCBI) protein database or the NCBI virus variation resource. We used BLASTP to find regions of identity between viruses. We quantified the identity between the Zika virus and each of the other viruses, as well as within-Zika virus polymorphism for all amino acid k -mers across the proteome, with k ranging from 6 to 100. We assessed accessibility of protein fragments by calculating the solvent accessible surface area for the envelope and nonstructural-1 (NS1) proteins. In total, we identified 294 Zika virus protein fragments with both low proportion of identity with other viruses and low levels of polymorphisms among Zika virus strains. The list includes protein fragments from all Zika virus proteins, except NS3. NS4A has the highest number (190 k -mers) of protein fragments on the list. We provide a candidate list of protein fragments that could be used when developing a sensitive and specific serological test to detect previous Zika virus infections.

A No-Notice Drill of Hospital Preparedness in Responding to Ebola Virus Disease in Taiwan.

PubMed

Hsu, Shih-Min; Chien, Li-Jung; Tseng, Shu-Hui; Kuo, Steve H S

2015-01-01

The Ebola virus was first discovered in 1976, but the outbreak of Ebola virus disease that began in Guinea, West Africa, in December 2013 shocked the world. It is the largest and most severe epidemic of Ebola virus disease to date. The US Centers for Disease Control and Prevention confirmed that inadequate implementation of the policy of acquiring travel history led to a delay in identifying the first imported Ebola virus disease case. The Taiwan Centers for Disease Control developed a no-notice drill that used a simulated patient to assess hospitals' emergency preparedness capacity in responding to Ebola virus disease. Despite the fact that regular inspection shows that more than 90% of regional hospitals and medical centers inquired about patients' travel history, occupation, contact history, and cluster information, the no-notice drill revealed that more than 40% of regional hospitals and medical centers failed to ask emergency room patients about these factors. Therefore, to assist in inquiries about travel history, occupation, contact history, and cluster information in emergency triage and outpatient settings, the Taiwan CDC revised the criteria for hospital infection control inspection. It requested that hospitals issue appropriate reminders and implement process control mechanisms to block diagnostic processes in instances in which healthcare workers do not inquire about travel history, occupation, contact history, and cluster information. Furthermore, the Taiwan CDC will continue no-notice inspections in order to strengthen hospitals' infection control measures and reduce the risk of infectious disease transmission in the healthcare system.

Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010

PubMed Central

Comach, Guillermo; Teneza-Mora, Nimfa; Kochel, Tadeusz J.; Espino, Carlos; Sierra, Gloria; Camacho, Daria E.; Laguna-Torres, V. Alberto; Garcia, Josefina; Chauca, Gloria; Gamero, Maria E.; Sovero, Merly; Bordones, Slave; Villalobos, Iris; Melchor, Angel; Halsey, Eric S.

2012-01-01

Background Limited information exists on the epidemiology of acute febrile respiratory illnesses in tropical South American countries such as Venezuela. The objective of the present study was to examine the epidemiology of influenza-like illness (ILI) in two hospitals in Maracay, Venezuela. Methodology/Principal Findings We performed a prospective surveillance study of persons with ILI who presented for care at two hospitals in Maracay, Venezuela, from October 2006 to December 2010. A respiratory specimen and clinical information were obtained from each participant. Viral isolation and identification with immunofluorescent antibodies and molecular methods were employed to detect respiratory viruses such as adenovirus, influenza A and B, parainfluenza, and respiratory sincytial virus, among others. There were 916 participants in the study (median age: 17 years; range: 1 month – 86 years). Viruses were identified in 143 (15.6%) subjects, and one participant was found to have a co-infection with more than one virus. Influenza viruses, including pandemic H1N1 2009, were the most frequently detected pathogens, accounting for 67.4% (97/144) of the viruses detected. Adenovirus (15/144), parainfluenza virus (13/144), and respiratory syncytial virus (11/144) were also important causes of ILI in this study. Pandemic H1N1 2009 virus became the most commonly isolated influenza virus during its initial appearance in 2009. Two waves of the pandemic were observed: the first which peaked in August 2009 and the second - higher than the preceding - that peaked in October 2009. In 2010, influenza A/H3N2 re-emerged as the most predominant respiratory virus detected. Conclusions/Significance Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Pandemic H1N1 2009 influenza virus did not completely replace other circulating influenza viruses during its initial appearance in 2009. Seasonal influenza A/H3N2 was the most common influenza virus in the post-pandemic phase. PMID:22984519

Hepatitis E virus and fulminant hepatitis--a virus or host-specific pathology?

PubMed

Smith, Donald B; Simmonds, Peter

2015-04-01

Fulminant hepatitis is a rare outcome of infection with hepatitis E virus. Several recent reports suggest that virus variation is an important determinant of disease progression. To critically examine the evidence that virus-specific factors underlie the development of fulminant hepatitis following hepatitis E virus infection. Published sequence information of hepatitis E virus isolates from patients with and without fulminant hepatitis was collected and analysed using statistical tests to identify associations between virus polymorphisms and disease outcome. Fulminant hepatitis has been reported following infection with all four hepatitis E virus genotypes that infect humans comprising multiple phylogenetic lineages within genotypes 1, 3 and 4. Analysis of virus sequences from individuals infected by a common source did not detect any common substitutions associated with progression to fulminant hepatitis. Re-analysis of previously reported associations between virus substitutions and fulminant hepatitis suggests that these were probably the result of sampling biases. Host-specific factors rather than virus genotype, variants or specific substitutions appear to be responsible for the development of fulminant hepatitis. © 2014 The Authors. Liver International Published by John Wiley & Sons Ltd.

Serodiagnosis for Tumor Viruses

PubMed Central

Morrison, Brian J.; Labo, Nazzarena; Miley, Wendell J.; Whitby, Denise

2015-01-01

The known human tumor viruses include the DNA viruses Epstein-Barr virus, Kaposi sarcoma herpesvirus, Merkel cell polyomavirus, human papillomavirus, and hepatitis B virus. RNA tumor viruses include Human T-cell lymphotrophic virus type-1 and hepatitis C virus. The serological identification of antigens/antibodies in plasma serum is a rapidly progressing field with utility for both scientists and clinicians. Serology is useful for conducting seroepidemiology studies and to inform on the pathogenesis and host immune response to a particular viral agent. Clinically, serology is useful for diagnosing current or past infection and for aiding in clinical management decisions. Serology is useful for screening blood donations for infectious agents and for monitoring the outcome of vaccination against these viruses. Serodiagnosis of human tumor viruses has improved in recent years with increased specificity and sensitivity of the assays, as well as reductions in cost and the ability to assess multiple antibody/antigens in single assays. Serodiagnosis of tumor viruses plays an important role in our understanding of the prevalence and transmission of these viruses and ultimately in the ability to develop treatments/preventions for these globally important diseases. PMID:25843726

Poxvirus viability and signatures in historical relics.

PubMed

McCollum, Andrea M; Li, Yu; Wilkins, Kimberly; Karem, Kevin L; Davidson, Whitni B; Paddock, Christopher D; Reynolds, Mary G; Damon, Inger K

2014-02-01

Although it has been >30 years since the eradication of smallpox, the unearthing of well-preserved tissue material in which the virus may reside has called into question the viability of variola virus decades or centuries after its original occurrence. Experimental data to address the long-term stability and viability of the virus are limited. There are several instances of well-preserved corpses and tissues that have been examined for poxvirus viability and viral DNA. These historical specimens cause concern for potential exposures, and each situation should be approached cautiously and independently with the available information. Nevertheless, these specimens provide information on the history of a major disease and vaccination against it.

Household transmission of influenza virus

PubMed Central

Tsang, Tim K.; Lau, Lincoln L. H.; Cauchemez, Simon; Cowling, Benjamin J.

2015-01-01

Human influenza viruses cause regular epidemics and occasional pandemics with a substantial public health burden. Household transmission studies have provided valuable information on the dynamics of influenza transmission. We reviewed published studies and found that once one household member is infected with influenza, the risk of infection in a household contact can be up to 38%, and the delay between onset in index and secondary cases is around 3 days. Younger age was associated with higher susceptibility. In the future, household transmission studies will provide information on transmission dynamics including the correlation of virus shedding and symptoms with transmission, and the correlation of new measures of immunity with protection against infection. PMID:26612500

Broad cross-reactive T cell receptor repertoires recognizing dissimilar Epstein-Barr and influenza A virus epitopes

PubMed Central

Clute, Shalyn C.; Naumov, Yuri N.; Watkin, Levi B.; Aslan, Nuray; Sullivan, John L.; Thorley-Lawson, David A.; Luzuriaga, Katherine; Welsh, Raymond M.; Puzone, Roberto; Celada, Franco; Selin, Liisa K.

2013-01-01

Memory T cells cross-reactive with epitopes encoded by related or even unrelated viruses may alter the immune response and pathogenesis of infection by a process known as heterologous immunity. Because a challenge virus epitope may react with only a subset of the T cell repertoire in a cross-reactive epitope-specific memory pool, the vigorous cross-reactive response may be narrowly focused, or oligoclonal. We show here, by examining human T cell cross-reactivity between the HLA-A2-restricted influenza A virus-encoded M158-66 epitope (GILGFVFTL) and the dissimilar Epstein-Barr virus-encoded BMLF1280-288 epitope (GLCTLVAML), that under some conditions heterologous immunity can lead to a significant broadening rather than a narrowing of the T cell receptor repertoire. We suggest that dissimilar cross-reactive epitopes might generate a broad rather than narrow T cell repertoire if there is a lack of dominant high affinity clones, and this hypothesis is supported by computer simulation. PMID:21048112

Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments

DOE PAGES

Hraber, Peter; Rademeyer, Cecilia; Williamson, Carolyn; ...

2017-07-26

In the search for effective immunologic interventions to prevent and treat HIV-1 infection, standardized reference reagents are a cost-effective way to maintain robustness and reproducibility among immunological assays. To support planned and ongoing studies where clade C predominates, here we describe three virus panels, chosen from 200 well-characterized clade C envelope (Env)-pseudotyped viruses from early infection. All 200 Envs were expressed as a single round of replication pseudoviruses and were tested to quantify neutralization titers by 16 broadly neutralizing antibodies (bnAbs) and sera from 30 subjects with chronic clade C infections. We selected large panels of 50 and 100 Envsmore » either to characterize cross-reactive breadth for sera identified as having potent neutralization activity based on initial screening or to evaluate neutralization magnitude-breadth distributions of newly isolated antibodies. We identified these panels by downselection after hierarchical clustering of bnAb neutralization titers. The resulting panels represent the diversity of neutralization profiles throughout the range of virus sensitivities identified in the original panel of 200 viruses. A small 12-Env panel was chosen to screen sera from vaccine trials or natural-infection studies for neutralization responses. We considered panels selected by previously described methods but favored a computationally informed method that enabled selection of viruses representing diverse neutralization sensitivity patterns, given that we do nota prioriknow what the neutralization-response profile of vaccine sera will be relative to that of sera from infected individuals. The resulting 12-Env panel complements existing panels. Use of standardized panels enables direct comparisons of data from different trials and study sites testing HIV-1 clade C-specific products. HIV-1 group M includes nine clades and many recombinants. Clade C is the most common lineage, responsible for roughly half of current HIV-1 infections, and is a focus for vaccine design and testing. Standard reference reagents, particularly virus panels to study neutralization by antibodies, are crucial for developing cost-effective and yet rigorous and reproducible assays against diverse examples of this variable virus. We developed clade C-specific panels for use as standardized reagents to monitor complex polyclonal sera for neutralization activity and to characterize the potency and breadth of cross-reactive neutralization by monoclonal antibodies, whether engineered or isolated from infected individuals. We chose from 200 southern African, clade C envelope-pseudotyped viruses with neutralization titers against 16 broadly neutralizing antibodies and 30 sera from chronic clade C infections. We selected panels to represent the diversity of bnAb neutralization profiles and Env neutralization sensitivities. Finally, use of standard virus panels can facilitate comparison of results across studies and sites.« less

Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hraber, Peter; Rademeyer, Cecilia; Williamson, Carolyn

In the search for effective immunologic interventions to prevent and treat HIV-1 infection, standardized reference reagents are a cost-effective way to maintain robustness and reproducibility among immunological assays. To support planned and ongoing studies where clade C predominates, here we describe three virus panels, chosen from 200 well-characterized clade C envelope (Env)-pseudotyped viruses from early infection. All 200 Envs were expressed as a single round of replication pseudoviruses and were tested to quantify neutralization titers by 16 broadly neutralizing antibodies (bnAbs) and sera from 30 subjects with chronic clade C infections. We selected large panels of 50 and 100 Envsmore » either to characterize cross-reactive breadth for sera identified as having potent neutralization activity based on initial screening or to evaluate neutralization magnitude-breadth distributions of newly isolated antibodies. We identified these panels by downselection after hierarchical clustering of bnAb neutralization titers. The resulting panels represent the diversity of neutralization profiles throughout the range of virus sensitivities identified in the original panel of 200 viruses. A small 12-Env panel was chosen to screen sera from vaccine trials or natural-infection studies for neutralization responses. We considered panels selected by previously described methods but favored a computationally informed method that enabled selection of viruses representing diverse neutralization sensitivity patterns, given that we do nota prioriknow what the neutralization-response profile of vaccine sera will be relative to that of sera from infected individuals. The resulting 12-Env panel complements existing panels. Use of standardized panels enables direct comparisons of data from different trials and study sites testing HIV-1 clade C-specific products. HIV-1 group M includes nine clades and many recombinants. Clade C is the most common lineage, responsible for roughly half of current HIV-1 infections, and is a focus for vaccine design and testing. Standard reference reagents, particularly virus panels to study neutralization by antibodies, are crucial for developing cost-effective and yet rigorous and reproducible assays against diverse examples of this variable virus. We developed clade C-specific panels for use as standardized reagents to monitor complex polyclonal sera for neutralization activity and to characterize the potency and breadth of cross-reactive neutralization by monoclonal antibodies, whether engineered or isolated from infected individuals. We chose from 200 southern African, clade C envelope-pseudotyped viruses with neutralization titers against 16 broadly neutralizing antibodies and 30 sera from chronic clade C infections. We selected panels to represent the diversity of bnAb neutralization profiles and Env neutralization sensitivities. Finally, use of standard virus panels can facilitate comparison of results across studies and sites.« less

76 FR 6694 - Disclosure of Medical Information to the Surrogate of a Patient Who Lacks Decision-Making Capacity

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-08

... virus, or sickle cell anemia, without first obtaining the written consent of the patient. 38 U.S.C. 7332... virus, or sickle cell anemia in VA records and are applicable in combination with other regulations..., infection with the human immunodeficiency virus, or sickle cell anemia to a surrogate of the patient who is...

In-vitro infection of pupae with Israeli Acute Paralysis Virus suggests variation for susceptibility and disturbance of transcriptional homeostasis in honey bees (Apis mellifera)

USDA-ARS?s Scientific Manuscript database

The ongoing decline of honey bee health worldwide is a serious economic and ecological concern. One major contributor to the decline are pathogens, including several honey bee viruses. However, information is limited on the biology of bee viruses and molecular interactions with their hosts. An exper...

A phylogenomic data-driven exploration of viral origins and evolution

PubMed Central

Nasir, Arshan; Caetano-Anollés, Gustavo

2015-01-01

The origin of viruses remains mysterious because of their diverse and patchy molecular and functional makeup. Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data. We take full advantage of the wealth of available protein structural and functional data to explore the evolution of the proteomic makeup of thousands of cells and viruses. Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the “viral supergroup” and the existence of widespread episodes of horizontal transfer of genetic information. Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells. The model for the origin and evolution of viruses and cells is backed by strong genomic and structural evidence and can be reconciled with existing models of viral evolution if one considers viruses to have originated from ancient cells and not from modern counterparts. PMID:26601271

Spontaneous Regression of Pulmonary Nodules Presenting as Epstein-Barr Virus-related Atypical Infectious Mononucleosis.

PubMed

Shinozuka, Jun; Awaguni, Hitoshi; Tanaka, Shin-Ichiro; Makino, Shigeru; Maruyama, Rikken; Inaba, Tohru; Imashuku, Shinsaku

2016-07-01

Pulmonary nodules associated with Epstein-Barr virus (EBV)-related atypical infectious mononucleosis have rarely been described. A 12-year-old Japanese boy, upon admission, revealed multiple small round nodules (a total of 7 nodules in 4 to 8 mm size) in the lungs on computed tomography. The hemorrhagic pharyngeal tonsils with hot signals on 18F-fluorodeoxyglucose-positron emission tomography-computed tomography were biopsied revealing the presence of EBV-encoded small nuclear RNA (EBER)-positive cells; however, no lymphoma was noted. The patient was diagnosed as having atypical EBV-infectious mononucleosis associated with primary EBV infection. Pulmonary nodules markedly reduced in numbers and sizes spontaneously over a 2-year period. Differential diagnosis of pulmonary nodules in childhood should include atypical EBV infection.

Open Reading Frame Phylogenetic Analysis on the Cloud

PubMed Central

2013-01-01

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

National Computer Security Conference (15th) held in Baltimore, Maryland on October 13-16, 1992. Volume 1: Proceedings

DTIC Science & Technology

1992-10-16

The Spread of Viruses Programs have been developed to attack some of these problems , primarily in the virus arena. Pick up any PC magazine and you...a particular DBMS-specific research area. These documents discuss the research problem , present an overview of relevant research and development ...MITRE has developed to date and a brief discussion those documents currently under development . For each companion document, the problem being

Mutagenesis of the La Crosse Virus glycoprotein supports a role for Gc (1066-1087) as the fusion peptide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plassmeyer, Matthew L.; Graduate Group Molecular and Cell Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6058; Soldan, Samantha S.

The La Crosse Virus (LACV) M segment encodes two glycoproteins (Gn and Gc), and plays a critical role in the neuropathogenesis of LACV infection as the primary determinant of neuroinvasion. A recent study from our group demonstrated that the region comprising the membrane proximal two-thirds of Gc, amino acids 860-1442, is critical in mediating LACV fusion and entry. Furthermore, computational analysis identified structural similarities between a portion of this region, amino acids 970-1350, and the E1 fusion protein of two alphaviruses: Sindbis virus and Semliki Forrest virus (SFV). Within the region 970-1350, a 22-amino-acid hydrophobic segment (1066-1087) is predicted tomore » correlate structurally with the fusion peptides of class II fusion proteins. We performed site-directed mutagenesis of key amino acids in this 22-amino acid segment and determined the functional consequences of these mutations on fusion and entry. Several mutations within this hydrophobic domain affected glycoprotein expression to some extent, but all mutations either shifted the pH threshold of fusion below that of the wild-type protein, reduced fusion efficiency, or abrogated cell-to-cell fusion and pseudotype entry altogether. These results, coupled with the aforementioned computational modeling, suggest that the LACV Gc functions as a class II fusion protein and support a role for the region Gc 1066-1087 as a fusion peptide.« less

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

PubMed Central

Farkas, Kata; Harrison, Christian; Jones, David L.; McCarthy, Alan J.

2018-01-01

ABSTRACT Detection of viruses in the environment is heavily dependent on PCR-based approaches that require reference sequences for primer design. While this strategy can accurately detect known viruses, it will not find novel genotypes or emerging and invasive viral species. In this study, we investigated the use of viromics, i.e., high-throughput sequencing of the biosphere’s viral fraction, to detect human-/animal-pathogenic RNA viruses in the Conwy river catchment area in Wales, United Kingdom. Using a combination of filtering and nuclease treatment, we extracted the viral fraction from wastewater and estuarine river water and sediment, followed by high-throughput RNA sequencing (RNA-Seq) analysis on the Illumina HiSeq platform, for the discovery of RNA virus genomes. We found a higher richness of RNA viruses in wastewater samples than in river water and sediment, and we assembled a complete norovirus genotype GI.2 genome from wastewater effluent, which was not contemporaneously detected by conventional reverse transcription-quantitative PCR (qRT-PCR). The simultaneous presence of diverse rotavirus signatures in wastewater indicated the potential for zoonotic infections in the area and suggested runoff from pig farms as a possible origin of these viruses. Our results show that viromics can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided appropriate and rigorous controls are included. IMPORTANCE Enteric viruses cause gastrointestinal illness and are commonly transmitted through the fecal-oral route. When wastewater is released into river systems, these viruses can contaminate the environment. Our results show that we can use viromics to find the range of potentially pathogenic viruses that are present in the environment and identify prevalent genotypes. The ultimate goal is to trace the fate of these pathogenic viruses from origin to the point where they are a threat to human health, informing reference-based detection methods and water quality management. PMID:29795788

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses.

PubMed

Adriaenssens, Evelien M; Farkas, Kata; Harrison, Christian; Jones, David L; Allison, Heather E; McCarthy, Alan J

2018-01-01

Detection of viruses in the environment is heavily dependent on PCR-based approaches that require reference sequences for primer design. While this strategy can accurately detect known viruses, it will not find novel genotypes or emerging and invasive viral species. In this study, we investigated the use of viromics, i.e., high-throughput sequencing of the biosphere's viral fraction, to detect human-/animal-pathogenic RNA viruses in the Conwy river catchment area in Wales, United Kingdom. Using a combination of filtering and nuclease treatment, we extracted the viral fraction from wastewater and estuarine river water and sediment, followed by high-throughput RNA sequencing (RNA-Seq) analysis on the Illumina HiSeq platform, for the discovery of RNA virus genomes. We found a higher richness of RNA viruses in wastewater samples than in river water and sediment, and we assembled a complete norovirus genotype GI.2 genome from wastewater effluent, which was not contemporaneously detected by conventional reverse transcription-quantitative PCR (qRT-PCR). The simultaneous presence of diverse rotavirus signatures in wastewater indicated the potential for zoonotic infections in the area and suggested runoff from pig farms as a possible origin of these viruses. Our results show that viromics can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided appropriate and rigorous controls are included. IMPORTANCE Enteric viruses cause gastrointestinal illness and are commonly transmitted through the fecal-oral route. When wastewater is released into river systems, these viruses can contaminate the environment. Our results show that we can use viromics to find the range of potentially pathogenic viruses that are present in the environment and identify prevalent genotypes. The ultimate goal is to trace the fate of these pathogenic viruses from origin to the point where they are a threat to human health, informing reference-based detection methods and water quality management.

Viral etiologies of influenza-like illness and severe acute respiratory infections in Thailand.

PubMed

Chittaganpitch, Malinee; Waicharoen, Sunthareeya; Yingyong, Thitipong; Praphasiri, Prabda; Sangkitporn, Somchai; Olsen, Sonja J; Lindblade, Kim A

2018-07-01

Information on the burden, characteristics and seasonality of non-influenza respiratory viruses is limited in tropical countries. Describe the epidemiology of selected non-influenza respiratory viruses in Thailand between June 2010 and May 2014 using a sentinel surveillance platform established for influenza. Patients with influenza-like illness (ILI; history of fever or documented temperature ≥38°C, cough, not requiring hospitalization) or severe acute respiratory infection (SARI; history of fever or documented temperature ≥38°C, cough, onset <10 days, requiring hospitalization) were enrolled from 10 sites. Throat swabs were tested for influenza viruses, respiratory syncytial virus (RSV), metapneumovirus (MPV), parainfluenza viruses (PIV) 1-3, and adenoviruses by polymerase chain reaction (PCR) or real-time reverse transcriptase-PCR. We screened 15 369 persons with acute respiratory infections and enrolled 8106 cases of ILI (5069 cases <15 years old) and 1754 cases of SARI (1404 cases <15 years old). Among ILI cases <15 years old, influenza viruses (1173, 23%), RSV (447, 9%), and adenoviruses (430, 8%) were the most frequently identified respiratory viruses tested, while for SARI cases <15 years old, RSV (196, 14%) influenza (157, 11%) and adenoviruses (90, 6%) were the most common. The RSV season significantly overlapped the larger influenza season from July to November in Thailand. The global expansion of influenza sentinel surveillance provides an opportunity to gather information on the characteristics of cases positive for non-influenza respiratory viruses, particularly seasonality, although adjustments to case definitions may be required. © 2018 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

A Mixed-Methods Study on the Acceptability of Using eHealth for HIV Prevention and Sexual Health Care Among Men Who Have Sex With Men in China

PubMed Central

Bien, Cedric H; Wei, Chongyi; Lo, Elaine J; Yang, Min; Tucker, Joseph D; Yang, Ligang; Meng, Gang; Hightow-Weidman, Lisa B

2015-01-01

Background Human immunodeficiency virus (HIV) infection disproportionately affects men who have sex with men (MSM). Over half of all HIV-positive MSM in China may not know their HIV status. Mobile phones and Web interventions (eHealth) are underutilized resources that show promise for supporting HIV education, testing, and linkage to care. Objective This mixed-methods study among MSM in China assessed technology utilization and eHealth acceptability for sexual health care. Methods We conducted in-depth interviews and an online survey. Qualitative analyses informed the development of the Internet survey, which was administered through two popular MSM websites. Bivariate and multivariate analysis assessed characteristics of MSM interested in eHealth for sexual health care. Results The qualitative sample included MSM across a range of ages, education, marital status, sexuality, and HIV testing experience. Qualitative findings included the importance of the Internet as the primary source of information about sexual health, HIV and other sexually transmitted diseases (STDs), use of the Internet to enable HIV testing opportunities by facilitating connections with both the gay community and health care providers, and mixed perceptions regarding the confidentiality of eHealth tools for sexual health. Among the Internet sample (N=1342), the average age was 30.6 years old, 82.81% (1098/1342) were single, and 53.42% (711/1331) had completed college. In the past 3 months, 38.66% (382/988) had condomless sex and 60.53% (805/1330) self-reported having ever tested for HIV. The majority of men owned computers (94.14%, 1220/1296) and mobile phones (92.32%, 1239/1342), which many had used to search for HIV/STD information and testing sites. In multivariate analysis, interest in using computers or mobile phones to support their sexual health care was associated with being a student, prior use of computers or mobile phones to search for general health information, prior use of computers or mobile phones to search for HIV/STD information, and confidentiality concerns. Conclusions MSM in this sample had high utilization of technology and interest in eHealth despite confidentiality concerns. Future eHealth interventions can thoughtfully and creatively address these concerns as a priority for successful implementation. PMID:25900881

Prevention and control of seasonal influenza with vaccines. Recommendations of the Advisory Committee on Immunization Practices--United States, 2013-2014.

PubMed

2013-09-20

This report updates the 2012 recommendations by CDC's Advisory Committee on Immunization Practices (ACIP) regarding the use of influenza vaccines for the prevention and control of seasonal influenza (CDC. Prevention and control of influenza with vaccines: recommendations of the Advisory Committee on Immunization Practices [ACIP]. MMWR 2012;61:613-8). Routine annual influenza vaccination is recommended for all persons aged ≥ 6 months. For the 2013-14 influenza season, it is expected that trivalent live attenuated influenza vaccine (LAIV3) will be replaced by a quadrivalent LAIV formulation (LAIV4). Inactivated influenza vaccines (IIVs) will be available in both trivalent (IIV3) and quadrivalent (IIV4) formulations. Vaccine virus strains included in the 2013-14 U.S. trivalent influenza vaccines will be an A/California/7/2009 (H1N1)-like virus, an H3N2 virus antigenically like the cell-propagated prototype virus A/Victoria/361/2011, and a B/Massachusetts/2/2012-like virus. Quadrivalent vaccines will include an additional influenza B virus strain, a B/Brisbane/60/2008-like virus, intended to ensure that both influenza B virus antigenic lineages (Victoria and Yamagata) are included in the vaccine. This report describes recently approved vaccines, including LAIV4, IIV4, trivalent cell culture-based inactivated influenza vaccine (ccIIV3), and trivalent recombinant influenza vaccine (RIV3). No preferential recommendation is made for one influenza vaccine product over another for persons for whom more than one product is otherwise appropriate. This information is intended for vaccination providers, immunization program personnel, and public health personnel. These recommendations and other information are available at CDC's influenza website (http://www.cdc.gov/flu); any updates also will be found at this website. Vaccination and health-care providers should check the CDC influenza website periodically for additional information.

The mathematics of virus shell assembly. Progress report 1995--1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berger, B.

1996-08-01

This research focuses on applying computational and mathematical techniques to problems in biology, and more specifically to problems in protein folding. Significant progress has been made in the following areas relating to virus shell assembly: the local rules theory has been further developed; development has begun on a second-generation simulator which provides a more physically realistic model of assembly, collaborative efforts have continued with an experimental biologist to verify and inspire the local rules theory; an investigation has been initiated into the mechanics of virus shell assembly; laboratory experiments have been conducted on bacteriophage T4 which verify that the previouslymore » believed structure for the core may be incorrect.« less

Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns

DOE PAGES

Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; ...

2015-01-23

Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox( cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set ofmore » diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.« less

Management of the infant with respiratory syncytial virus.

PubMed

Corey, M A; Clore, E R

1991-04-01

This article examines updated clinical information concerning respiratory syncytial virus (RSV) infection including epidemiology, pathology, clinical manifestations, diagnosis, treatment, nosocomial infection, and prognosis. Also presented is current information on ribavirin therapy, its side effects, and precautions. Research related to the most effective isolation methodology is discussed, as well as nursing diagnoses based on Gordon's Functional Health Patterns and interventions for the infant hospitalized with RSV bronchiolitis and/or pneumonia.

Host-Based Multivariate Statistical Computer Operating Process Anomaly Intrusion Detection System (PAIDS)

DTIC Science & Technology

2009-03-01

viii 3.2.3 Sub7 ...from TaskInfo in Excel Format. 3.2.3 Sub7 Also known as SubSeven, this is one of the best known, most widely distributed backdoor programs on the...engineering the spread of viruses, worms, backdoors and other malware. The Sub7 Trojan establishes a server on the victim computer that

Behavior-Based Fault Monitoring

DTIC Science & Technology

1990-12-03

processor targeted for avionics and space applications . It appears that the signature monitoring technique can be extended to detect computer viruses as...most common approach is structural duplication. Although effective, duplication is too expensive for all but a few applications . Redundancy can also be...Signature Monitoring and Encryption," Int. Conf. on Dependable Computing for Critical Applications , August 1989. 7. K.D. Wilken and J.P. Shen

Preventing Catastrophes from Data Loss

ERIC Educational Resources Information Center

Goldsborough, Reid

2004-01-01

What's the worst thing that can happen to a computer? Worse than a hard disk crash, virus infection, spare assault, denial-of-service attack, hacker take-over, fire, flood or some other human, mechanical or natural disaster is a faulty backup when it is really needed. If the computer blows up, as long as the data is backed up securely, it can be…

Bottlenecks in HIV-1 transmission: insights from the study of founder viruses.

PubMed

Joseph, Sarah B; Swanstrom, Ronald; Kashuba, Angela D M; Cohen, Myron S

2015-07-01

HIV-1 infection typically results from the transmission of a single viral variant, the transmitted/founder (T/F) virus. Studies of these HIV-1 variants provide critical information about the transmission bottlenecks and the selective pressures acting on the virus in the transmission fluid and in the recipient tissues. These studies reveal that T/F virus phenotypes are shaped by stochastic and selective forces that restrict transmission and may be targets for prevention strategies. In this Review, we highlight how studies of T/F viruses contribute to a better understanding of the biology of HIV-1 transmission and discuss how these findings affect HIV-1 prevention strategies.

[Dutch computer domestication, 1975-1990].

PubMed

Veraart, Frank

2008-01-01

A computer seems an indispensable tool among twenty-first century households. Computers however, did not come as manna from heaven. The domestication and appropriation of computers in Dutch households was a result of activities by various intermediary actors. Computers became household commodities only gradually. Technophile computer hobbyists imported the first computers into the Netherlands from the USA, and started small businesses from 1975 onwards. They developed a social network in which computer technology was made available for use by individuals. This network extended itself via shops, clubs, magazines, and other means of acquiring and exchanging computer hard- and software. Hobbyist culture established the software-copying habits of private computer users as well as their ambivalence to commercial software. They also made the computer into a game machine. Under the impulse of a national policy that aimed at transforming society into an 'Information Society', clubs and other actors extended their activities and tailored them to this new agenda. Hobby clubs presented themselves as consumer organizations and transformed into intermediary actors that filled the gap between suppliers and a growing group of users. They worked hard to give meaning to (proper) use of computers. A second impulse to the increasing use of computers in the household came from so-called 'private-PC' projects in the late 1980s. In these projects employers financially aided employees in purchasing their own private PCs'. The initially important intermediary actors such as hobby clubs lost control and the agenda for personal computers was shifted to interoperability with office equipment. IBM compatible PC's flooded the households. In the household the new equipment blended with the established uses, such as gaming. The copying habits together with the PC standard created a risky combination in which computer viruses could spread easily. New roles arose for intermediary actors in guiding and educating computer users. The activities of intermediaries had a lasting influence on contemporary computer use and user preferences. Technical choices and the nature of Dutch computer use in households can be explained by analyzing the historical developments of intermediaries and users.

Complexities in Ferret Influenza Virus Pathogenesis and Transmission Models

PubMed Central

Eckert, Alissa M.; Tumpey, Terrence M.; Maines, Taronna R.

2016-01-01

SUMMARY Ferrets are widely employed to study the pathogenicity, transmissibility, and tropism of influenza viruses. However, inherent variations in inoculation methods, sampling schemes, and experimental designs are often overlooked when contextualizing or aggregating data between laboratories, leading to potential confusion or misinterpretation of results. Here, we provide a comprehensive overview of parameters to consider when planning an experiment using ferrets, collecting data from the experiment, and placing results in context with previously performed studies. This review offers information that is of particular importance for researchers in the field who rely on ferret data but do not perform the experiments themselves. Furthermore, this review highlights the breadth of experimental designs and techniques currently available to study influenza viruses in this model, underscoring the wide heterogeneity of protocols currently used for ferret studies while demonstrating the wealth of information which can benefit risk assessments of emerging influenza viruses. PMID:27412880

Complexities in Ferret Influenza Virus Pathogenesis and Transmission Models.

PubMed

Belser, Jessica A; Eckert, Alissa M; Tumpey, Terrence M; Maines, Taronna R

2016-09-01

Ferrets are widely employed to study the pathogenicity, transmissibility, and tropism of influenza viruses. However, inherent variations in inoculation methods, sampling schemes, and experimental designs are often overlooked when contextualizing or aggregating data between laboratories, leading to potential confusion or misinterpretation of results. Here, we provide a comprehensive overview of parameters to consider when planning an experiment using ferrets, collecting data from the experiment, and placing results in context with previously performed studies. This review offers information that is of particular importance for researchers in the field who rely on ferret data but do not perform the experiments themselves. Furthermore, this review highlights the breadth of experimental designs and techniques currently available to study influenza viruses in this model, underscoring the wide heterogeneity of protocols currently used for ferret studies while demonstrating the wealth of information which can benefit risk assessments of emerging influenza viruses. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Revalidation and genetic characterization of new members of Group C (Orthobunyavirus genus, Peribunyaviridae family) isolated in the Americas.

PubMed

Nunes, Márcio Roberto Teixeira; de Souza, William Marciel; Acrani, Gustavo Olszanski; Cardoso, Jedson Ferreira; da Silva, Sandro Patroca; Badra, Soraya Jabur; Figueiredo, Luiz Tadeu Moraes; Vasconcelos, Pedro Fernando da Costa

2018-01-01

Group C serogroup includes members of the Orthobunyavirus genus (family Peribunyaviridae) and comprises 15 arboviruses that can be associated with febrile illness in humans. Although previous studies described the genome characterization of Group C orthobunyavirus, there is a gap in genomic information about the other viruses in this group. Therefore, in this study, complete genomes of members of Group C serogroup were sequenced or re-sequenced and used for genetic characterization, as well as to understand their phylogenetic and evolutionary aspects. Thus, our study reported the genomes of three new members in Group C virus (Apeu strain BeAn848, Itaqui strain BeAn12797 and Nepuyo strain BeAn10709), as well as re-sequencing of original strains of five members: Caraparu (strain BeAn3994), Madrid (strain BT4075), Murucutu (strain BeAn974), Oriboca (strain BeAn17), and Marituba (strain BeAn15). These viruses presented a typical genomic organization related to members of the Orthobunyavirus genus. Interestingly, all viruses of this serogroup showed an open reading frame (ORF) that encodes the putative nonstructural NSs protein that precedes the nucleoprotein ORF, an unprecedented fact in Group C virus. Also, we confirmed the presence of natural reassortment events. This study expands the genomic information of Group C viruses, as well as revalidates the genomic organization of viruses that were previously reported.

Instrumentation for noninvasive express-diagnostics bacteriophages and viruses by optical method

NASA Astrophysics Data System (ADS)

Moguilnaia, Tatiana A.; Andreev, Gleb I.; Agibalov, Andrey A.; Botikov, Andrey G.; Kosenkov, Evgeniy; Saguitova, Elena

2004-03-01

The theoretical and the experimental researches of spectra of absent-minded radiation in medium containing viruses were carried out. The information on spectra luminescence 31 viruses was written down.The new method the express - analysis of viruses in organism of the man was developed. It shall be mentioned that the proposed method of express diagnostics allows detection of infection agent in the organism several hours after infection. It makes it suitable for high efficient testing in blood services for detection and rejection of potential donors infected with such viruses as hepatitis, herpes, Epstein-Barre, cytomegalovirus, and immunodeficiency. Methods of serum diagnostics used for that purpose can detect antibodies to virus only 1-3 months after the person has been infected. The device for the express analysis of 31 viruses of the man was created.

A universal mammalian vaccine cell line substrate.

PubMed

Murray, Jackelyn; Todd, Kyle V; Bakre, Abhijeet; Orr-Burks, Nichole; Jones, Les; Wu, Weilin; Tripp, Ralph A

2017-01-01

Using genome-wide small interfering RNA (siRNA) screens for poliovirus, influenza A virus and rotavirus, we validated the top 6 gene hits PV, RV or IAV to search for host genes that when knocked-down (KD) enhanced virus permissiveness and replication over wild type Vero cells or HEp-2 cells. The enhanced virus replication was tested for 12 viruses and ranged from 2-fold to >1000-fold. There were variations in virus-specific replication (strain differences) across the cell lines examined. Some host genes (CNTD2, COQ9, GCGR, NDUFA9, NEU2, PYCR1, SEC16G, SVOPL, ZFYVE9, and ZNF205) showed that KD resulted in enhanced virus replication. These findings advance platform-enabling vaccine technology, the creation of diagnostic cells substrates, and are informative about the host mechanisms that affect virus replication in mammalian cells.

Live Attenuated Influenza Vaccines by Computer-Aided Rational Design

PubMed Central

Mueller, Steffen; Coleman, J. Robert; Papamichail, Dimitris; Ward, Charles B.; Nimnual, Anjaruwee; Futcher, Bruce; Skiena, Steven; Wimmer, Eckard

2010-01-01

Influenza claims 250,000 - 500,000 lives annually worldwide. Despite existing vaccines and enormous efforts in biomedical research, these staggering numbers have not changed significantly over the last two decades1, motivating the search for new, more effective, vaccines that can be rapidly designed and easily produced. Using influenza virus strain A/PR/8/34, we describe a systematic, rational approach, termed Synthetic Attenuated Virus Engineering (SAVE), to develop new, efficacious live attenuated influenza virus vaccine candidates through genome-scale changes in codon pair bias. Attenuation is based on many hundreds of nucleotide changes across the viral genome, offering high genetic stability and a wide margin of safety. The method can be applied rapidly to any emerging influenza virus in its entirety, an advantage that is significant for dealing with seasonal epidemics and pandemic threats, such as H5N1- or 2009-H1N1 influenza. PMID:20543832

Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface.

PubMed

Knodel, Markus M; Nägel, Arne; Reiter, Sebastian; Vogel, Andreas; Targett-Adams, Paul; McLauchlan, John; Herrmann, Eva; Wittum, Gabriel

2018-01-08

Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles.

Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, Shea N.; Jaing, Crystal J.; Elsheikh, Maher M.

Background . Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. Degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. Results . A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. The new script, run_tiled_primers, is part of the PriMux software. Primers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses, Arenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus. Eachmore » group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross reactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to specifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo. Conclusions . This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family.« less

Classification of viral zoonosis through receptor pattern analysis.

PubMed

Bae, Se-Eun; Son, Hyeon Seok

2011-04-13

Viral zoonosis, the transmission of a virus from its primary vertebrate reservoir species to humans, requires ubiquitous cellular proteins known as receptor proteins. Zoonosis can occur not only through direct transmission from vertebrates to humans, but also through intermediate reservoirs or other environmental factors. Viruses can be categorized according to genotype (ssDNA, dsDNA, ssRNA and dsRNA viruses). Among them, the RNA viruses exhibit particularly high mutation rates and are especially problematic for this reason. Most zoonotic viruses are RNA viruses that change their envelope proteins to facilitate binding to various receptors of host species. In this study, we sought to predict zoonotic propensity through the analysis of receptor characteristics. We hypothesized that the major barrier to interspecies virus transmission is that receptor sequences vary among species--in other words, that the specific amino acid sequence of the receptor determines the ability of the viral envelope protein to attach to the cell. We analysed host-cell receptor sequences for their hydrophobicity/hydrophilicity characteristics. We then analysed these properties for similarities among receptors of different species and used a statistical discriminant analysis to predict the likelihood of transmission among species. This study is an attempt to predict zoonosis through simple computational analysis of receptor sequence differences. Our method may be useful in predicting the zoonotic potential of newly discovered viral strains.

Questing for an optimal, universal viral agent for oncolytic virotherapy

NASA Astrophysics Data System (ADS)

Paiva, L. R.; Martins, M. L.; Ferreira, S. C.

2011-10-01

One of the most promising strategies to treat cancer is attacking it with viruses designed to exploit specific altered pathways. Here, the effects of oncolytic virotherapy on tumors having compact, papillary, and disconnected morphologies are investigated through computer simulations of a multiscale model coupling macroscopic reaction-diffusion equations for the nutrients with microscopic stochastic rules for the actions of individual cells and viruses. The interaction among viruses and tumor cells involves cell infection, intracellular virus replication, and the release of new viruses in the tissue after cell lysis. The evolution over time of both the viral load and cancer cell population, as well as the probabilities for tumor eradication, were evaluated for a range of multiplicities of infection, viral entries, and burst sizes. It was found that in immunosuppressed hosts, the antitumor efficacy of a virus is primarily determined by its entry efficiency, its replicative capacity within the tumor, and its ability to spread over the tissue. However, the optimal traits for oncolytic viruses depend critically on the tumor growth dynamics and do not necessarily include rapid replication, cytolysis, or spreading, currently assumed as necessary conditions for a successful therapeutic outcome. Our findings have potential implications on the design of new vectors for the viral therapy of cancer.

Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface

PubMed Central

Nägel, Arne; Reiter, Sebastian; Vogel, Andreas; McLauchlan, John; Herrmann, Eva; Wittum, Gabriel

2018-01-01

Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles. PMID:29316722

Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes

DOE PAGES

Gardner, Shea N.; Jaing, Crystal J.; Elsheikh, Maher M.; ...

2014-01-01

Background . Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. Degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. Results . A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. The new script, run_tiled_primers, is part of the PriMux software. Primers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses, Arenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus. Eachmore » group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross reactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to specifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo. Conclusions . This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family.« less

Theoretical and experimental analysis of the impacts of removable storage media and antivirus software on viral spread

NASA Astrophysics Data System (ADS)

Gan, Chenquan; Yang, Xiaofan

2015-05-01

In this paper, a new computer virus propagation model, which incorporates the effects of removable storage media and antivirus software, is proposed and analyzed. The global stability of the unique equilibrium of the model is independent of system parameters. Numerical simulations not only verify this result, but also illustrate the influences of removable storage media and antivirus software on viral spread. On this basis, some applicable measures for suppressing virus prevalence are suggested.

Electron microscopy and antigenic studies of uncharacterized viruses. I. Evidence suggesting the placement of viruses in families Arenaviridae, Paramyxoviridae, or Poxviridae.

PubMed

Zeller, H G; Karabatsos, N; Calisher, C H; Digoutte, J P; Murphy, F A; Shope, R E

1989-01-01

During approximately 35 years, investigators in various laboratories studying arbovirus ecology and epidemiology accumulated many virus isolates, more than 60 of which were not characterized or placed in taxa. By a combination of electron microscopic and antigenic studies we collected information sufficient to provisionally classify 60 isolates. Electron microscopic observations suggest that 20 are members of the virus family Bunyaviridae, 20 Rhabdoviridae, 14 Reoviridae, one Togaviridae, one Paramyxoviridae (Mapuera virus, from a bat), and one Poxviridae (Yoka virus, from mosquitoes). Serologic studies provided evidence sufficient to place some of these viruses in recognized antigenic groups, within families and genera, and to establish new antigenic groups and taxa for others. Three viruses were found to have morphologic and morphogenetic characteristics consistent with those of members of the family Arenaviridae: Quaranfil virus, a human pathogen, Johnston Atoll virus, isolated from birds and ticks, and Araguari virus, isolated from an opossum. This, the first in a series of three papers, described methods used for these investigations and also presents descriptions of viruses provisionally placed in the families Arenaviridae, Paramyxoviridae, or Poxviridae. Descriptions of viruses provisionally placed in families Bunyaviridae and Reoviridae are published in the second and third papers, respectively. Viruses of the family Rhabdoviridae have been described separately.

Restriction of virus infection by plants. Final report, July 1, 1987--June 30, 1992

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruening, G.

1992-12-31

The basis of genotypic resistance of the Arlington line of cowpea (Vigna unguiculata) against cowpea mosaic virus (CPMV) has been attributed, to an inhibitor of the processing of CPMV polyproteins. We sought to purify the protein that is postulated to be the inhibitor of polyprotein processing and to characterize the inhibitor and its gene. Such information can be the basis for engineering resistance to specific viruses in plants. In studies with cherry leafroll virus (CLRV) we sought understanding of the biochemical basis of the resistance.

RNA-Seq reveals virus–virus and virus–plant interactions in nature

PubMed Central

Kamitani, Mari; Nagano, Atsushi J.; Honjo, Mie N.; Kudoh, Hiroshi

2016-01-01

Abstract As research on plant viruses has focused mainly on crop diseases, little is known about these viruses in natural environments. To understand the ecology of viruses in natural systems, comprehensive information on virus–virus and virus–host interactions is required. We applied RNA-Seq to plants from a natural population of Arabidopsis halleri subsp. gemmifera to simultaneously determine the presence/absence of all sequence-reported viruses, identify novel viruses and quantify the host transcriptome. By introducing the criteria of read number and genome coverage, we detected infections by Turnip mosaic virus (TuMV), Cucumber mosaic virus and Brassica yellows virus. Active TuMV replication was observed by ultramicroscopy. De novo assembly further identified a novel partitivirus, Arabidopsis halleri partitivirus 1. Interestingly, virus reads reached a maximum level that was equivalent to that of the host's total mRNA, although asymptomatic infection was common. AhgAGO2, a key gene in host defence systems, was upregulated in TuMV-infected plants. Multiple infection was frequent in TuMV-infected leaves, suggesting that TuMV facilitates multiple infection, probably by suppressing host RNA silencing. Revealing hidden plant–virus interactions in nature can enhance our understanding of biological interactions and may have agricultural applications. PMID:27549115

Propagation and immunization of infection on general networks with both homogeneous and heterogeneous components

NASA Astrophysics Data System (ADS)

Liu, Zonghua; Lai, Ying-Cheng; Ye, Nong

2003-03-01

We consider the entire spectrum of architectures of general networks, ranging from being heterogeneous (scale-free) to homogeneous (random), and investigate the infection dynamics by using a three-state epidemiological model that does not involve the mechanism of self-recovery. This model is relevant to realistic situations such as the propagation of a flu virus or information over a social network. Our heuristic analysis and computations indicate that (1) regardless of the network architecture, there exists a substantial fraction of nodes that can never be infected and (2) heterogeneous networks are relatively more robust against spreads of infection as compared with homogeneous networks. We have also considered the problem of immunization for preventing wide spread of infection, with the result that targeted immunization is effective for heterogeneous networks.

Help Control Mosquitoes that Spread Dengue, Chikungunya, and Zika Viruses

MedlinePlus

Help Control Mosquitoes that Spread Dengue, Chikungunya, and Zika Viruses B Z Z Z Z . Aside from being itchy ... for your information only. The Centers for Disease Control and Prevention and the U.S. Department of Health ...

An operational epidemiological model for calibrating agent-based simulations of pandemic influenza outbreaks.

PubMed

Prieto, D; Das, T K

2016-03-01

Uncertainty of pandemic influenza viruses continue to cause major preparedness challenges for public health policymakers. Decisions to mitigate influenza outbreaks often involve tradeoff between the social costs of interventions (e.g., school closure) and the cost of uncontrolled spread of the virus. To achieve a balance, policymakers must assess the impact of mitigation strategies once an outbreak begins and the virus characteristics are known. Agent-based (AB) simulation is a useful tool for building highly granular disease spread models incorporating the epidemiological features of the virus as well as the demographic and social behavioral attributes of tens of millions of affected people. Such disease spread models provide excellent basis on which various mitigation strategies can be tested, before they are adopted and implemented by the policymakers. However, to serve as a testbed for the mitigation strategies, the AB simulation models must be operational. A critical requirement for operational AB models is that they are amenable for quick and simple calibration. The calibration process works as follows: the AB model accepts information available from the field and uses those to update its parameters such that some of its outputs in turn replicate the field data. In this paper, we present our epidemiological model based calibration methodology that has a low computational complexity and is easy to interpret. Our model accepts a field estimate of the basic reproduction number, and then uses it to update (calibrate) the infection probabilities in a way that its effect combined with the effects of the given virus epidemiology, demographics, and social behavior results in an infection pattern yielding a similar value of the basic reproduction number. We evaluate the accuracy of the calibration methodology by applying it for an AB simulation model mimicking a regional outbreak in the US. The calibrated model is shown to yield infection patterns closely replicating the input estimates of the basic reproduction number. The calibration method is also tested to replicate an initial infection incidence trend for a H1N1 outbreak like that of 2009.

Detection of viruses in used ventilation filters from two large public buildings.

PubMed

Goyal, Sagar M; Anantharaman, Senthilvelan; Ramakrishnan, M A; Sajja, Suchitra; Kim, Seung Won; Stanley, Nicholas J; Farnsworth, James E; Kuehn, Thomas H; Raynor, Peter C

2011-09-01

Viral and bacterial pathogens may be present in the air after being released from infected individuals and animals. Filters are installed in the heating, ventilation, and air-conditioning (HVAC) systems of buildings to protect ventilation equipment and maintain healthy indoor air quality. These filters process enormous volumes of air. This study was undertaken to determine the utility of sampling used ventilation filters to assess the types and concentrations of virus aerosols present in buildings. The HVAC filters from 2 large public buildings in Minneapolis and Seattle were sampled to determine the presence of human respiratory viruses and viruses with bioterrorism potential. Four air-handling units were selected from each building, and a total of 64 prefilters and final filters were tested for the presence of influenza A, influenza B, respiratory syncytial, corona, parainfluenza 1-3, adeno, orthopox, entero, Ebola, Marburg, Lassa fever, Machupo, eastern equine encephalitis, western equine encephalitis, and Venezuelan equine encephalitis viruses. Representative pieces of each filter were cut and eluted with a buffer solution. Attempts were made to detect viruses by inoculation of these eluates in cell cultures (Vero, MDCK, and RK-13) and specific pathogen-free embryonated chicken eggs. Two passages of eluates in cell cultures or these eggs did not reveal the presence of any live virus. The eluates were also examined by polymerase chain reaction or reverse-transcription polymerase chain reaction to detect the presence of viral DNA or RNA, respectively. Nine of the 64 filters tested were positive for influenza A virus, 2 filters were positive for influenza B virus, and 1 filter was positive for parainfluenza virus 1. These findings indicate that existing building HVAC filters may be used as a method of detection for airborne viruses. As integrated long-term bioaerosol sampling devices, they may yield valuable information on the epidemiology and aerobiology of viruses in air that can inform the development of methods to prevent airborne transmission of viruses and possible deterrents against the spread of bioterrorism agents. Copyright © 2011 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

VIP: an integrated pipeline for metagenomics of virus identification and discovery

PubMed Central

Li, Yang; Wang, Hao; Nie, Kai; Zhang, Chen; Zhang, Yi; Wang, Ji; Niu, Peihua; Ma, Xuejun

2016-01-01

Identification and discovery of viruses using next-generation sequencing technology is a fast-developing area with potential wide application in clinical diagnostics, public health monitoring and novel virus discovery. However, tremendous sequence data from NGS study has posed great challenge both in accuracy and velocity for application of NGS study. Here we describe VIP (“Virus Identification Pipeline”), a one-touch computational pipeline for virus identification and discovery from metagenomic NGS data. VIP performs the following steps to achieve its goal: (i) map and filter out background-related reads, (ii) extensive classification of reads on the basis of nucleotide and remote amino acid homology, (iii) multiple k-mer based de novo assembly and phylogenetic analysis to provide evolutionary insight. We validated the feasibility and veracity of this pipeline with sequencing results of various types of clinical samples and public datasets. VIP has also contributed to timely virus diagnosis (~10 min) in acutely ill patients, demonstrating its potential in the performance of unbiased NGS-based clinical studies with demand of short turnaround time. VIP is released under GPLv3 and is available for free download at: https://github.com/keylabivdc/VIP. PMID:27026381

Inhibitor designing, virtual screening, and docking studies for methyltransferase: A potential target against dengue virus

PubMed Central

Singh, Jagbir; Kumar, Mahesh; Mansuri, Rani; Sahoo, Ganesh Chandra; Deep, Aakash

2016-01-01

Aim: Aim of this work was to design and identify some S-adenosyl-L-homocysteine (SAH) analogs as inhibitors of S-adenosyl-L-methionine-dependent methyltransferase (MTase) protein using computational approaches. Introduction: According to the current scenario the dengue has been a global burden. The people are being killed by dengue virus in an abundant number. Despite of lot of research being going on dengue worldwide, there is no single drug which can kill its virus. This creates an urge for new drug target identification and designing. MTase has been reported as an effective target against dengue virus as it catalyzes an essential step in methylation and capping of viral RNA for viral replication. Materials and Methods: The crystal structure of MTase in complex with SAH was used for designing new analogs of SAH. SAH analogs designed were analyzed on the basis of docking, ADMET, and toxicity analysis done using Discovery Studio 3.5. Results: Seventeen analogs found noncarcinogenic, nonmutagenic, as well as good ADMET properties and good drug-like profile. Conclusion: These SAH analogs, inhibitors of MTase may act as drugs against dengue virus. Further synthesis and biological testing against dengue virus is under observation. PMID:27413346

Improving Remote Voting Security with CodeVoting

NASA Astrophysics Data System (ADS)

Joaquim, Rui; Ribeiro, Carlos; Ferreira, Paulo

One of the major problems that prevents the spread of elections with the possibility of remote voting over electronic networks, also called Internet Voting, is the use of unreliable client platforms, such as the voter's computer and the Internet infrastructure connecting it to the election server. A computer connected to the Internet is exposed to viruses, worms, Trojans, spyware, malware and other threats that can compromise the election's integrity. For instance, it is possible to write a virus that changes the voter's vote to a predetermined vote on election's day. Another possible attack is the creation of a fake election web site where the voter uses a malicious vote program on the web site that manipulates the voter's vote (phishing/pharming attack). Such attacks may not disturb the election protocol, therefore can remain undetected in the eyes of the election auditors.

Prediction of the binding mode of N2-phenylguanine derivative inhibitors to herpes simplex virus type 1 thymidine kinase

NASA Astrophysics Data System (ADS)

Gaudio, Anderson Coser; Takahata, Yuji; Richards, William Graham

1998-01-01

The probable binding mode of the herpes simplex virus thymidine kinase (HSV1 TK) N2-[substituted]-phenylguanine inhibitors is proposed. A computational experiment was designed to check some qualitative binding parameters and to calculate the interaction binding energies of alternative binding modes of N2-phenylguanines. The known binding modes of the HSV1 TK natural substrate deoxythymidine and one of its competitive inhibitors ganciclovir were used as templates. Both the qualitative and quantitative parts of the computational experiment indicated that the N2-phenylguanine derivatives bind to the HSV1 TK active site in the deoxythymidine-like binding mode. An experimental observation that N2-phenylguanosine derivatives are not phosphorylated during the interaction with the HSV1 TK gives support to the proposed binding mode.

Possible sexual transmission of Ebola virus - Liberia, 2015.

PubMed

Christie, Athalia; Davies-Wayne, Gloria J; Cordier-Lassalle, Thierry; Cordier-Lasalle, Thierry; Blackley, David J; Laney, A Scott; Williams, Desmond E; Shinde, Shivam A; Badio, Moses; Lo, Terrence; Mate, Suzanne E; Ladner, Jason T; Wiley, Michael R; Kugelman, Jeffrey R; Palacios, Gustavo; Holbrook, Michael R; Janosko, Krisztina B; de Wit, Emmie; van Doremalen, Neeltje; Munster, Vincent J; Pettitt, James; Schoepp, Randal J; Verhenne, Leen; Evlampidou, Iro; Kollie, Karsor K; Sieh, Sonpon B; Gasasira, Alex; Bolay, Fatorma; Kateh, Francis N; Nyenswah, Tolbert G; De Cock, Kevin M

2015-05-08

On March 20, 2015, 30 days after the most recent confirmed Ebola Virus Disease (Ebola) patient in Liberia was isolated, Ebola was laboratory confirmed in a woman in Monrovia. The investigation identified only one epidemiologic link to Ebola: unprotected vaginal intercourse with a survivor. Published reports from previous outbreaks have demonstrated Ebola survivors can continue to harbor virus in immunologically privileged sites for a period of time after convalescence. Ebola virus has been isolated from semen as long as 82 days after symptom onset and viral RNA has been detected in semen up to 101 days after symptom onset. One instance of possible sexual transmission of Ebola has been reported, although the accompanying evidence was inconclusive. In addition, possible sexual transmission of Marburg virus, a filovirus related to Ebola, was documented in 1968. This report describes the investigation by the Government of Liberia and international response partners of the source of Liberia's latest Ebola case and discusses the public health implications of possible sexual transmission of Ebola virus. Based on information gathered in this investigation, CDC now recommends that contact with semen from male Ebola survivors be avoided until more information regarding the duration and infectiousness of viral shedding in body fluids is known. If male survivors have sex (oral, vaginal, or anal), a condom should be used correctly and consistently every time.

Matched Case-Control Study of Effectiveness of Live, Attenuated S79 Mumps Virus Vaccine against Clinical Mumps▿

PubMed Central

Fu, Chuanxi; Liang, Jianhua; Wang, Ming

2008-01-01

Mumps virus infection is a potentially serious viral infection of childhood and early adulthood. In China, live, attenuated S79 mumps virus vaccine has been licensed for pediatric use since 1990. There has been no assessment of its efficacy. Thus, the objective of this study was to determine the effectiveness of live, attenuated S79 mumps virus vaccine against clinical mumps. Cases were selected from the China Information System for Disease Control and Prevention during September 2004 to March 2005. Each case was matched to a control by gender, age, and area of residency. In all, 469 cases and 469 controls were enrolled in the study. Vaccination information was obtained from the Children's EPI Administrative Computerized System. Vaccine effectiveness (VE) was calculated for one or two doses of S79 vaccine, with 95% confidence intervals (CI). VE of mumps virus vaccine for one dose versus none was protection of 86.0% (95% CI, 77.2% to 91.5%) of recipients, and VE was much higher in the first 4 years than in the 5 to 12 years after vaccination. The S79 vaccine can effectively prevent clinical mumps, and a second dose of mumps virus vaccine is necessary for the protection of children in China. PMID:18667635

A Novel H1N2 Influenza Virus Related to the Classical and Human Influenza Viruses from Pigs in Southern China.

PubMed

Song, Yafen; Wu, Xiaowei; Wang, Nianchen; Ouyang, Guowen; Qu, Nannan; Cui, Jin; Qi, Yan; Liao, Ming; Jiao, Peirong

2016-01-01

Southern China has long been considered to be an epicenter of pandemic influenza viruses. The special environment, breeding mode, and lifestyle in southern China provides more chances for wild aquatic birds, domestic poultry, pigs, and humans to be in contact. This creates the opportunity for interspecies transmission and generation of new influenza viruses. In this study, we reported a novel reassortant H1N2 influenza virus from pigs in southern China. According to the phylogenetic trees and homology of the nucleotide sequence, the virus was confirmed to be a novel triple-reassortant H1N2 virus containing genes from classical swine (PB2, PB1, HA, NP, and NS genes), triple-reassortant swine (PA and M genes), and recent human (NA gene) lineages. It indicated that the novel reassortment virus among human and swine influenza viruses occurred in pigs in southern China. The isolation of the novel reassortant H1N2 influenza viruses provides further evidence that pigs are "mixing vessels," and swine influenza virus surveillance in southern China will provide important information about genetic evaluation and antigenic variation of swine influenza virus to formulate the prevention and control measures for the viruses.

A Novel H1N2 Influenza Virus Related to the Classical and Human Influenza Viruses from Pigs in Southern China

PubMed Central

Song, Yafen; Wu, Xiaowei; Wang, Nianchen; Ouyang, Guowen; Qu, Nannan; Cui, Jin; Qi, Yan; Liao, Ming; Jiao, Peirong

2016-01-01

Southern China has long been considered to be an epicenter of pandemic influenza viruses. The special environment, breeding mode, and lifestyle in southern China provides more chances for wild aquatic birds, domestic poultry, pigs, and humans to be in contact. This creates the opportunity for interspecies transmission and generation of new influenza viruses. In this study, we reported a novel reassortant H1N2 influenza virus from pigs in southern China. According to the phylogenetic trees and homology of the nucleotide sequence, the virus was confirmed to be a novel triple-reassortant H1N2 virus containing genes from classical swine (PB2, PB1, HA, NP, and NS genes), triple-reassortant swine (PA and M genes), and recent human (NA gene) lineages. It indicated that the novel reassortment virus among human and swine influenza viruses occurred in pigs in southern China. The isolation of the novel reassortant H1N2 influenza viruses provides further evidence that pigs are “mixing vessels,” and swine influenza virus surveillance in southern China will provide important information about genetic evaluation and antigenic variation of swine influenza virus to formulate the prevention and control measures for the viruses. PMID:27458456

Computational design of hepatitis C vaccines using empirical fitness landscapes and population dynamics

NASA Astrophysics Data System (ADS)

Hart, Gregory; Ferguson, Andrew

Hepatitis C virus (HCV) afflicts 170 million people and kills 350,000 annually. Vaccination offers the most realistic and cost effective hope of controlling this epidemic. Despite 25 years of research, no vaccine is available. A major obstacle is the virus' extreme genetic variability and rapid mutational escape from immune pressure. Improvements in the vaccine design process are urgently needed. Coupling data mining and maximum entropy inference, we have developed a computational approach to translate sequence databases into empirical fitness landscapes. These landscapes explicitly connect viral genotype to phenotypic fitness and reveal vulnerable targets that can be exploited to rationally design vaccines. These landscapes represent the mutational ''playing field'' over which the virus evolves. We have integrated them with agent-based models of the viral mutational and host immune response, establishing a data-driven multi-scale immune simulator. We have used this simulator to perform in silico screening of HCV immunogens to rationally design vaccines to both cripple viral fitness and block escape. By systematically identifying a small number of promising vaccine candidates, these models can accelerate the search for a vaccine by massively reducing the experimental search space.

Computational design of hepatitis C vaccines using maximum entropy models and population dynamics

NASA Astrophysics Data System (ADS)

Hart, Gregory; Ferguson, Andrew

Hepatitis C virus (HCV) afflicts 170 million people and kills 350,000 annually. Vaccination offers the most realistic and cost effective hope of controlling this epidemic. Despite 20 years of research, no vaccine is available. A major obstacle is the virus' extreme genetic variability and rapid mutational escape from immune pressure. Improvements in the vaccine design process are urgently needed. Coupling data mining with spin glass models and maximum entropy inference, we have developed a computational approach to translate sequence databases into empirical fitness landscapes. These landscapes explicitly connect viral genotype to phenotypic fitness and reveal vulnerable targets that can be exploited to rationally design immunogens. Viewing these landscapes as the mutational ''playing field'' over which the virus is constrained to evolve, we have integrated them with agent-based models of the viral mutational and host immune response dynamics, establishing a data-driven immune simulator of HCV infection. We have employed this simulator to perform in silico screening of HCV immunogens. By systematically identifying a small number of promising vaccine candidates, these models can accelerate the search for a vaccine by massively reducing the experimental search space.

Genomic Variability of Monkeypox Virus among Humans, Democratic Republic of the Congo

PubMed Central

Kugelman, Jeffrey R.; Johnston, Sara C.; Mulembakani, Prime M.; Kisalu, Neville; Lee, Michael S.; Koroleva, Galina; McCarthy, Sarah E.; Gestole, Marie C.; Wolfe, Nathan D.; Fair, Joseph N.; Schneider, Bradley S.; Wright, Linda L.; Huggins, John; Whitehouse, Chris A.; Wemakoy, Emile Okitolonda; Muyembe-Tamfum, Jean Jacques; Hensley, Lisa E.

2014-01-01

Monkeypox virus is a zoonotic virus endemic to Central Africa. Although active disease surveillance has assessed monkeypox disease prevalence and geographic range, information about virus diversity is lacking. We therefore assessed genome diversity of viruses in 60 samples obtained from humans with primary and secondary cases of infection from 2005 through 2007. We detected 4 distinct lineages and a deletion that resulted in gene loss in 10 (16.7%) samples and that seemed to correlate with human-to-human transmission (p = 0.0544). The data suggest a high frequency of spillover events from the pool of viruses in nonhuman animals, active selection through genomic destabilization and gene loss, and increased disease transmissibility and severity. The potential for accelerated adaptation to humans should be monitored through improved surveillance. PMID:24457084

Zika virus infection in Vietnam: current epidemic, strain origin, spreading risk, and perspective.

PubMed

Chu, Dinh-Toi; Ngoc, Vo Truong Nhu; Tao, Yang

2017-11-01

Zika virus infection and its associated microcephaly have being receiving global concern. This infection has spread widely since the first outbreak was recorded in Africa in 1952. Now, it has been reported in over 70 countries on five continents including Africa, North and South America, Asia, and Europe. Vietnam is one of the most recent countries which had cases of Zika virus infection at the end of 2016. This country has also reported the first case of a microcephaly-born baby which was probably linked to Zika virus infection. However, information on the Zika virus epidemic in Vietnam is still limited. This brief report intends to update the current Zika virus epidemic, and to discuss challenges and perspectives in controlling this infection in Vietnam.

Outbreaks of Foot-and-Mouth Disease in Libya and Saudi Arabia During 2013 Due to an Exotic O/ME-SA/Ind-2001 Lineage Virus.

PubMed

Knowles, N J; Bachanek-Bankowska, K; Wadsworth, J; Mioulet, V; Valdazo-González, B; Eldaghayes, I M; Dayhum, A S; Kammon, A M; Sharif, M A; Waight, S; Shamia, A M; Tenzin, S; Wernery, U; Grazioli, S; Brocchi, E; Subramaniam, S; Pattnaik, B; King, D P

2016-10-01

Foot-and-mouth disease viruses are often restricted to specific geographical regions and spread to new areas may lead to significant epidemics. Phylogenetic analysis of sequences of the VP1 genome region of recent outbreak viruses from Libya and Saudi Arabia has revealed a lineage, O-Ind-2001, normally found in the Indian subcontinent. This paper describes the characterization of field viruses collected from these cases and provides information about a new real-time RT-PCR assay that can be used to detect viruses from this lineage and discriminate them from other endemic FMD viruses that are co-circulating in North Africa and western Eurasia. © 2014 The Authors. Transboundary and Emerging Diseases Published by Blackwell Verlag GmbH.

Inhibition of Neurogenesis by Zika virus Infection.

PubMed

Ahmad, Fahim; Siddiqui, Amna; Kamal, Mohammad A; Sohrab, Sayed S

2018-02-01

The association between Zika virus infection and neurological disorder has raised urgent global alarm. The ongoing epidemic has triggered quick responses in the scientific community. The first case of Zika virus was reported in 2015 from Brazil and now has spread over 30 countries. Nearly four hundred cases of travel-associated Zika virus infection have also been reported in the United States. Zika virus is primarily transmitted by mosquito belongs to the genus Aedes that are widely distributed throughout the world including the Southern United States. Additionally, the virus can also be transmitted from males to females by sexual contact. The epidemiological investigations during the current outbreak found a causal link between infection in pregnant women and development of microcephaly in their unborn babies. This finding is a cause for grave concern since microcephaly is a serious neural developmental disorder that can lead to significant post-natal developmental abnormalities and disabilities. Recently, published data indicate that Zika virus infection affects the growth of fetal neural progenitor cells and cerebral neurons that results in malformation of cerebral cortex leading to microcephaly. Recently, it has been reported that Zika virus infection deregulates the signaling pathway of neuronal cell and inhibit the neurogenesis resulting into dementia. In this review we have discussed about the information about cellular and molecular mechanisms in neurodegeneration of human neuronal cells and inhibit the neurogenesis. Additionally, this information will be very helpful further not only in neuro-scientific research but also designing and development of management strategies for microcephaly and other mosquito borne disease. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Unique Safety Issues Associated with Virus Vectored Vaccines: Potential for and Theoretical Consequences of Recombination with Wild Type Virus Strains

PubMed Central

Condit, Richard C.; Williamson, Anna-Lise; Sheets, Rebecca; Seligman, Stephen J.; Monath, Thomas P.; Excler, Jean-Louis; Gurwith, Marc; Bok, Karin; Robertson, James S.; Kim, Denny; Hendry, Michael; Singh, Vidisha; Mac, Lisa M.; Chen, Robert T.

2016-01-01

In 2003 and 2013, the World Health Organization convened informal consultations on characterization and quality aspects of vaccines based on live virus vectors. In the resulting reports, one of several issues raised for future study was the potential for recombination of virus-vectored vaccines with wild type pathogenic virus strains. This paper presents an assessment of this issue formulated by the Brighton Collaboration. To provide an appropriate context for understanding the potential for recombination of virus-vectored vaccines, we review briefly the current status of virus vectored vaccines, mechanisms of recombination between viruses, experience with recombination involving live attenuated vaccines in the field, and concerns raised previously in the literature regarding recombination of virus-vectored vaccines with wild type virus strains. We then present a discussion of the major variables that could influence recombination between a virus-vectored vaccine and circulating wild type virus and the consequences of such recombination, including intrinsic recombination properties of the parent virus used as a vector; sequence relatedness of vector and wild virus; virus host range, pathogenesis and transmission; replication competency of vector in target host; mechanism of vector attenuation; additional factors potentially affecting virulence; and circulation of multiple recombinant vectors in the same target population. Finally, we present some guiding principles for vector design and testing intended to anticipate and mitigate the potential for and consequences of recombination of virus-vectored vaccines with wild type pathogenic virus strains. PMID:27346303

Modeling virus survival and transport in the subsurface

NASA Astrophysics Data System (ADS)

Yates, Marylynn V.; Yates, S. R.; Wagner, Jan; Gerba, Charles P.

1987-03-01

The significance of viruses as agents of waterborne disease in the United States is just beginning to be recognized. The ability to predict how far viruses can be transported and how long they can remain infective in soil and groundwater is desirable from the standpoint of planning the placement of sources of contamination so that they will not have an impact on drinking-water wells. This, in turn should have the effect of decreasing the number of waterborne disease outbreaks caused by viruses. This article reviews the factors that affect the survival and migration of viruses in soils and groundwater. It also discusses the efforts that have been made to mathematically model the movement of viruses in the subsurface, including the assumptions made by the modelers. At this time, it appears that modeling efforts are constrained by a lack of quantitative information on virus interactions with soil and fluid media, rather than on mathematical solution techniques.

Presence and Persistence of Zika Virus RNA in Semen, United Kingdom, 2016.

PubMed

Atkinson, Barry; Thorburn, Fiona; Petridou, Christina; Bailey, Daniel; Hewson, Roger; Simpson, Andrew J H; Brooks, Timothy J G; Aarons, Emma J

2017-04-01

Zika virus RNA has been detected in semen collected several months after onset of symptoms of infection. Given the potential for sexual transmission of Zika virus and for serious fetal abnormalities resulting from infection during pregnancy, information regarding the persistence of Zika virus in semen is critical for advancing our understanding of potential risks. We tested serial semen samples from symptomatic male patients in the United Kingdom who had a diagnosis of imported Zika virus infection. Among the initial semen samples from 23 patients, Zika virus RNA was detected at high levels in 13 (56.5%) and was not detected in 9 (39.1%); detection was indeterminate in 1 sample (4.4%). After symptomatic infection, a substantial proportion of men have detectable Zika virus RNA at high copy numbers in semen during early convalescence, suggesting high risk for sexual transmission. Viral RNA clearance times are not consistent and can be prolonged.

Visible light powered self-disinfecting coatings for influenza viruses

NASA Astrophysics Data System (ADS)

Weng, Ding; Qi, Hangfei; Wu, Ting-Ting; Yan, Ming; Sun, Ren; Lu, Yunfeng

2012-04-01

Influenza A viruses, the pathogens responsible for the recent swine flu outbreak and many historical pandemics, remain a threat to the public health. We report herein the fabrication of self-disinfecting surfaces from photoactive building nanocrystals, which can inactivate influenza viruses rapidly, spontaneously and continuously under visible light illumination.Influenza A viruses, the pathogens responsible for the recent swine flu outbreak and many historical pandemics, remain a threat to the public health. We report herein the fabrication of self-disinfecting surfaces from photoactive building nanocrystals, which can inactivate influenza viruses rapidly, spontaneously and continuously under visible light illumination. Electronic supplementary information (ESI) available: XRD, UV-Vis absorbance, TEM, AFM of as-prepared nanocrystals and as-fabricated self-disinfecting surfaces, disinfection of influenza A virus by TiO2 (P25) with UV irradiation as reference control, photoinactivation of influenza A virus envelope proteins and photoinactivation of trypsin. See DOI: 10.1039/c2nr30388d

Bottlenecks in HIV-1 transmission: insights from the study of founder viruses

PubMed Central

Joseph, Sarah B.; Swanstrom, Ronald; Kashuba, Angela D. M.; Cohen, Myron S.

2016-01-01

HIV-1 infection typically results from the transmission of a single viral variant, the transmitted/founder (T/F) virus. Studies of these HIV-1 variants provide critical information about the transmission bottlenecks and the selective pressures acting on the virus in the transmission fluid and in the recipient tissues. These studies reveal that T/F virus phenotypes are shaped by stochastic and selective forces that restrict transmission and may be targets for prevention strategies. In this Review, we highlight how studies of T/F viruses contribute to a better understanding of the biology of HIV-1 transmission and discuss how these findings affect HIV-1 prevention strategies. PMID:26052661

The A-Z of Zika drug discovery.

PubMed

Mottin, Melina; Borba, Joyce V V B; Braga, Rodolpho C; Torres, Pedro H M; Martini, Matheus C; Proenca-Modena, Jose Luiz; Judice, Carla C; Costa, Fabio T M; Ekins, Sean; Perryman, Alexander L; Andrade, Carolina Horta

2018-06-20

Despite the recent outbreak of Zika virus (ZIKV), there are still no approved treatments, and early-stage compounds are probably many years away from approval. A comprehensive A-Z review of the recent advances in ZIKV drug discovery efforts is presented, highlighting drug repositioning and computationally guided compounds, including discovered viral and host cell inhibitors. Promising ZIKV molecular targets are also described and discussed, as well as targets belonging to the host cell, as new opportunities for ZIKV drug discovery. All this knowledge is not only crucial to advancing the fight against the Zika virus and other flaviviruses but also helps us prepare for the next emerging virus outbreak to which we will have to respond. Copyright © 2018. Published by Elsevier Ltd.

Computational Modelling and Optimal Control of Ebola Virus Disease with non-Linear Incidence Rate

NASA Astrophysics Data System (ADS)

Takaidza, I.; Makinde, O. D.; Okosun, O. K.

2017-03-01

The 2014 Ebola outbreak in West Africa has exposed the need to connect modellers and those with relevant data as pivotal to better understanding of how the disease spreads and quantifying the effects of possible interventions. In this paper, we model and analyse the Ebola virus disease with non-linear incidence rate. The epidemic model created is used to describe how the Ebola virus could potentially evolve in a population. We perform an uncertainty analysis of the basic reproductive number R 0 to quantify its sensitivity to other disease-related parameters. We also analyse the sensitivity of the final epidemic size to the time control interventions (education, vaccination, quarantine and safe handling) and provide the cost effective combination of the interventions.

Understanding dengue virus evolution to support epidemic surveillance and counter-measure development.

PubMed

Pollett, S; Melendrez, M C; Maljkovic Berry, I; Duchêne, S; Salje, H; Dat, Cummings; Jarman, R G

2018-04-25

Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen. Copyright © 2018. Published by Elsevier B.V.

Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions.

PubMed

Zhang, Aidi; He, Libo; Wang, Yaping

2017-03-02

Grass carp hemorrhagic disease, caused by grass carp reovirus (GCRV), is the most fatal causative agent in grass carp aquaculture. Protein-protein interactions between virus and host are one avenue through which GCRV can trigger infection and induce disease. Experimental approaches for the detection of host-virus interactome have many inherent limitations, and studies on protein-protein interactions between GCRV and its host remain rare. In this study, based on known motif-domain interaction information, we systematically predicted the GCRV virus-host protein interactome by using motif-domain interaction pair searching strategy. These proteins derived from different domain families and were predicted to interact with different motif patterns in GCRV. JAM-A protein was successfully predicted to interact with motifs of GCRV Sigma1-like protein, and shared the similar binding mode compared with orthoreovirus. Differentially expressed genes during GCRV infection process were extracted and mapped to our predicted interactome, the overlapped genes displayed different tissue expression distributions on the whole, the overall expression level in intestinal is higher than that of other three tissues, which may suggest that the functions of these genes are more active in intestinal. Function annotation and pathway enrichment analysis revealed that the host targets were largely involved in signaling pathway and immune pathway, such as interferon-gamma signaling pathway, VEGF signaling pathway, EGF receptor signaling pathway, B cell activation, and T cell activation. Although the predicted PPIs may contain some false positives due to limited data resource and poor research background in non-model species, the computational method still provide reasonable amount of interactions, which can be further validated by high throughput experiments. The findings of this work will contribute to the development of system biology for GCRV infectious diseases, and help guide the identification of novel receptors of GCRV in its host.

Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data.

PubMed

Parker, Nicolas J; Parker, Andrew G

2008-04-18

The advent of pyrophosphate sequencing makes large volumes of sequencing data available at a lower cost than previously possible. However, the short read lengths are difficult to assemble and the large dataset is difficult to handle. During the sequencing of a virus from the tsetse fly, Glossina pallidipes, we found the need for tools to search quickly a set of reads for near exact text matches. A set of tools is provided to search a large data set of pyrophosphate sequence reads under a "live" CD version of Linux on a standard PC that can be used by anyone without prior knowledge of Linux and without having to install a Linux setup on the computer. The tools permit short lengths of de novo assembly, checking of existing assembled sequences, selection and display of reads from the data set and gathering counts of sequences in the reads. Demonstrations are given of the use of the tools to help with checking an assembly against the fragment data set; investigating homopolymer lengths, repeat regions and polymorphisms; and resolving inserted bases caused by incomplete chain extension. The additional information contained in a pyrophosphate sequencing data set beyond a basic assembly is difficult to access due to a lack of tools. The set of simple tools presented here would allow anyone with basic computer skills and a standard PC to access this information.

Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus.

PubMed

Squires, R Burke; Pickett, Brett E; Das, Sajal; Scheuermann, Richard H

2014-12-01

In 2009 a novel pandemic H1N1 influenza virus (H1N1pdm09) emerged as the first official influenza pandemic of the 21st century. Early genomic sequence analysis pointed to the swine origin of the virus. Here we report a novel computational approach to determine the evolutionary trajectory of viral sequences that uses data-driven estimations of nucleotide substitution rates to track the gradual accumulation of observed sequence alterations over time. Phylogenetic analysis and multiple sequence alignments show that sequences belonging to the resulting evolutionary trajectory of the H1N1pdm09 lineage exhibit a gradual accumulation of sequence variations and tight temporal correlations in the topological structure of the phylogenetic trees. These results suggest that our evolutionary trajectory analysis (ETA) can more effectively pinpoint the evolutionary history of viruses, including the host and geographical location traversed by each segment, when compared against either BLAST or traditional phylogenetic analysis alone. Copyright © 2014 Elsevier B.V. All rights reserved.

Satellite Tobacco Mosaic Virus (STMV)

NASA Technical Reports Server (NTRS)

2000-01-01

The structure of the Satellite Tobacco Mosaic Virus (STMV)--one of the smallest viruses known--has been successfully deduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the same time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystal grown on Earth, the crystals grown under microgravity conditions were viusally perfect, with no striations or clumping of crystals. Furthermore, the X-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This computer model shows the external coating or capsid. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, Univeristy of California at Irvin.

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.

PubMed

Zhou, Xinrui; Zheng, Jie; Ivan, Fransiskus Xaverius; Yin, Rui; Ranganathan, Shoba; Chow, Vincent T K; Kwoh, Chee-Keong

2018-05-09

Influenza viruses are undergoing continuous and rapid evolution. The fatal influenza A/H7N9 has drawn attention since the first wave of infections in March 2013, and raised more grave concerns with its increased potential to spread among humans. Experimental studies have revealed several host and virulence markers, indicating differential host binding preferences which can help estimate the potential of causing a pandemic. Here we systematically investigate the sequence pattern and structural characteristics of novel influenza A/H7N9 using computational approaches. The sequence analysis highlighted mutations in protein functional domains of influenza viruses. Molecular docking and molecular dynamics simulation revealed that the hemagglutinin (HA) of A/Taiwan/1/2017(H7N9) strain enhanced the binding with both avian and human receptor analogs, compared with the previous A/Shanghai/02/2013(H7N9) strain. The Molecular Mechanics - Poisson Boltzmann Surface Area (MM-PBSA) calculation revealed the change of residue-ligand interaction energy and detected the residues with conspicuous binding preference. The results are novel and specific to the emerging influenza A/Taiwan/1/2017(H7N9) strain compared with A/Shanghai/02/2013(H7N9). Its enhanced ability to bind human receptor analogs, which are abundant in the human upper respiratory tract, may be responsible for the recent outbreak. Residues showing binding preference were detected, which could facilitate monitoring the circulating influenza viruses.

Silicified virus-like nanoparticles in an extreme thermal environment: implications for the preservation of viruses in the geological record.

PubMed

Peng, X; Xu, H; Jones, B; Chen, S; Zhou, H

2013-11-01

Biofilms that grow around Gumingquan hot spring (T = 71 °C, pH = 9.2) in the Rehai geothermal area, Tengchong, China, are formed of various cyanobacteria, Firmicutes, Aquificae, Thermodesulfobacteria, Desulfurococcales, and Thermoproteales. Silicified virus-like nanoparticles, 40-200 nm in diameter, are common inside the microbial cells and the extracellular polymeric substances around the cells. These nanoparticles, which are formed of a core encased by a silica cortex, are morphologically akin to known viruses and directly comparable to silicified virus-like particles that were produced in biofilms cultured in the laboratory. The information obtained from examination of the natural and laboratory-produced samples suggests that viruses can be preserved by silicification, especially while they are still encased in their host cells. These results expand our views of virus-host mineral interaction in extreme thermal environments and imply that viruses can be potentially preserved and identified in the geological record. © 2013 John Wiley & Sons Ltd.

Influenza surveillance in animals: what is our capacity to detect emerging influenza viruses with zoonotic potential?

PubMed

VON Dobschuetz, S; DE Nardi, M; Harris, K A; Munoz, O; Breed, A C; Wieland, B; Dauphin, G; Lubroth, J; Stärk, K D C

2015-07-01

A survey of national animal influenza surveillance programmes was conducted to assess the current capacity to detect influenza viruses with zoonotic potential in animals (i.e. those influenza viruses that can be naturally transmitted between animals and humans) at regional and global levels. Information on 587 animal influenza surveillance system components was collected for 99 countries from Chief Veterinary Officers (CVOs) (n = 94) and published literature. Less than 1% (n = 4) of these components were specifically aimed at detecting influenza viruses with pandemic potential in animals (i.e. those influenza viruses that are capable of causing epidemic spread in human populations over large geographical regions or worldwide), which would have zoonotic potential as a prerequisite. Those countries that sought to detect influenza viruses with pandemic potential searched for such viruses exclusively in domestic pigs. This work shows the global need for increasing surveillance that targets potentially zoonotic influenza viruses in relevant animal species.

Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability.

PubMed

Ho, Daniel W H; Sze, Karen M F; Ng, Irene O L

2015-08-28

Viral integration into the human genome upon infection is an important risk factor for various human malignancies. We developed viral integration site detection tool called Virus-Clip, which makes use of information extracted from soft-clipped sequencing reads to identify exact positions of human and virus breakpoints of integration events. With initial read alignment to virus reference genome and streamlined procedures, Virus-Clip delivers a simple, fast and memory-efficient solution to viral integration site detection. Moreover, it can also automatically annotate the integration events with the corresponding affected human genes. Virus-Clip has been verified using whole-transcriptome sequencing data and its detection was validated to have satisfactory sensitivity and specificity. Marked advancement in performance was detected, compared to existing tools. It is applicable to versatile types of data including whole-genome sequencing, whole-transcriptome sequencing, and targeted sequencing. Virus-Clip is available at http://web.hku.hk/~dwhho/Virus-Clip.zip.

Distribution of mosquitoes and mosquito-borne arboviruses in Yunnan Province near the China-Myanmar-Laos border.

PubMed

Wang, Jinglin; Zhang, Hailin; Sun, Xiaohong; Fu, Shihong; Wang, Huanqin; Feng, Yun; Wang, Huanyu; Tang, Qing; Liang, Guo-Dong

2011-05-01

Economic development and increased tourism in the southern region of Yunnan Province in China, adjacent to several countries in Southeast Asia, has increased the likelihood of import and export of vectors and vector-borne diseases. We report the results of surveillance of mosquitoes and mosquito-borne arboviruses along the border of China-Myanmar-Laos in 2005 and 2006, and information associating several arboviruses with infections and possibly disease in local human populations. Seventeen mosquito species representing four genera were obtained, and 14 strains of mosquito-borne viruses representing six viruses in five genera were isolated from Culex tritaeniorhynchus. In addition, IgM against Japanese encephalitis virus, Sindbis virus, Yunnan orbivirus and novel Banna virus was detected in acute-phase serum samples obtained from hospitalized patients with fever and encephalitis near the areas where the viruses were isolated. This investigation suggests that Japanese encephalitis virus, Sindbis virus, and lesser-known arboviruses circulate and may be infecting humans in the China-Myanmar-Laos border region.

Computational screen and experimental validation of anti-influenza effects of quercetin and chlorogenic acid from traditional Chinese medicine

PubMed Central

Liu, Zekun; Zhao, Junpeng; Li, Weichen; Shen, Li; Huang, Shengbo; Tang, Jingjing; Duan, Jie; Fang, Fang; Huang, Yuelong; Chang, Haiyan; Chen, Ze; Zhang, Ran

2016-01-01

The Influenza A virus is a great threat for human health, while various subtypes of the virus made it difficult to develop drugs. With the development of state-of-art computational chemistry, computational molecular docking could serve as a virtual screen of potential leading compound. In this study, we performed molecular docking for influenza A H1N1 (A/PR/8/34) with small molecules such as quercetin and chlorogenic acid, which were derived from traditional Chinese medicine. The results showed that these small molecules have strong binding abilities with neuraminidase from H1N1 (A/PR/8/34). Further details showed that the structural features of the molecules might be helpful for further drug design and development. The experiments in vitro, in vivo have validated the anti-influenza effect of quercetin and chlorogenic acid, which indicating comparable protection effects as zanamivir. Taken together, it was proposed that chlorogenic acid and quercetin could be employed as the effective lead compounds for anti-influenza A H1N1. PMID:26754609

Computational screen and experimental validation of anti-influenza effects of quercetin and chlorogenic acid from traditional Chinese medicine

NASA Astrophysics Data System (ADS)

Liu, Zekun; Zhao, Junpeng; Li, Weichen; Shen, Li; Huang, Shengbo; Tang, Jingjing; Duan, Jie; Fang, Fang; Huang, Yuelong; Chang, Haiyan; Chen, Ze; Zhang, Ran

2016-01-01

The Influenza A virus is a great threat for human health, while various subtypes of the virus made it difficult to develop drugs. With the development of state-of-art computational chemistry, computational molecular docking could serve as a virtual screen of potential leading compound. In this study, we performed molecular docking for influenza A H1N1 (A/PR/8/34) with small molecules such as quercetin and chlorogenic acid, which were derived from traditional Chinese medicine. The results showed that these small molecules have strong binding abilities with neuraminidase from H1N1 (A/PR/8/34). Further details showed that the structural features of the molecules might be helpful for further drug design and development. The experiments in vitro, in vivo have validated the anti-influenza effect of quercetin and chlorogenic acid, which indicating comparable protection effects as zanamivir. Taken together, it was proposed that chlorogenic acid and quercetin could be employed as the effective lead compounds for anti-influenza A H1N1.

Zika: what we do and do not know based on the experiences of Brazil.

PubMed

Possas, Cristina

2016-01-01

Zika virus, which was first discovered in 1947, has become a global threat to human health as it is rapidly spreading through Latin America, the Caribbean, the US and Asia, after causing a large outbreak in the Northeast region of Brazil in 2015. There is ample evidence to support that Zika virus is associated with neurological complications such as microcephaly. The review aims to provide an overview on the complex issues involved in the emergence of Zika virus's neurological disorders and to discuss possible explanations of Zika virus introduction and dissemination in Brazil. We also suggest national and global strategies to adequately respond to the Zika virus emergence. We provide an analytical evaluation of the main issues related to the Zika outbreak in Brazil, based on available scientific literature, including government documents, and on epidemiological information from national surveillance databases. The studies on the clinical manifestations of the Zika virus infection coupled with the epidemiological surveillance information in Brazil have provided significant evidence that the Zika virus is associated with neurological disorders such as microcephaly and Guillain-Barré syndrome. Based on phylogenetic and molecular analysis, the hypothesis regarding the introduction of Zika virus in the country is that it took place following international events in 2013 and 2014, when many foreign visitors could have brought Zika virus into Brazil. The immunologically naïve status of populations in the Americas, previous infection with dengue virus, and the increased activity of Aedes aegypti might be the contributing factors for such an outbreak in Brazil. The Zika virus emergence emphasized the importance of cross-disciplinary perspective. Besides the scientific-based vector control strategies, it is important to understand the nature of the evolutionary processes involved in the viral evolution in complex ecosystems and to have social and anthropological knowledge on the conditions related to the spread of the disease in order to properly respond to the spread of the Zika virus. The experiences of Brazil have demonstrated the significance of multi-disciplinary approach in response to new and resurgent arboviral diseases and provided important lessons that could be applied to other developing countries.

Reviews: Software.

ERIC Educational Resources Information Center

Mackenzie, Norma N.; And Others

1988-01-01

Reviews four computer software packages including: "The Physical Science Series: Sound" which demonstrates making waves, speed of sound, doppler effect, and human hearing; "Andromeda" depicting celestial motions in any direction; "Biology Quiz: Humans" covering chemistry, cells, viruses, and human biology; and…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koizumi, Yoshiki; Nakajim, Syo; Ohash, Hirofumi

Cell culture study combing a mathematical model and computer simulation quantifies the anti-hepatitis C virus drug efficacy at any concentrations and any combinations in preclinical settings, and can obtain rich basic evidences for selecting optimal treatments prior to costly clinical trials.

Woodcock reovirus

USGS Publications Warehouse

Docherty, D.E.

1999-01-01

This chapter provides information on a recently identified disease of the American woodcock. Little is known about the disease or the virus that causes it. It has been included in this Manual to enhance awareness that such a disease exists and to stimulate additional interest in further investigations to define the importance of woodcock reovirus. More information about this disease is needed because it is not known whether or not this virus is a factor in the decline of woodcock populations within the United States.

Breast milk transmission of flaviviruses in the context of Zika virus: A systematic review.

PubMed

Mann, Taylor Z; Haddad, Lisa B; Williams, Tonya R; Hills, Susan L; Read, Jennifer S; Dee, Deborah L; Dziuban, Eric J; Pérez-Padilla, Janice; Jamieson, Denise J; Honein, Margaret A; Shapiro-Mendoza, Carrie K

2018-06-08

Since the Zika virus epidemic in the Americas began in 2015, Zika virus transmission has occurred throughout the Americas. However, limited information exists regarding possible risks of transmission of Zika virus and other flaviviruses through breast feeding and human milk. We conducted a systematic review of the evidence regarding flaviviruses detection in and transmission through milk, specifically regarding Zika virus, Japanese encephalitis virus, tick-borne encephalitis virus, Powassan virus, West Nile virus, dengue virus, and yellow fever virus. Medline, Embase, Global Health, CINAHL, Cochrane Library, Scopus, Popline, Virtual Health Library, and WorldCat were searched through June 2017. Two authors independently screened potential studies for inclusion and extracted data. Human and nonhuman (animal) studies describing: 1) confirmed or suspected cases of mother-to-child transmission through milk; or 2) the presence of flavivirus genomic material in milk. Seventeen studies were included, four animal models and thirteen observational studies. Dengue virus, West Nile virus, and Zika virus viral ribonucleic acid was detected in human milk, including infectious Zika virus and dengue virus viral particles. Human breast-feeding transmission was confirmed for only yellow fever virus. There was evidence of milk-related transmission of dengue virus, Powassan virus, and West Nile virus in animal studies. Because the health advantages of breast feeding are considered greater than the potential risk of transmission, the World Health Organization recommends that mothers with possible or confirmed Zika virus infection or exposure continue to breast feed. This review did not identify any data that might alter this recommendation. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

The effectiveness of risk communication regarding drug safety information: a nationwide survey by the Japanese public health insurance claims data.

PubMed

Hagiwara, Hiromi; Nakano, Shun; Ogawa, Yoshihiro; Tohkin, Masahiro

2015-06-01

We evaluated the effectiveness of warning letters published by the pharmaceutical regulatory agency in Japan on communication of drug safety and risk by quantitative analysis of the national health insurance claims database (NHICD). We then explored what factors may have affected risk communication. We measured the implementation rate of the hepatitis virus-monitoring test among methotrexate (MTX)-treated patients; a warning letter had been issued regarding the use of MTX, as it apparently activates the hepatitis virus. Data from the NHICD, which include 99·3% of Japanese residents, were used. A total of 4,933,481 patients with rheumatoid arthritis (RA) (January-June, 2010) were the focus of this study. The implementation rate of the hepatitis virus-monitoring test increased from 1·4% before to 1·8% after the warning letter announcement. Logistic regression analysis suggested that the installation of a drug information management room is one of the important factors affecting risk communication. Further analysis revealed that the hepatitis virus monitoring rates in hospitals without drug information management rooms increased from 2·3% to 4·1% due to the issue of the warning letter. The warning letter from the regulatory agency plays an important role in risk communication in hospitals without drug information management rooms. © 2015 John Wiley & Sons Ltd.

Viruses and viruslike particles of eukaryotic algae.

PubMed Central

Van Etten, J L; Lane, L C; Meints, R H

1991-01-01

Until recently there was little interest or information on viruses and viruslike particles of eukaryotic algae. However, this situation is changing. In the past decade many large double-stranded DNA-containing viruses that infect two culturable, unicellular, eukaryotic green algae have been discovered. These viruses can be produced in large quantities, assayed by plaque formation, and analyzed by standard bacteriophage techniques. The viruses are structurally similar to animal iridoviruses, their genomes are similar to but larger (greater than 300 kbp) than that of poxviruses, and their infection process resembles that of bacteriophages. Some of the viruses have DNAs with low levels of methylated bases, whereas others have DNAs with high concentrations of 5-methylcytosine and N6-methyladenine. Virus-encoded DNA methyltransferases are associated with the methylation and are accompanied by virus-encoded DNA site-specific (restriction) endonucleases. Some of these enzymes have sequence specificities identical to those of known bacterial enzymes, and others have previously unrecognized specificities. A separate rod-shaped RNA-containing algal virus has structural and nucleotide sequence affinities to higher plant viruses. Quite recently, viruses have been associated with rapid changes in marine algal populations. In the next decade we envision the discovery of new algal viruses, clarification of their role in various ecosystems, discovery of commercially useful genes in these viruses, and exploitation of algal virus genetic elements in plant and algal biotechnology. Images PMID:1779928

A computational method for predicting regulation of human microRNAs on the influenza virus genome

PubMed Central

2013-01-01

Background While it has been suggested that host microRNAs (miRNAs) may downregulate viral gene expression as an antiviral defense mechanism, such a mechanism has not been explored in the influenza virus for human flu studies. As it is difficult to conduct related experiments on humans, computational studies can provide some insight. Although many computational tools have been designed for miRNA target prediction, there is a need for cross-species prediction, especially for predicting viral targets of human miRNAs. However, finding putative human miRNAs targeting influenza virus genome is still challenging. Results We developed machine-learning features and conducted comprehensive data training for predicting interactions between H1N1 genome segments and host miRNA. We defined our seed region as the first ten nucleotides from the 5' end of the miRNA to the 3' end of the miRNA and integrated various features including the number of consecutive matching bases in the seed region of 10 bases, a triplet feature in seed regions, thermodynamic energy, penalty of bulges and wobbles at binding sites, and the secondary structure of viral RNA for the prediction. Conclusions Compared to general predictive models, our model fully takes into account the conservation patterns and features of viral RNA secondary structures, and greatly improves the prediction accuracy. Our model identified some key miRNAs including hsa-miR-489, hsa-miR-325, hsa-miR-876-3p and hsa-miR-2117, which target HA, PB2, MP and NS of H1N1, respectively. Our study provided an interesting hypothesis concerning the miRNA-based antiviral defense mechanism against influenza virus in human, i.e., the binding between human miRNA and viral RNAs may not result in gene silencing but rather may block the viral RNA replication. PMID:24565017

Information Assurance Technical Framework (IATF). Release 3.1

DTIC Science & Technology

2002-09-01

used in the United States and Europe for both cordless phones and wireless PBXs. In addition to DECT, some cordless telephones use other signaling...1.544 Mbps. Europe and Japan use a different standard for primary rate service. Government equipment is being designed for N-ISDN. This device was...There are three main components of a polymorphic virus: a scrambled virus body, a decryption routine, and a mutation engine. In a polymorphic virus, the

Use of Influenza Risk Assessment Tool for Prepandemic Preparedness

PubMed Central

Trock, Susan C.

2018-01-01

In 2010, the Centers for Disease Control and Prevention began to develop an Influenza Risk Assessment Tool (IRAT) to methodically capture and assess information relating to influenza A viruses not currently circulating among humans. The IRAT uses a multiattribute, additive model to generate a summary risk score for each virus. Although the IRAT is not intended to predict the next pandemic influenza A virus, it has provided input into prepandemic preparedness decisions. PMID:29460739

A 1-Year Quantitative Survey of Noro-, Adeno-, Human Boca-, and Hepatitis E Viruses in Raw and Secondarily Treated Sewage from Two Plants in Norway.

PubMed

Myrmel, M; Lange, H; Rimstad, E

2015-09-01

A study of enteric viruses in raw and treated sewage from two secondary treatment plants, which received sewage from Oslo city (plant A) and small municipalities in Hedmark county in Norway (plant B), showed high levels of noro-, adeno-, and bocavirus throughout the year. A seasonal variation was observed for adeno- and GII norovirus with higher levels during winter and bocavirus that had more positive samples during winter. The virus concentrations in raw sewage were comparable in the two plants, with medians (log10 genome copies per liter) of 6.1, 6.3, 6.0, and 4.5 for noro GI, noro GII, adeno-, and bocavirus, respectively. The level of hepatitis E virus was not determined as it was below the limit of quantification. The mean log10 virus reduction was 0.55 (plant A) and 1.44 (plant B) with the highest reduction found in the plant with longer hydraulic retention time. The adenoviruses were dominantly serotype 41, while serotype 12 appeared sporadically. Of the 102 raw and treated sewage samples that were tested, eight were positive for hepatitis E virus of which four were from treated sewage. Two of the four obtained gene sequences from hepatitis E virus originated from the rural sewage samples and showed high similarity with a genotype 3 strain of hepatitis E virus detected in local piglets. Two other hepatitis E virus sequences obtained from urban sewage samples showed high similarities with genotype 3 strains isolated from urban sewage in Spain and a human genotype 1 isolate from India. The study gives information on the levels of noroviruses in raw and treated sewage, which is valuable to risk assessment, information indicating that some infections with hepatitis E viruses in Norway have a regional origin and that human bocavirus 2 and 3 are prevalent in the Norwegian population.

Influenza A viruses of avian origin circulating in pigs and other mammals.

PubMed

Urbaniak, Kinga; Kowalczyk, Andrzej; Markowska-Daniel, Iwona

2014-01-01

Influenza A viruses (IAVs) are zoonotic agents, capable of crossing the species barriers. Nowadays, they still constitute a great challenge worldwide. The natural reservoir of all influenza A viruses are wild aquatic birds, despite the fact they have been isolated from a number of avian and mammalian species, including humans. Even when influenza A viruses are able to get into another than waterfowl population, they are often unable to efficiently adapt and transmit between individuals. Only in rare cases, these viruses are capable of establishing a new lineage. To succeed a complete adaptation and further transmission between species, influenza A virus must overcome a species barrier, including adaptation to the receptors of a new host, which would allow the virus-cell binding, virus replication and, then, animal-to-animal transmission. For many years, pigs were thought to be intermediate host for adaptation of avian influenza viruses to humans, because of their susceptibility to infection with both, avian and human influenza viruses, which supported hypothesis of pigs as a 'mixing vessel'. In this review, the molecular factors necessary for interspecies transmission are described, with special emphasis on adaptation of avian influenza viruses to the pig population. In addition, this review gives the information about swine influenza viruses circulating around the world with special emphasis on Polish strains.

Acanthamoeba polyphaga mimivirus and other giant viruses: an open field to outstanding discoveries

PubMed Central

2014-01-01

In 2003, Acanthamoeba polyphaga mimivirus (APMV) was first described and began to impact researchers around the world, due to its structural and genetic complexity. This virus founded the family Mimiviridae. In recent years, several new giant viruses have been isolated from different environments and specimens. Giant virus research is in its initial phase and information that may arise in the coming years may change current conceptions of life, diversity and evolution. Thus, this review aims to condense the studies conducted so far about the features and peculiarities of APMV, from its discovery to its clinical relevance. PMID:24976356

A Student's Guide to Giant Viruses Infecting Small Eukaryotes: From Acanthamoeba to Zooxanthellae.

PubMed

Wilhelm, Steven W; Bird, Jordan T; Bonifer, Kyle S; Calfee, Benjamin C; Chen, Tian; Coy, Samantha R; Gainer, P Jackson; Gann, Eric R; Heatherly, Huston T; Lee, Jasper; Liang, Xiaolong; Liu, Jiang; Armes, April C; Moniruzzaman, Mohammad; Rice, J Hunter; Stough, Joshua M A; Tams, Robert N; Williams, Evan P; LeCleir, Gary R

2017-03-17

The discovery of infectious particles that challenge conventional thoughts concerning "what is a virus" has led to the evolution a new field of study in the past decade. Here, we review knowledge and information concerning "giant viruses", with a focus not only on some of the best studied systems, but also provide an effort to illuminate systems yet to be better resolved. We conclude by demonstrating that there is an abundance of new host-virus systems that fall into this "giant" category, demonstrating that this field of inquiry presents great opportunities for future research.

Climate Change and the Arboviruses: Lessons from the Evolution of the Dengue and Yellow Fever Viruses.

PubMed

Tabachnick, Walter J

2016-09-29

The impact of anticipated changes in global climate on the arboviruses and the diseases they cause poses a significant challenge for public health. The past evolution of the dengue and yellow fever viruses provides clues about the influence of changes in climate on their future evolution. The evolution of both viruses has been influenced by virus interactions involving the mosquito species and the primate hosts involved in virus transmission, and by their domestic and sylvatic cycles. Information is needed on how viral genes in general influence phenotypic variance for important viral functions. Changes in global climate will alter the interactions of mosquito species with their primate hosts and with the viruses in domestic cycles, and greater attention should be paid to the sylvatic cycles. There is great danger for the evolution of novel viruses, such as new serotypes, that could compromise vaccination programs and jeopardize public health. It is essential to understand (a) both sylvatic and domestic cycles and (b) the role of virus genetic and environmental variances in shaping virus phenotypic variance to more fully assess the impact of global climate change.

Metagenomic characterization of viral communities in Goseong Bay, Korea

NASA Astrophysics Data System (ADS)

Hwang, Jinik; Park, So Yun; Park, Mirye; Lee, Sukchan; Jo, Yeonhwa; Cho, Won Kyong; Lee, Taek-Kyun

2016-12-01

In this study, seawater samples were collected from Goseong Bay, Korea in March 2014 and viral populations were examined by metagenomics assembly. Enrichment of marine viral particles using FeCl3 followed by next-generation sequencing produced numerous sequences. De novo assembly and BLAST search showed that most of the obtained contigs were unknown sequences and only 0.74% of sequences were associated with known viruses. As a result, 138 viruses, including bacteriophages (87%), viruses infecting algae and others (13%) were identified. The identified 138 viruses were divided into 11 orders, 14 families, 34 genera, and 133 species. The dominant viruses were Pelagibacter phage HTVC010P and Roseobacter phage SIO1. The viruses infecting algae, including the Ostreococcus species, accounted for 9.4% of total identified viruses. In addition, we identified pathogenic herpes viruses infecting fishes and giant viruses infecting parasitic acanthamoeba species. This is a comprehensive study to reveal the viral populations in the Goseong Bay using metagenomics. The information associated with the marine viral community in Goseong Bay, Korea will be useful for comparative analysis in other marine viral communities.

Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique.

PubMed

Zou, Xiaohui; Tang, Guangpeng; Zhao, Xiang; Huang, Yan; Chen, Tao; Lei, Mingyu; Chen, Wenbing; Yang, Lei; Zhu, Wenfei; Zhuang, Li; Yang, Jing; Feng, Zhaomin; Wang, Dayan; Wang, Dingming; Shu, Yuelong

2017-03-01

Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples. Human rhinovirus C was the virus most frequently detected and was identified in seven samples. Human measles virus, adenovirus B 55 and coxsackievirus A10 were also identified. Metagenomic sequencing also provided virus genomic sequences, which enabled genotype characterization and phylogenetic analysis. For cases of multiple infection, metagenomic sequencing afforded information regarding the quantity of each virus in the sample, which could be used to evaluate each viruses' role in the disease. Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.

Swine Influenza Virus (H1N2) Characterization and Transmission in Ferrets, Chile.

PubMed

Bravo-Vasquez, Nicolás; Karlsson, Erik A; Jimenez-Bluhm, Pedro; Meliopoulos, Victoria; Kaplan, Bryan; Marvin, Shauna; Cortez, Valerie; Freiden, Pamela; Beck, Melinda A; Hamilton-West, Christopher; Schultz-Cherry, Stacey

2017-02-01

Phylogenetic analysis of the influenza hemagglutinin gene (HA) has suggested that commercial pigs in Chile harbor unique human seasonal H1-like influenza viruses, but further information, including characterization of these viruses, was unavailable. We isolated influenza virus (H1N2) from a swine in a backyard production farm in Central Chile and demonstrated that the HA gene was identical to that in a previous report. Its HA and neuraminidase genes were most similar to human H1 and N2 viruses from the early 1990s and internal segments were similar to influenza A(H1N1)pdm09 virus. The virus replicated efficiently in vitro and in vivo and transmitted in ferrets by respiratory droplet. Antigenically, it was distinct from other swine viruses. Hemagglutination inhibition analysis suggested that antibody titers to the swine Chilean H1N2 virus were decreased in persons born after 1990. Further studies are needed to characterize the potential risk to humans, as well as the ecology of influenza in swine in South America.

Swine Influenza Virus (H1N2) Characterization and Transmission in Ferrets, Chile

PubMed Central

Bravo-Vasquez, Nicolás; Karlsson, Erik A.; Jimenez-Bluhm, Pedro; Meliopoulos, Victoria; Kaplan, Bryan; Marvin, Shauna; Cortez, Valerie; Freiden, Pamela; Beck, Melinda A.

2017-01-01

Phylogenetic analysis of the influenza hemagglutinin gene (HA) has suggested that commercial pigs in Chile harbor unique human seasonal H1-like influenza viruses, but further information, including characterization of these viruses, was unavailable. We isolated influenza virus (H1N2) from a swine in a backyard production farm in Central Chile and demonstrated that the HA gene was identical to that in a previous report. Its HA and neuraminidase genes were most similar to human H1 and N2 viruses from the early 1990s and internal segments were similar to influenza A(H1N1)pdm09 virus. The virus replicated efficiently in vitro and in vivo and transmitted in ferrets by respiratory droplet. Antigenically, it was distinct from other swine viruses. Hemagglutination inhibition analysis suggested that antibody titers to the swine Chilean H1N2 virus were decreased in persons born after 1990. Further studies are needed to characterize the potential risk to humans, as well as the ecology of influenza in swine in South America. PMID:28098524

The study of virus structure and function: a personal history

NASA Astrophysics Data System (ADS)

Rossmann, Michael G.

2014-09-01

I describe my gradually evolving role as a scientist from my birth in Frankfurt (Germany) to my education in the UK, my post-doc years and my experiences as an independent investigator at Purdue University1. I discuss the significance of my post-doctoral work in Minnesota where I had my first encounter with an electronic computer and subsequently in Cambridge where I participated in the first structure determination of proteins. After six years back in England my family moved to Indiana (USA) where my home remains to this day. At Purdue University I first studied the structure of enzymes and in the process I discovered the organization and slow evolution of protein domains, each with a specific function. With this success I started what had been on my mind already for a long time, namely the structural analysis of viruses. Initially we studied plant viruses but then switched to small RNA animal viruses, discovering that some plant and animal RNA viruses have closely similar structures and therefore presumably had a common evolutionary origin. Next I became interested in somewhat larger viruses that had lipid membrane envelopes. In turn that has led to the study of very large dsDNA viruses as big as small bacteria as well as studies of bacterial viruses that require complex molecular motors for different parts of their life cycle. While developing crystallographic techniques for the study of viruses it has become progressively more apparent that electron microscopy is an important new tool that is likely to eclipse x-ray crystallography in the next decade.

Representing virus-host interactions and other multi-organism processes in the Gene Ontology.

PubMed

Foulger, R E; Osumi-Sutherland, D; McIntosh, B K; Hulo, C; Masson, P; Poux, S; Le Mercier, P; Lomax, J

2015-07-28

The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms. To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms. Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution

PubMed Central

Vrancken, Bram; Lemey, Philippe; Rambaut, Andrew; Bedford, Trevor; Longdon, Ben; Günthard, Huldrych F.; Suchard, Marc A.

2014-01-01

Phylogenetic signal quantifies the degree to which resemblance in continuously-valued traits reflects phylogenetic relatedness. Measures of phylogenetic signal are widely used in ecological and evolutionary research, and are recently gaining traction in viral evolutionary studies. Standard estimators of phylogenetic signal frequently condition on data summary statistics of the repeated trait observations and fixed phylogenetics trees, resulting in information loss and potential bias. To incorporate the observation process and phylogenetic uncertainty in a model-based approach, we develop a novel Bayesian inference method to simultaneously estimate the evolutionary history and phylogenetic signal from molecular sequence data and repeated multivariate traits. Our approach builds upon a phylogenetic diffusion framework that model continuous trait evolution as a Brownian motion process and incorporates Pagel’s λ transformation parameter to estimate dependence among traits. We provide a computationally efficient inference implementation in the BEAST software package. We evaluate the synthetic performance of the Bayesian estimator of phylogenetic signal against standard estimators, and demonstrate the use of our coherent framework to address several virus-host evolutionary questions, including virulence heritability for HIV, antigenic evolution in influenza and HIV, and Drosophila sensitivity to sigma virus infection. Finally, we discuss model extensions that will make useful contributions to our flexible framework for simultaneously studying sequence and trait evolution. PMID:25780554

Granulomatous herpes simplex encephalitis in an infant with multicystic encephalopathy: a distinct clinicopathologic entity?

PubMed

Schutz, Peter W; Fauth, Clarissa T; Al-Rawahi, Ghada N; Pugash, Denise; White, Valerie A; Stockler, Sylvia; Dunham, Christopher P

2014-04-01

Herpes simplex virus encephalitis can manifest as a range of clinical presentations including classic adult, neonatal, and biphasic chronic-granulomatous herpes encephalitis. We report an infant with granulomatous herpes simplex virus type 2 encephalitis with a subacute course and multicystic encephalopathy. A 2-month-old girl presented with lethargy and hypothermia. Computed tomography scan of the head showed multicystic encephalopathy and calcifications. Cerebrospinal fluid analysis by polymerase chain reaction testing for herpes simplex virus 1 and 2, enterovirus, and cytomegalovirus was negative. Normal cerebrospinal fluid interferon-α levels argued against Aicardi-Goutières syndrome. The patient died 2 weeks after presentation. At autopsy, multicystic encephalopathy was confirmed with bilateral gliosis, granulomatous inflammation with multinucleated giant cells, and calcifications. Bilateral healing necrotizing retinitis suggested a viral etiology, but retina and brain were free of viral inclusions and immunohistochemically negative for herpes simplex virus-2 and cytomegalovirus. However, polymerase chain reaction analysis showed herpes simplex virus-2 DNA in four cerebral paraffin blocks. Subsequent repeat testing of the initial cerebrospinal fluid sample using a different polymerase chain reaction assay was weakly positive for herpes simplex virus-2 DNA. Granulomatous herpes simplex virus encephalitis in infants can present with subacute course and result in multicystic encephalopathy with mineralization and minimal cerebrospinal fluid herpes simplex virus DNA load. Infectious etiologies should be carefully investigated in the differential diagnosis of multicystic encephalopathy with mineralization, in particular if multinucleated giant cells are present. Copyright © 2014 Elsevier Inc. All rights reserved.

VIRUS NOMENCLATURE BELOW THE SPECIES LEVEL: A STANDARDIZED NOMENCLATURE FOR LABORATORY ANIMAL-ADAPTED STRAINS AND VARIANTS OF VIRUSES ASSIGNED TO THE FAMILY FILOVIRIDAE

PubMed Central

Kuhn, Jens H.; Bao, Yiming; Bavari, Sina; Becker, Stephan; Bradfute, Steven; Brister, J. Rodney; Bukreyev, Alexander A.; Caì, Yíngyún; Chandran, Kartik; Davey, Robert A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Gonzalez, Jean-Paul; Formenty, Pierre; Freiberg, Alexander N.; Hensley, Lisa E.; Honko, Anna N.; Ignatyev, Georgy M.; Jahrling, Peter B.; Johnson, Karl M.; Klenk, Hans-Dieter; Kobinger, Gary; Lackemeyer, Matthew G.; Leroy, Eric M.; Lever, Mark S.; Lofts, Loreen L.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Palacios, Gustavo; Patterson, Jean L.; Paweska, Janusz T.; Pitt, Louise; Radoshitzky, Sheli R.; Ryabchikova, Elena I.; Saphire, Erica Ollmann; Shestopalov, Aleksandr M.; Smither, Sophie J.; Sullivan, Nancy J.; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Warren, Travis K.; Warfield, Kelly L.; Weidmann, Manfred; Nichol, Stuart T.

2013-01-01

The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming ( ///-) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed. PMID:23358612

Persistence of enteroviruses in sewage sludge*

PubMed Central

Subrahmanyan, T. P.

1977-01-01

Sewage from residential areas often contains viruses pathogenic for man and significant amounts are probably associated with solids in sewage sludge. Information on the survival of viruses in sewage sludge is necessary in order to develop guidelines for recycling programmes that involve spreading the sludge on land. In the present study, a number of enteroviruses were added to sewage sludge and the artificially contaminated sludges were tested for viruses at intervals over a 12-week period. Most of the viruses survived for many weeks at room temperature. It is clear that sewage sludge destined for land application should be adequately treated for virus inactivation. In interpreting these results, it should be borne in mind that the survival of hepatitis A virus might be similar. Recent reports about the reappearance of poliomyelitis in regions with immunization programmes should also be taken into consideration. PMID:202416

Newcastle Disease Virus (PDQ®)—Health Professional Version

Cancer.gov

Newcastle disease virus (NDV)- based therapy has been reported to be of benefit in clinical studies, but results are considered inconclusive. Study designs were weak and the study reports were generally incomplete. Get detailed information about NDV use in cancer in this summary for clinicians.

Porcine reproductive and respiratory syndrome virus (PRRSV): pathogenesis and interaction with the immune System

USDA-ARS?s Scientific Manuscript database

This review addresses important issues of porcine reproductive and respiratory syndrome virus (PRRSV) infection, immunity, pathogenesis and control. Worldwide PRRS is the most economically important infectious disease of pigs. We highlight the latest information on viral genome structure, pathogenic...

GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records.

PubMed

Tahsin, Tasnia; Weissenbacher, Davy; O'Connor, Karen; Magge, Arjun; Scotch, Matthew; Gonzalez-Hernandez, Graciela

2018-05-01

GeoBoost is a command-line software package developed to address sparse or incomplete metadata in GenBank sequence records that relate to the location of the infected host (LOIH) of viruses. Given a set of GenBank accession numbers corresponding to virus GenBank records, GeoBoost extracts, integrates and normalizes geographic information reflecting the LOIH of the viruses using integrated information from GenBank metadata and related full-text publications. In addition, to facilitate probabilistic geospatial modeling, GeoBoost assigns probability scores for each possible LOIH. Binaries and resources required for running GeoBoost are packed into a single zipped file and freely available for download at https://tinyurl.com/geoboost. A video tutorial is included to help users quickly and easily install and run the software. The software is implemented in Java 1.8, and supported on MS Windows and Linux platforms. gragon@upenn.edu. Supplementary data are available at Bioinformatics online.

Detection of respiratory viruses on air filters from aircraft.

PubMed

Korves, T M; Johnson, D; Jones, B W; Watson, J; Wolk, D M; Hwang, G M

2011-09-01

To evaluate the feasibility of identifying viruses from aircraft cabin air, we evaluated whether respiratory viruses trapped by commercial aircraft air filters can be extracted and detected using a multiplex PCR, bead-based assay. The ResPlex II assay was first tested for its ability to detect inactivated viruses applied to new filter material; all 18 applications of virus at a high concentration were detected. The ResPlex II assay was then used to test for 18 respiratory viruses on 48 used air filter samples from commercial aircraft. Three samples tested positive for viruses, and three viruses were detected: rhinovirus, influenza A and influenza B. For 33 of 48 samples, internal PCR controls performed suboptimally, suggesting sample matrix effect. In some cases, influenza and rhinovirus RNA can be detected on aircraft air filters, even more than 10 days after the filters were removed from aircraft. With protocol modifications to overcome PCR inhibition, air filter sampling and the ResPlex II assay could be used to characterize viruses in aircraft cabin air. Information about viruses in aircraft could support public health measures to reduce disease transmission within aircraft and between cities. © The MITRE corporation. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

Guidelines for Network Security in the Learning Environment.

ERIC Educational Resources Information Center

Littman, Marlyn Kemper

1996-01-01

Explores security challenges and practical approaches to safeguarding school networks against invasion. Highlights include security problems; computer viruses; privacy assaults; Internet invasions; building a security policy; authentication; passwords; encryption; firewalls; and acceptable use policies. (Author/LRW)

RNA structural constraints in the evolution of the influenza A virus genome NP segment

PubMed Central

Gultyaev, Alexander P; Tsyganov-Bodounov, Anton; Spronken, Monique IJ; van der Kooij, Sander; Fouchier, Ron AM; Olsthoorn, René CL

2014-01-01

Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed. PMID:25180940

[Prevalence of transmission of zidovudine-resistant viruses in Switzerland. l'Etude suisse de cohorte VIH].

PubMed

Yerly, S; Rakik, A; Kinloch-de-Loes, S; Erb, P; Vernazza, P; Hirschel, B; Perrin, L

1996-10-26

Zidovudine (ZDV) was the most widely used anti-HIV drug between 1987 and 1995, and, as already reported, transmission of ZDV-resistant viruses occurs. Several mutations of the reverse transcriptase gene have been identified; one of them affects the 215 codon and is associated with a high degree of resistance. We have determined, using selective PCR, the prevalence of transmission of 215 mutant isolates in 134 patients with primary HIV infection (PHI) and have identified 8 patients with 215 mutant virus between 1989 and 1995 in Switzerland. Mutant resistant viruses have been isolated from patients treated with most antiviral drugs. A systematic search for mutant viruses may provide useful information for the adaptation of treatment strategies.

Differential Immune Responses to New World and Old World Mammalian Arenaviruses

PubMed Central

Ly, Hinh

2017-01-01

Some New World (NW) and Old World (OW) mammalian arenaviruses are emerging, zoonotic viruses that can cause lethal hemorrhagic fever (HF) infections in humans. While these are closely related RNA viruses, the infected hosts appear to mount different types of immune responses against them. Lassa virus (LASV) infection, for example, results in suppressed immune function in progressive disease stage, whereas patients infected with Junín virus (JUNV) develop overt pro-inflammatory cytokine production. These viruses have also evolved different molecular strategies to evade host immune recognition and activation. This paper summarizes current progress in understanding the differential immune responses to pathogenic arenaviruses and how the information can be exploited toward the development of vaccines against them. PMID:28498311

Primary central nervous system lymphoma in an human immunodeficiency virus-infected patient mimicking bilateral eye sign in brain seen in fluorine-18 fluorodeoxyglucose-positron emission tomography/computed tomography.

PubMed

Kamaleshwaran, Koramadai Karuppusany; Thirugnanam, Rajasekar; Shibu, Deepu; Kalarikal, Radhakrishnan Edathurthy; Shinto, Ajit Sugunan

2014-04-01

Fluorodeoxyglucose-positron emission tomography/computed tomography (FDG PET/CT) has proven useful in the diagnosis, staging, and detection of metastasis and posttreatment monitoring of several malignancies in human immunodeficiency virus (HIV)-infected patients. It also has the ability to make the important distinction between malignancy and infection in the evaluation of central nervous system (CNS) lesions, leading to the initiation of the appropriate treatment and precluding the need for invasive biopsy. We report an interesting case of HIV positive 35-year-old woman presented with headache, disorientation, and decreased level of consciousness. She underwent whole body PET/CT which showed multiple lesions in the cerebrum which mimics bilateral eye in brain. A diagnosis of a primary CNS lymphoma was made and patient was started on chemotherapy.

Towards multiscale modeling of influenza infection

PubMed Central

Murillo, Lisa N.; Murillo, Michael S.; Perelson, Alan S.

2013-01-01

Aided by recent advances in computational power, algorithms, and higher fidelity data, increasingly detailed theoretical models of infection with influenza A virus are being developed. We review single scale models as they describe influenza infection from intracellular to global scales, and, in particular, we consider those models that capture details specific to influenza and can be used to link different scales. We discuss the few multiscale models of influenza infection that have been developed in this emerging field. In addition to discussing modeling approaches, we also survey biological data on influenza infection and transmission that is relevant for constructing influenza infection models. We envision that, in the future, multiscale models that capitalize on technical advances in experimental biology and high performance computing could be used to describe the large spatial scale epidemiology of influenza infection, evolution of the virus, and transmission between hosts more accurately. PMID:23608630

Computational biology approach to uncover hepatitis C virus helicase operation.

PubMed

Flechsig, Holger

2014-04-07

Hepatitis C virus (HCV) helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings.

VIOLIN: vaccine investigation and online information network.

PubMed

Xiang, Zuoshuang; Todd, Thomas; Ku, Kim P; Kovacic, Bethany L; Larson, Charles B; Chen, Fang; Hodges, Andrew P; Tian, Yuying; Olenzek, Elizabeth A; Zhao, Boyang; Colby, Lesley A; Rush, Howard G; Gilsdorf, Janet R; Jourdian, George W; He, Yongqun

2008-01-01

Vaccines are among the most efficacious and cost-effective tools for reducing morbidity and mortality caused by infectious diseases. The vaccine investigation and online information network (VIOLIN) is a web-based central resource, allowing easy curation, comparison and analysis of vaccine-related research data across various human pathogens (e.g. Haemophilus influenzae, human immunodeficiency virus (HIV) and Plasmodium falciparum) of medical importance and across humans, other natural hosts and laboratory animals. Vaccine-related peer-reviewed literature data have been downloaded into the database from PubMed and are searchable through various literature search programs. Vaccine data are also annotated, edited and submitted to the database through a web-based interactive system that integrates efficient computational literature mining and accurate manual curation. Curated information includes general microbial pathogenesis and host protective immunity, vaccine preparation and characteristics, stimulated host responses after vaccination and protection efficacy after challenge. Vaccine-related pathogen and host genes are also annotated and available for searching through customized BLAST programs. All VIOLIN data are available for download in an eXtensible Markup Language (XML)-based data exchange format. VIOLIN is expected to become a centralized source of vaccine information and to provide investigators in basic and clinical sciences with curated data and bioinformatics tools for vaccine research and development. VIOLIN is publicly available at http://www.violinet.org.

Using epidemiological information to develop effective integrated virus disease management strategies.

PubMed

Jones, Roger A C

2004-03-01

Virus diseases cause serious losses in yield and quality of cultivated plants worldwide. These losses and the resulting financial damage can be limited by controlling epidemics using measures that minimise virus infection sources or suppress virus spread. For each combination of virus, cultivated plant and production system, there is an 'economic threshold' above which the financial damage is sufficient to justify using such measures. However, individual measures used alone may bring only small benefits and they may become ineffective, especially over the long term. When diverse control measures that act in different ways are combined and used together, their effects are complementary resulting in far more effective overall control. Such experiences have led to the development of integrated management concepts for virus diseases that combine available host resistance, cultural, chemical and biological control measures. Selecting the ideal mix of measures for each pathosystem and production situation requires detailed knowledge of the epidemiology of the causal virus and the mode of action of each individual control measure so that diverse responses can be devised to meet the unique features of each of the different scenarios considered. The strategies developed must be robust and necessitate minimal extra expense, labour demands and disruption to standard practices. Examples of how epidemiological information can be used to develop effective integrated disease management (IDM) strategies for diverse situations are described. They involve circumstances where virus transmission from plant-to-plant occurs in four different ways: by contact, non-persistently or persistently by insect vectors, and by root-infecting fungi. The examples are: Subterranean clover mottle virus (SCMoV) (contact-transmitted) and Bean yellow mosaic virus (BYMV) (non-persistently aphid-transmitted) in annually self-regenerating clover pasture; three seed-borne viruses (all non-persistently aphid-transmitted) plots of pasture legume improvement programmes; Tomato spotted wilt virus (TSWV) (persistently thrips-transmitted) in vegetables in seedling nurseries, protected cropping or field systems; and lettuce big-vein disease (fungus-transmitted) in lettuce in seedling nursery, hydroponic, infested field or uninfested field situations. By describing the kinds of approaches required, this article is intended to help future research and extension programmes devise integrated disease management strategies that not only function effectively to diminish the losses caused by economically important plant virus diseases but also fulfill the requirement of being environmentally and socially responsible.

Virtual virus, a semester-long interdisciplinary project on the crossroads of creativity and knowledge integration.

PubMed

Marintcheva, Boriana

2017-05-01

Virtual virus is a semester-long interdisciplinary project offered as part of upper level elective course in virology. Students are challenged to apply key concepts from multiple biological sub-disciplines to 'synthesize' a plausible virtual virus. The project is executed as a scaffolded series of hands-on sessions and mini-projects that are integrated into continuous story leading to mock conference presentation and comprehensive report modeling article publication. It complements classroom instruction helping students to meet overarching learning targets traditionally associated undergraduate virology courses such as viral structure and function, mode of viral propagation and flow of genetic information and virus/host interactions on the cellular and organismal level. Formal instructor and informal peer feedback were used as tools to prompt reflection and guide revisions of the final report. Student learning gains and attitudes toward the approach were studied by evaluating project work product and end of the semester survey. Outcome analysis demonstrated that students exit the course with elaborated conceptual understanding of viruses and ownership of their work. The project can be viewed as an approach to model the process of scientific discovery in fast-forward mode by combining active learning, creativity and problem solving to assemble and communicate a virtual virus story. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Structural Transitions and Energy Landscape for Cowpea Chlorotic Mottle Virus Capsid Mechanics from Nanomanipulation in Vitro and in Silico

NASA Astrophysics Data System (ADS)

Kononova, Olga; Snijder, Joost; Brasch, Melanie; Cornelissen, Jeroen; Dima, Ruxandra I.; Marx, Kenneth A.; Wuite, Gijs J. L.; Roos, Wouter H.; Barsegov, Valeri

2013-10-01

Physical properties of capsids of plant and animal viruses are important factors in capsid self-assembly, survival of viruses in the extracellular environment, and their cell infectivity. Virus shells can have applications as nanocontainers and delivery vehicles in biotechnology and medicine. Combined AFM experiments and computational modeling on sub-second timescales of the indentation nanomechanics of Cowpea Chlorotic Mottle Virus (CCMV) capsid show that the capsid's physical properties are dynamic and local characteristics of the structure, which depend on the magnitude and geometry of mechanical input. Surprisingly, under large deformations the CCMV capsid transitions to the collapsed state without substantial local structural alterations. The enthalpy change in this deformation state dH = 11.5 - 12.8 MJ/mol is mostly due to large-amplitude out-of-plane excitations, which contribute to the capsid bending, and the entropy change TdS = 5.1 - 5.8 MJ/mol is mostly due to coherent in-plane rearrangements of protein chains, which result in the capsid stiffening. Dynamic coupling of these modes defines the extent of elasticity and reversibility of capsid mechanical deformation. This emerging picture illuminates how unique physico-chemical properties of protein nanoshells help define their structure and morphology, and determine their viruses' biological function.

Zika: what we do and do not know based on the experiences of Brazil

PubMed Central

2016-01-01

OBJECTIVES: Zika virus, which was first discovered in 1947, has become a global threat to human health as it is rapidly spreading through Latin America, the Caribbean, the US and Asia, after causing a large outbreak in the Northeast region of Brazil in 2015. There is ample evidence to support that Zika virus is associated with neurological complications such as microcephaly. The review aims to provide an overview on the complex issues involved in the emergence of Zika virus’s neurological disorders and to discuss possible explanations of Zika virus introduction and dissemination in Brazil. We also suggest national and global strategies to adequately respond to the Zika virus emergence. METHODS: We provide an analytical evaluation of the main issues related to the Zika outbreak in Brazil, based on available scientific literature, including government documents, and on epidemiological information from national surveillance databases. RESULTS: The studies on the clinical manifestations of the Zika virus infection coupled with the epidemiological surveillance information in Brazil have provided significant evidence that the Zika virus is associated with neurological disorders such as microcephaly and Guillain-Barré syndrome. Based on phylogenetic and molecular analysis, the hypothesis regarding the introduction of Zika virus in the country is that it took place following international events in 2013 and 2014, when many foreign visitors could have brought Zika virus into Brazil. The immunologically naïve status of populations in the Americas, previous infection with dengue virus, and the increased activity of Aedes aegypti might be the contributing factors for such an outbreak in Brazil. The Zika virus emergence emphasized the importance of cross-disciplinary perspective. Besides the scientific-based vector control strategies, it is important to understand the nature of the evolutionary processes involved in the viral evolution in complex ecosystems and to have social and anthropological knowledge on the conditions related to the spread of the disease in order to properly respond to the spread of the Zika virus. CONCLUSIONS: The experiences of Brazil have demonstrated the significance of multi-disciplinary approach in response to new and resurgent arboviral diseases and provided important lessons that could be applied to other developing countries. PMID:27283140

Optimizing Hybrid Spreading in Metapopulations

PubMed Central

Zhang, Changwang; Zhou, Shi; Miller, Joel C.; Cox, Ingemar J.; Chain, Benjamin M.

2015-01-01

Epidemic spreading phenomena are ubiquitous in nature and society. Examples include the spreading of diseases, information, and computer viruses. Epidemics can spread by local spreading, where infected nodes can only infect a limited set of direct target nodes and global spreading, where an infected node can infect every other node. In reality, many epidemics spread using a hybrid mixture of both types of spreading. In this study we develop a theoretical framework for studying hybrid epidemics, and examine the optimum balance between spreading mechanisms in terms of achieving the maximum outbreak size. We show the existence of critically hybrid epidemics where neither spreading mechanism alone can cause a noticeable spread but a combination of the two spreading mechanisms would produce an enormous outbreak. Our results provide new strategies for maximising beneficial epidemics and estimating the worst outcome of damaging hybrid epidemics. PMID:25923411

Optimizing hybrid spreading in metapopulations.

PubMed

Zhang, Changwang; Zhou, Shi; Miller, Joel C; Cox, Ingemar J; Chain, Benjamin M

2015-04-29

Epidemic spreading phenomena are ubiquitous in nature and society. Examples include the spreading of diseases, information, and computer viruses. Epidemics can spread by local spreading, where infected nodes can only infect a limited set of direct target nodes and global spreading, where an infected node can infect every other node. In reality, many epidemics spread using a hybrid mixture of both types of spreading. In this study we develop a theoretical framework for studying hybrid epidemics, and examine the optimum balance between spreading mechanisms in terms of achieving the maximum outbreak size. We show the existence of critically hybrid epidemics where neither spreading mechanism alone can cause a noticeable spread but a combination of the two spreading mechanisms would produce an enormous outbreak. Our results provide new strategies for maximising beneficial epidemics and estimating the worst outcome of damaging hybrid epidemics.

Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation

PubMed Central

Romero-Severson, Ethan O.; Bulla, Ingo; Hengartner, Nick; Bártolo, Inês; Abecasis, Ana; Azevedo-Pereira, José M.; Taveira, Nuno; Leitner, Thomas

2017-01-01

Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections, there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods, and the reconstruction of epidemiologic histories. To infer who-infected-whom, and to compute the probability of alternative transmission scenarios while explicitly taking phylogenetic uncertainty into account, we created an approximate Bayesian computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity. We applied our method to a suspected heterosexual transmission case involving three individuals, showing a complex monophyletic-paraphyletic-polyphyletic phylogenetic topology. We detected that seven phylogenetic lineages had been transmitted between two of the individuals based on the available samples, implying that many more unsampled lineages had also been transmitted. Testing whether the lineages had been transmitted at one time or over some length of time suggested that an ongoing superinfection process over several years was most likely. While one individual was found unlinked to the other two, surprisingly, when evaluating two competing epidemiological priors, the donor of the two that did infect each other was not identified by the host root-label, and was also not the primary suspect in that transmission. This highlights that it is important to take epidemiological information into account when analyzing support for one transmission hypothesis over another, as results may be nonintuitive and sensitive to details about sampling dates relative to possible infection dates. Our study provides a formal inference framework to include information on infection and sampling times, and to investigate ancestral node-label states, transmission direction, transmitted genetic diversity, and frequency of transmission. PMID:28912340

The 6th International Conference on Computer Science and Computational Mathematics (ICCSCM 2017)

NASA Astrophysics Data System (ADS)

2017-09-01

The ICCSCM 2017 (The 6th International Conference on Computer Science and Computational Mathematics) has aimed to provide a platform to discuss computer science and mathematics related issues including Algebraic Geometry, Algebraic Topology, Approximation Theory, Calculus of Variations, Category Theory; Homological Algebra, Coding Theory, Combinatorics, Control Theory, Cryptology, Geometry, Difference and Functional Equations, Discrete Mathematics, Dynamical Systems and Ergodic Theory, Field Theory and Polynomials, Fluid Mechanics and Solid Mechanics, Fourier Analysis, Functional Analysis, Functions of a Complex Variable, Fuzzy Mathematics, Game Theory, General Algebraic Systems, Graph Theory, Group Theory and Generalizations, Image Processing, Signal Processing and Tomography, Information Fusion, Integral Equations, Lattices, Algebraic Structures, Linear and Multilinear Algebra; Matrix Theory, Mathematical Biology and Other Natural Sciences, Mathematical Economics and Financial Mathematics, Mathematical Physics, Measure Theory and Integration, Neutrosophic Mathematics, Number Theory, Numerical Analysis, Operations Research, Optimization, Operator Theory, Ordinary and Partial Differential Equations, Potential Theory, Real Functions, Rings and Algebras, Statistical Mechanics, Structure Of Matter, Topological Groups, Wavelets and Wavelet Transforms, 3G/4G Network Evolutions, Ad-Hoc, Mobile, Wireless Networks and Mobile Computing, Agent Computing & Multi-Agents Systems, All topics related Image/Signal Processing, Any topics related Computer Networks, Any topics related ISO SC-27 and SC- 17 standards, Any topics related PKI(Public Key Intrastructures), Artifial Intelligences(A.I.) & Pattern/Image Recognitions, Authentication/Authorization Issues, Biometric authentication and algorithms, CDMA/GSM Communication Protocols, Combinatorics, Graph Theory, and Analysis of Algorithms, Cryptography and Foundation of Computer Security, Data Base(D.B.) Management & Information Retrievals, Data Mining, Web Image Mining, & Applications, Defining Spectrum Rights and Open Spectrum Solutions, E-Comerce, Ubiquitous, RFID, Applications, Fingerprint/Hand/Biometrics Recognitions and Technologies, Foundations of High-performance Computing, IC-card Security, OTP, and Key Management Issues, IDS/Firewall, Anti-Spam mail, Anti-virus issues, Mobile Computing for E-Commerce, Network Security Applications, Neural Networks and Biomedical Simulations, Quality of Services and Communication Protocols, Quantum Computing, Coding, and Error Controls, Satellite and Optical Communication Systems, Theory of Parallel Processing and Distributed Computing, Virtual Visions, 3-D Object Retrievals, & Virtual Simulations, Wireless Access Security, etc. The success of ICCSCM 2017 is reflected in the received papers from authors around the world from several countries which allows a highly multinational and multicultural idea and experience exchange. The accepted papers of ICCSCM 2017 are published in this Book. Please check http://www.iccscm.com for further news. A conference such as ICCSCM 2017 can only become successful using a team effort, so herewith we want to thank the International Technical Committee and the Reviewers for their efforts in the review process as well as their valuable advices. We are thankful to all those who contributed to the success of ICCSCM 2017. The Secretary

How much reduction of virus is needed for recycled water: A continuous changing need for assessment?

PubMed

Gerba, Charles P; Betancourt, Walter Q; Kitajima, Masaaki

2017-01-01

To ensure the safety of wastewater reuse for irrigation of food crops and drinking water pathogenic viruses must be reduced to levels that pose no significant risk. To achieve this goal minimum reduction of viruses by treatment trains have been suggested. For use of edible crops a 6-log reduction and for production of potable drinking water a 12-log reduction has been suggested. These reductions were based on assuming infective virus concentrations of 10 5 to 10 6 per liter. Recent application of molecular methods suggests that some pathogenic viruses may be occurring in concentrations of 10 7 to 10 9 per liter. Factors influencing these levels include the development of molecular methods for virus detection, emergence of newly recognized viruses, decrease in per capita water use due to conservation measures, and outbreaks. Since neither cell culture nor molecular methods can assess all the potentially infectious virus in wastewater conservative estimates should be used to assess the virus load in untreated wastewater. This review indicates that an additional 2- to 3-log reduction of viruses above current recommendations may be needed to ensure the safety of recycled water. Information is needed on peak loading of viruses. In addition, more virus groups need to be quantified using better methods of virus quantification, including more accurate methods for measuring viral infectivity in order to better quantify risks from viruses in recycled water. Copyright © 2016 Elsevier Ltd. All rights reserved.

Antibody responses of raccoons naturally exposed to influenza A virus.

PubMed

Root, J Jeffrey; Bentler, Kevin T; Sullivan, Heather J; Blitvich, Bradley J; McLean, Robert G; Franklin, Alan B

2010-10-01

An investigation was performed to describe the responses of naturally acquired antibodies to influenza A virus in raccoons (Procyon lotor) over time. Seven wild raccoons, some of which had been exposed to multiple subtypes of influenza A virus, were held in captivity for 279 days, and serum samples were collected on 10 occasions during this interval. Serum samples from 9 of 10 bleeding occasions were tested using an epitope-blocking enzyme-linked immunosorbent assay for the presence of antibodies to influenza A virus. Although titer declines were noted in most animals over time, all animals maintained detectable antibodies for the duration of the study. These data indicate that naturally acquired antibodies to influenza A virus can remain detectable in raccoons for many months, with the actual duration presumably being much longer because all animals had been exposed to influenza A virus before this study commenced. This information is important to surveillance programs because the duration of naturally acquired antibodies to influenza A virus in wildlife populations is largely unknown.

Novel flaviviruses from mosquitoes: Mosquito-specific evolutionary lineages within the phylogenetic group of mosquito-borne flaviviruses

PubMed Central

Huhtamo, Eili; Cook, Shelley; Moureau, Gregory; Uzcátegui, Nathalie Y.; Sironen, Tarja; Kuivanen, Suvi; Putkuri, Niina; Kurkela, Satu; Harbach, Ralph E.; Firth, Andrew E.; Vapalahti, Olli; Gould, Ernest A.; de Lamballerie, Xavier

2014-01-01

Novel flaviviruses that are genetically related to pathogenic mosquito-borne flaviviruses (MBFV) have been isolated from mosquitoes in various geographical locations, including Finland. We isolated and characterized another novel virus of this group from Finnish mosquitoes collected in 2007, designated as Ilomantsi virus (ILOV). Unlike the MBFV that infect both vertebrates and mosquitoes, the MBFV-related viruses appear to be specific to mosquitoes similar to the insect-specific flaviviruses (ISFs). In this overview of MBFV-related viruses we conclude that they differ from the ISFs genetically and antigenically. Phylogenetic analyses separated the MBFV-related viruses isolated in Africa, the Middle East and South America from those isolated in Europe and Asia. Serological cross-reactions of MBFV-related viruses with other flaviviruses and their potential for vector-borne transmission require further characterization. The divergent MBFV-related viruses are probably significantly under sampled to date and provide new information on the variety, properties and evolution of vector-borne flaviviruses. PMID:25108382

Structure and organization of paramyxovirus particles.

PubMed

Cox, Robert M; Plemper, Richard K

2017-06-01

The paramyxovirus family comprises major human and animal pathogens such as measles virus (MeV), mumps virus (MuV), the parainfluenzaviruses, Newcastle disease virus (NDV), and the highly pathogenic zoonotic hendra (HeV) and nipah (NiV) viruses. Paramyxovirus particles are pleomorphic, with a lipid envelope, nonsegmented RNA genomes of negative polarity, and densely packed glycoproteins on the virion surface. A number of crystal structures of different paramyxovirus proteins and protein fragments were solved, but the available information concerning overall virion organization remains limited. However, recent studies have reported cryo-electron tomography-based reconstructions of Sendai virus (SeV), MeV, NDV, and human parainfluenza virus type 3 (HPIV3) particles and a surface assessment of NiV-derived virus-like particles (VLPs), which have yielded innovative hypotheses concerning paramyxovirus particle assembly, budding, and organization. Following a summary of the current insight into paramyxovirus virion morphology, this review will focus on discussing the implications of these particle reconstructions on the present models of paramyxovirus assembly and infection. Copyright © 2017 Elsevier B.V. All rights reserved.

A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system.

PubMed

Oba, Mami; Tsuchiaka, Shinobu; Omatsu, Tsutomu; Katayama, Yukie; Otomaru, Konosuke; Hirata, Teppei; Aoki, Hiroshi; Murata, Yoshiteru; Makino, Shinji; Nagai, Makoto; Mizutani, Tetsuya

2018-01-08

We tested usefulness of a target enrichment system SureSelect, a comprehensive viral nucleic acid detection method, for rapid identification of viral pathogens in feces samples of cattle, pigs and goats. This system enriches nucleic acids of target viruses in clinical/field samples by using a library of biotinylated RNAs with sequences complementary to the target viruses. The enriched nucleic acids are amplified by PCR and subjected to next generation sequencing to identify the target viruses. In many samples, SureSelect target enrichment method increased efficiencies for detection of the viruses listed in the biotinylated RNA library. Furthermore, this method enabled us to determine nearly full-length genome sequence of porcine parainfluenza virus 1 and greatly increased Breadth, a value indicating the ratio of the mapping consensus length in the reference genome, in pig samples. Our data showed usefulness of SureSelect target enrichment system for comprehensive analysis of genomic information of various viruses in field samples. Copyright © 2017 Elsevier Inc. All rights reserved.

Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

PubMed Central

Rubio, Luis; Guerri, José; Moreno, Pedro

2013-01-01

RNA viruses have a great potential for genetic variation, rapid evolution and adaptation. Characterization of the genetic variation of viral populations provides relevant information on the processes involved in virus evolution and epidemiology and it is crucial for designing reliable diagnostic tools and developing efficient and durable disease control strategies. Here we performed an updated analysis of sequences available in Genbank and reviewed present knowledge on the genetic variability and evolutionary processes of viruses of the family Closteroviridae. Several factors have shaped the genetic structure and diversity of closteroviruses. (I) A strong negative selection seems to be responsible for the high genetic stability in space and time for some viruses. (2) Long distance migration, probably by human transport of infected propagative plant material, have caused that genetically similar virus isolates are found in distant geographical regions. (3) Recombination between divergent sequence variants have generated new genotypes and plays an important role for the evolution of some viruses of the family Closteroviridae. (4) Interaction between virus strains or between different viruses in mixed infections may alter accumulation of certain strains. (5) Host change or virus transmission by insect vectors induced changes in the viral population structure due to positive selection of sequence variants with higher fitness for host-virus or vector-virus interaction (adaptation) or by genetic drift due to random selection of sequence variants during the population bottleneck associated to the transmission process. PMID:23805130

Molecular characterization of a novel reassortant H1N2 influenza virus containing genes from the 2009 pandemic human H1N1 virus in swine from eastern China.

PubMed

Peng, Xiuming; Wu, Haibo; Xu, Lihua; Peng, Xiaorong; Cheng, Linfang; Jin, Changzhong; Xie, Tiansheng; Lu, Xiangyun; Wu, Nanping

2016-06-01

Pandemic outbreaks of H1N1 swine influenza virus have been reported since 2009. Reassortant H1N2 viruses that contain genes from the pandemic H1N1 virus have been isolated in Italy and the United States. However, there is limited information regarding the molecular characteristics of reassortant H1N2 swine influenza viruses in eastern China. Active influenza surveillance programs in Zhejiang Province identified a novel H1N2 influenza virus isolated from pigs displaying clinical signs of influenza virus infection. Whole-genome sequencing was performed and this strain was compared with other influenza viruses available in GenBank. Phylogenetic analysis suggested that the novel strain contained genes from the 2009 pandemic human H1N1 and swine H3N2 viruses. BALB/c mice were infected with the isolated virus to assess its virulence in mice. While the novel H1N2 isolate replicated well in mice, it was found to be less virulent. These results provide additional evidence that swine serve as intermediate hosts or 'mixing vessels' for novel influenza viruses. They also emphasize the importance of surveillance in the swine population for use as an early warning system for influenza outbreaks in swine and human populations.

Influenza virus vaccine for neglected hosts: horses and dogs

PubMed Central

2016-01-01

This study provides information regarding vaccine research and the epidemiology of influenza virus in neglected hosts (horses and dogs). Equine influenza virus (EIV) causes a highly contagious disease in horses and other equids, and outbreaks have occurred worldwide. EIV has resulted in costly damage to the horse industry and has the ability of cross the host species barrier from horses to dogs. Canine influenza is a virus of equine or avian origin and infects companion animals that live in close contact with humans; this results in possible exposure to the seasonal epizootic influenza virus. There have been case reports of genetic reassortment between human and canine influenza viruses, which results in high virulence and the ability of transmission to ferrets. This emphasizes the need for vaccine research on neglected hosts to update knowledge on current strains and to advance technology for controlling influenza outbreaks for public health. PMID:27489801

New Measles Genotype, Uganda

PubMed Central

Muwonge, Apollo; Nanyunja, Miriam; Bwogi, Josephine; Lowe, Luis; Liffick, Stephanie L.; Bellini, William J.; Sylvester, Sempala

2005-01-01

We report the first genetic characterization of wildtype measles viruses from Uganda. Thirty-six virus isolates from outbreaks in 6 districts were analyzed from 2000 to 2002. Analyses of sequences of the nucleoprotein (N) and hemagglutinin (H) genes showed that the Ugandan isolates were all closely related, and phylogenetic analysis indicated that these viruses were members of a unique group within clade D. Sequences of the Ugandan viruses were not closely related to any of the World Health Organization reference sequences representing the 22 currently recognized genotypes. The minimum nucleotide divergence between the Ugandan viruses and the most closely related reference strain, genotype D2, was 3.1% for the N gene and 2.6% for the H gene. Therefore, Ugandan viruses should be considered a new, proposed genotype (d10). This new sequence information will expand the utility of molecular epidemiologic techniques for describing measles transmission patterns in eastern Africa. PMID:16318690

Virus Infection and Death Receptor-Mediated Apoptosis.

PubMed

Zhou, Xingchen; Jiang, Wenbo; Liu, Zhongshun; Liu, Shuai; Liang, Xiaozhen

2017-10-27

Virus infection can trigger extrinsic apoptosis. Cell-surface death receptors of the tumor necrosis factor family mediate this process. They either assist persistent viral infection or elicit the elimination of infected cells by the host. Death receptor-mediated apoptosis plays an important role in viral pathogenesis and the host antiviral response. Many viruses have acquired the capability to subvert death receptor-mediated apoptosis and evade the host immune response, mainly by virally encoded gene products that suppress death receptor-mediated apoptosis. In this review, we summarize the current information on virus infection and death receptor-mediated apoptosis, particularly focusing on the viral proteins that modulate death receptor-mediated apoptosis.

Virus Infection and Death Receptor-Mediated Apoptosis

PubMed Central

Zhou, Xingchen; Jiang, Wenbo; Liu, Zhongshun; Liu, Shuai; Liang, Xiaozhen

2017-01-01

Virus infection can trigger extrinsic apoptosis. Cell-surface death receptors of the tumor necrosis factor family mediate this process. They either assist persistent viral infection or elicit the elimination of infected cells by the host. Death receptor-mediated apoptosis plays an important role in viral pathogenesis and the host antiviral response. Many viruses have acquired the capability to subvert death receptor-mediated apoptosis and evade the host immune response, mainly by virally encoded gene products that suppress death receptor-mediated apoptosis. In this review, we summarize the current information on virus infection and death receptor-mediated apoptosis, particularly focusing on the viral proteins that modulate death receptor-mediated apoptosis. PMID:29077026

Transcriptional profiling of the host cell response to feline immunodeficiency virus infection.

PubMed

Ertl, Reinhard; Klein, Dieter

2014-03-19

Feline immunodeficiency virus (FIV) is a widespread pathogen of the domestic cat and an important animal model for human immunodeficiency virus (HIV) research. In contrast to HIV, only limited information is available on the transcriptional host cell response to FIV infections. This study aims to identify FIV-induced gene expression changes in feline T-cells during the early phase of the infection. Illumina RNA-sequencing (RNA-seq) was used identify differentially expressed genes (DEGs) at 24 h after FIV infection. After removal of low-quality reads, the remaining sequencing data were mapped against the cat genome and the numbers of mapping reads were counted for each gene. Regulated genes were identified through the comparison of FIV and mock-infected data sets. After statistical analysis and the removal of genes with insufficient coverage, we detected a total of 69 significantly DEGs (44 up- and 25 down-regulated genes) upon FIV infection. The results obtained by RNA-seq were validated by reverse transcription qPCR analysis for 10 genes. Out of the most distinct DEGs identified in this study, several genes are already known to interact with HIV in humans, indicating comparable effects of both viruses on the host cell gene expression and furthermore, highlighting the importance of FIV as a model system for HIV. In addition, a set of new genes not previously linked to virus infections could be identified. The provided list of virus-induced genes may represent useful information for future studies focusing on the molecular mechanisms of virus-host interactions in FIV pathogenesis.

Interplays between Soil-Borne Plant Viruses and RNA Silencing-Mediated Antiviral Defense in Roots

PubMed Central

Andika, Ida Bagus; Kondo, Hideki; Sun, Liying

2016-01-01

Although the majority of plant viruses are transmitted by arthropod vectors and invade the host plants through the aerial parts, there is a considerable number of plant viruses that infect roots via soil-inhabiting vectors such as plasmodiophorids, chytrids, and nematodes. These soil-borne viruses belong to diverse families, and many of them cause serious diseases in major crop plants. Thus, roots are important organs for the life cycle of many viruses. Compared to shoots, roots have a distinct metabolism and particular physiological characteristics due to the differences in development, cell composition, gene expression patterns, and surrounding environmental conditions. RNA silencing is an important innate defense mechanism to combat virus infection in plants, but the specific information on the activities and molecular mechanism of RNA silencing-mediated viral defense in root tissue is still limited. In this review, we summarize and discuss the current knowledge regarding RNA silencing aspects of the interactions between soil-borne viruses and host plants. Overall, research evidence suggests that soil-borne viruses have evolved to adapt to the distinct mechanism of antiviral RNA silencing in roots. PMID:27695446

Diversity of Papaya ringspot virus isolates in Puerto Rico

USDA-ARS?s Scientific Manuscript database

Papaya ringspot virus (PRSV) devastates papaya production worldwide. In Puerto Rico, papaya fields can be completely infected with PRSV within a year of planting. Information about the diversity of the Puerto Rican PRSV population is relevant in order to establish a control strategy in the island. T...

76 FR 41803 - Guidance for Industry and Food and Drug Administration Staff; Establishing the Performance...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-15

... of In Vitro Diagnostic Devices for the Detection or Detection and Differentiation of Influenza... of Influenza Viruses.'' FDA is issuing this guidance to inform industry and Agency staff of its... diagnostic devices intended for the detection or detection and differentiation of influenza viruses. DATES...

EXPRESSION AND SELF-ASSEMBLY OF NORWALK VIRUS CAPSID PROTEIN FROM VENEZUELAN EQUINE ENCEPHALITIS VIRUS REPLICONS. (R826139)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Development and Evaluation of EPA Method 1615 for Detection of Enterovirus and Norovirus in Water

EPA Science Inventory

The U.S. EPA developed a sample concentration and preparation assay in conjunction with the Total Culturable Virus Assay for concentrating and measuring culturable viruses in source and drinking waters as part of the Information Collection Rule promulgated in 1996. In an effort...

Viruses 2018 - Breakthroughs in Viral Replication - Barcelona, Spain | Center for Cancer Research

Cancer.gov

This Conference is held in Barcelona, Spain on February 7 - 9, 2018. For registration information please go to the conference website at https://sciforum.net/conference/Viruses-2018 Dates to remember: Abstract Submission: 31 Oct. 2017 Acceptance Notification: 25 Nov. 2017 Full Paper Submission: 1 Aug. 2018