ATIVS: analytical tool for influenza virus surveillance

Liao, Yu-Chieh; Ko, Chin-Yu; Tsai, Ming-Hsin; Lee, Min-Shi; Hsiung, Chao A.

doi:10.1093/nar/gkp321

Cited by 16 publications

(19 citation statements)

References 6 publications

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“…Large tabular serological data are hard to summarize and are recently analyzed using antigenic cartography (i.e., antigenic map) [11], [21], [22]. Briefly, antigenic cartography is a way to visualize and increase the resolution of serological data, such as neutralization data.…”

Section: Methodsmentioning

confidence: 99%

“…The result is a map in which the distance between points represents antigenic distance as measured by the binding assay [11]. In this study, an antigenic map was generated using a web-based analytic tool [22].…”

Section: Methodsmentioning

confidence: 99%

“…The GMTs of cross-reactive neutralizing antibody titers were further used to generate an antigenic map using a web-based analytical tool [22]. The relative positions of strains and antisera were adjusted such that the distances between strains and antisera in the map represent the corresponding ratios between homologous and heterologous neutralizing antibody titers.…”

Section: Methodsmentioning

confidence: 99%

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Cross-reactive Neutralizing Antibody Responses to Enterovirus 71 Infections in Young Children: Implications for Vaccine Development

et al. 2013

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BackgroundRecently, enterovirus 71 (EV71) has caused life-threatening outbreaks involving neurological and cardiopulmonary complications in Asian children with unknown mechanism. EV71 has one single serotype but can be phylogenetically classified into 3 main genogroups (A, B and C) and 11 genotypes (A, B1∼B5 and C1∼C5). In Taiwan, nationwide EV71 epidemics with different predominant genotypes occurred in 1998 (C2), 2000–2001 (B4), 2004–2005 (C4), and 2008 (B5). In this study, sera were collected to measure cross-reactive neutralizing antibody titers against different genotypes.MethodsWe collected historical sera from children who developed an EV71 infection in 1998, 2000, 2005, 2008, or 2010 and measured cross-reactive neutralizing antibody titers against all 11 EV71 genotypes. In addition, we aligned and compared the amino acid sequences of P1 proteins of the tested viruses.ResultsSerology data showed that children infected with genogroups B and C consistently have lower neutralizing antibody titers against genogroup A (>4-fold difference). The sequence comparisons revealed that five amino acid signatures (N143D in VP2; K18R, H116Y, D167E, and S275A in VP1) are specific for genogroup A and may be related to the observed antigenic variations.ConclusionsThis study documented antigenic variations among different EV71 genogroups and identified potential immunodominant amino acid positions. Enterovirus surveillance and vaccine development should monitor these positions.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Cross-reactive Neutralizing Antibody Responses to Enterovirus 71 Infections in Young Children: Implications for Vaccine Development

et al. 2013

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“…In order to understand and monitor the evolution and migration of strains, an Influenza Sequence and Epitope Database (ISED) was established that catalogs sequence and epitope information of viruses from Asian countries (10). Another useful Web server is ATIVS (Analytical Tool for Influenza Virus Surveillance), which analyzes serological data of all influenza subtypes and hemagglutinin sequence data of influenza A/H3N2 viruses so as to generate antigenic maps for influenza surveillance and vaccine strain selection (11). Recently, OpenFluDB (an isolate-centered inventory) was developed; it contains general information about an isolate, including virus type, host, and collection date and geographical location as well as computationally predicted antiviral resistance, enhanced pathogenicity, or human adaptation propensity (12).…”

Section: Virus-centered Resources and The Virus Pathogen Database Andmentioning

confidence: 99%

Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research

Sharma

Priyadarshini

Vrati

2015

J Virol

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The beginning of the second century of research in the field of virology (the first virus was discovered in 1898) was marked by its amalgamation with bioinformatics, resulting in the birth of a new domain-viroinformatics. The availability of more than 100 Web servers and databases embracing all or specific viruses ( Viruses, known to have infected humankind since approximately the 15th century BC, are found in all cellular forms of life, from bacteria to chordates. Pathogenic human viruses are causative agents of many morbid diseases such as influenza, AIDS, dengue fever, encephalitis, hepatitis, diarrhea, and severe acute respiratory syndrome (SARS). However, despite the availability of effective vaccines and treatments for several diseases, ϳ6 million deaths occur every year due to viruses. Thus, it is imperative to develop remedies against these viral invaders. Advances in molecular biology and bioinformatics have resulted in a deluge of genomic and experimental data. To store, examine, and disseminate all this information, 112 viroinformatics resources have been developed (as of May 2014; Table 1). The International Committee on Taxonomy of Viruses (ICTV) that performs the task of naming and classifying viruses lists 2,618 species. Strikingly, the genomes of ϳ40,000 viral strains, across more than 900 species, have been sequenced (NCBI Viral Genome Resource, NCBI Influenza Virus Resource [NCBI-IVR], and http://www .viprbrc.org/).The aims of this article are manyfold. The first aim is to provide an extensive list of viroinformatics resources. At present, the information about these resources is so disparate that it is almost impossible to be aware of all the tools (many of which have been developed recently). The second aim is to categorize the resources based on their specificity for a particular virus, application, or task. The third aim is to compare tools performing similar tasks on the basis of (i) importance, popularity, and reliability (reflected by the citation index of a tool), (ii) the number of genomes and sequences included, (iii) the unique features of a given resource, and (iv) ease of use (whether a Web interface is available). If available, references to publications comparing similar tools have also been provided. The fourth aim is to provide information about tools that have been succeeded by a newer resource, have not been updated for more than past 2 years, or are currently inaccessible. The fifth (and most important) aim is to enable virologists to get an overview of tools capable of carrying out a desired task and select the most suitable one(s). For compiling the comprehensive index of resources presented here, an initial list was first prepared by extensively searching the literature (PubMed [http://www.ncbi.nlm.nih.gov/pubmed] and ScienceDirect [http://www.sciencedirect.com]) using all possible combinations of various keywords. Subsequently, all the publications describing these tools were thoroughly explored to find other resources mentioned in them. This greatly expanded the initia...

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“…Analysis Tool for Influenza Virus Surveillance (ATIVS) from Division of Biostatistics and Bioinformatics, National Health Research Institutes, Zhunan, Taiwan available at web-address http://influenza.nhri.org. tw/ATIVS/index.jsp [8]. The bar chart was also generated by the same software which determined the range of antigenic coverage.…”

Section: Cross Hi Titration and Antigenic Cartographymentioning

confidence: 99%

Genetic and antigenic analysis of H5N1 viruses for selection of HA-donor virus for vaccine strains

et al. 2013

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ATIVS: analytical tool for influenza virus surveillance

Cited by 16 publications

References 6 publications

Cross-reactive Neutralizing Antibody Responses to Enterovirus 71 Infections in Young Children: Implications for Vaccine Development

Cross-reactive Neutralizing Antibody Responses to Enterovirus 71 Infections in Young Children: Implications for Vaccine Development

Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research

Genetic and antigenic analysis of H5N1 viruses for selection of HA-donor virus for vaccine strains

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