A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes

In recent years, an increasing number of outbreaks of Dengue, Chikungunya and Zika viruses have been reported in Asia and the Americas. Monitoring virus genotype diversity is crucial to understand the emergence and spread of outbreaks, both aspects that are vital to develop effective prevention and...

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Vydáno v:	PLoS neglected tropical diseases Ročník 13; číslo 5; s. e0007231
Hlavní autoři:	Fonseca, Vagner, Libin, Pieter J. K., Theys, Kristof, Faria, Nuno R., Nunes, Marcio R. T., Restovic, Maria I., Freire, Murilo, Giovanetti, Marta, Cuypers, Lize, Nowé, Ann, Abecasis, Ana, Deforche, Koen, Santiago, Gilberto A., Siqueira, Isadora C. de, San, Emmanuel J., Machado, Kaliane C. B., Azevedo, Vasco, Filippis, Ana Maria Bispo-de, Cunha, Rivaldo Venâncio da, Pybus, Oliver G., Vandamme, Anne-Mieke, Alcantara, Luiz C. J., de Oliveira, Tulio
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	United States Public Library of Science 01.05.2019 Public Library of Science (PLoS)
Témata:	Animal behavior Artificial intelligence Automation Bioinformatics Biology and life sciences Chikungunya fever Chikungunya Fever - virology Chikungunya virus Chikungunya virus - classification Chikungunya virus - genetics Chikungunya virus - isolation & purification Computational Biology - methods Computer and Information Sciences Computer applications Computer science Computer simulation Computers Dengue Dengue - virology Dengue fever Dengue Virus - classification Dengue Virus - genetics Dengue Virus - isolation & purification DNA sequencing Gene sequencing Genetic aspects Genome, Viral Genomes Genomics Genotype Genotypes Health sciences Human diseases Immunology Infectious diseases Medical research Medicine and Health Sciences Outbreaks Phylogenetics Phylogeny Prevention Research and Analysis Methods Risk factors Software Species Species classification Tropical diseases Vector-borne diseases Viral diseases Virology Viruses Zika virus Zika Virus - classification Zika Virus - genetics Zika Virus - isolation & purification Zika Virus Infection - virology Zoology Asia America Rio de Janeiro Brazil United Kingdom > UK Belgium England Brazil South Africa Portugal
ISSN:	1935-2735, 1935-2727, 1935-2735
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Popis
Shrnutí:	In recent years, an increasing number of outbreaks of Dengue, Chikungunya and Zika viruses have been reported in Asia and the Americas. Monitoring virus genotype diversity is crucial to understand the emergence and spread of outbreaks, both aspects that are vital to develop effective prevention and treatment strategies. Hence, we developed an efficient method to classify virus sequences with respect to their species and sub-species (i.e. serotype and/or genotype). This tool provides an easy-to-use software implementation of this new method and was validated on a large dataset assessing the classification performance with respect to whole-genome sequences and partial-genome sequences. Available online: http://krisp.org.za/tools.php.
Bibliografie:	new_version ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Article-2 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23 Dr. Koen Deforche is one of the owners of the commercial company, EMWEB.
ISSN:	1935-2735 1935-2727 1935-2735
DOI:	10.1371/journal.pntd.0007231