A computational method for the identification of dengue, zika and chikungunya virus species and genotypes

Fonseca, Vagner S., Libin, Pieter J.K., Kristof Theys, Nuno Rodrigues Faria, Nunes, Márcio Roberto Texeira, Restovic, Maria I., Freire, Murilo, Giovanetti, Marta, Lize Cuypers, Ann Nowé, AB Abecasis, Koen Deforche, Santiago, Gilberto A., de Siqueira, Isadora Cristina, Machado, Kaliane C.B., San, Emmanuel J., Machado, Kaliane C.B., Azevedo, Vasco Ariston De Carvalho, de Filippis, Ana Maria Bispo, da Cunha, Rivaldo VenâncioPybus, Oliver George, AM Vandamme, Júnior Alcântara, Luiz Carlos, Túlio de Oliveira

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Abstract

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.
Original languageEnglish
Article numbere0007231
Pages (from-to)e0007231-e0007246
Number of pages15
JournalPLoS Neglected Tropical Diseases
VolumeVol. 13
Issue numbern.º 5
DOIs
Publication statusPublished - 8 May 2019

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Vagner S., F., Pieter J.K., L., Theys, K., Faria, N. R., Márcio Roberto Texeira, N., Maria I., R., ... de Oliveira, T. (2019). A computational method for the identification of dengue, zika and chikungunya virus species and genotypes. PLoS Neglected Tropical Diseases, Vol. 13(n.º 5), e0007231-e0007246. [e0007231]. https://doi.org/10.1371/journal.pntd.0007231