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 Venâncio & 4 others Pybus, Oliver George, AM Vandamme, Júnior Alcântara, Luiz Carlos, Túlio de Oliveira

Research output: Contribution to journalArticle

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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Chikungunya virus
Dengue Virus
Disease Outbreaks
Genotype
Genome
Viruses
Software
Zika Virus

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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
Vagner S., Fonseca, ; Pieter J.K., Libin, ; Theys, Kristof ; Faria, Nuno Rodrigues ; Márcio Roberto Texeira, Nunes, ; Maria I., Restovic, ; Murilo, Freire, ; Marta, Giovanetti, ; Cuypers, Lize ; Nowé, Ann ; Abecasis, AB ; Deforche, Koen ; Gilberto A., Santiago, ; Isadora Cristina, de Siqueira, ; Kaliane C.B., Machado, ; Emmanuel J., San, ; Kaliane C.B., Machado, ; Vasco Ariston De Carvalho, Azevedo, ; Ana Maria Bispo, de Filippis, ; Rivaldo Venâncio, da Cunha, ; Oliver George, Pybus, ; Vandamme, AM ; Luiz Carlos, Júnior Alcântara, ; de Oliveira, Túlio. / A computational method for the identification of dengue, zika and chikungunya virus species and genotypes. In: PLoS Neglected Tropical Diseases. 2019 ; Vol. Vol. 13, No. n.º 5. pp. e0007231-e0007246.
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Vagner S., F, Pieter J.K., L, Theys, K, Faria, NR, Márcio Roberto Texeira, N, Maria I., R, Murilo, F, Marta, G, Cuypers, L, Nowé, A, Abecasis, AB, Deforche, K, Gilberto A., S, Isadora Cristina, DS, Kaliane C.B., M, Emmanuel J., S, Kaliane C.B., M, Vasco Ariston De Carvalho, A, Ana Maria Bispo, DF, Rivaldo Venâncio, DC, Oliver George, P, Vandamme, AM, Luiz Carlos, JA & de Oliveira, T 2019, 'A computational method for the identification of dengue, zika and chikungunya virus species and genotypes' PLoS Neglected Tropical Diseases, vol. Vol. 13, no. n.º 5, e0007231, pp. e0007231-e0007246. https://doi.org/10.1371/journal.pntd.0007231

A computational method for the identification of dengue, zika and chikungunya virus species and genotypes. / Vagner S., Fonseca, ; Pieter J.K., Libin, ; Theys, Kristof; Faria, Nuno Rodrigues; Márcio Roberto Texeira, Nunes, ; Maria I., Restovic, ; Murilo, Freire, ; Marta, Giovanetti, ; Cuypers, Lize; Nowé, Ann; Abecasis, AB; Deforche, Koen; Gilberto A., Santiago, ; Isadora Cristina, de Siqueira, ; Kaliane C.B., Machado, ; Emmanuel J., San, ; Kaliane C.B., Machado, ; Vasco Ariston De Carvalho, Azevedo, ; Ana Maria Bispo, de Filippis, ; Rivaldo Venâncio, da Cunha, ; Oliver George, Pybus, ; Vandamme, AM; Luiz Carlos, Júnior Alcântara,; de Oliveira, Túlio.

In: PLoS Neglected Tropical Diseases, Vol. Vol. 13, No. n.º 5, e0007231, 08.05.2019, p. e0007231-e0007246.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A computational method for the identification of dengue, zika and chikungunya virus species and genotypes

AU - Vagner S., Fonseca,

AU - Pieter J.K., Libin,

AU - Theys, Kristof

AU - Faria, Nuno Rodrigues

AU - Márcio Roberto Texeira, Nunes,

AU - Maria I., Restovic,

AU - Murilo, Freire,

AU - Marta, Giovanetti,

AU - Cuypers, Lize

AU - Nowé, Ann

AU - Abecasis, AB

AU - Deforche, Koen

AU - Gilberto A., Santiago,

AU - Isadora Cristina, de Siqueira,

AU - Kaliane C.B., Machado,

AU - Emmanuel J., San,

AU - Kaliane C.B., Machado,

AU - Vasco Ariston De Carvalho, Azevedo,

AU - Ana Maria Bispo, de Filippis,

AU - Rivaldo Venâncio, da Cunha,

AU - Oliver George, Pybus,

AU - Vandamme, AM

AU - Luiz Carlos, Júnior Alcântara,

AU - de Oliveira, Túlio

PY - 2019/5/8

Y1 - 2019/5/8

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U2 - 10.1371/journal.pntd.0007231

DO - 10.1371/journal.pntd.0007231

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JO - PLoS Neglected Tropical Diseases

JF - PLoS Neglected Tropical Diseases

SN - 1935-2727

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ER -

Vagner S. F, Pieter J.K. L, Theys K, Faria NR, Márcio Roberto Texeira N, Maria I. R et al. A computational method for the identification of dengue, zika and chikungunya virus species and genotypes. PLoS Neglected Tropical Diseases. 2019 May 8;Vol. 13(n.º 5):e0007231-e0007246. e0007231. https://doi.org/10.1371/journal.pntd.0007231