Vagner Fonseca, Pieter J K Libin, Kristof Theys, Nuno R Faria, Marcio R T Nunes, Maria I Restovic, Murilo Freire, Marta Giovanetti, Lize Cuypers, Ann Nowé, Ana Abecasis, Koen Deforche, Gilberto A Santiago, Isadora C de Siqueira, Emmanuel J San, Kaliane C B Machado, Vasco Azevedo, Ana Maria Bispo-de Filippis, Rivaldo Venâncio da Cunha, Oliver G Pybus, Anne-Mieke Vandamme, Luiz C J Alcantara, Tulio de Oliveira
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.
Fonseca, V, Libin, PJK, Theys, K, Faria, NR, Nunes, MRT, Restovic, MI, Freire, M, Giovanetti, M, Cuypers, L, Nowé, A, Abecasis, A, Deforche, K, Santiago, GA, Siqueira, ICD, San, EJ, Machado, KCB, Azevedo, V, Filippis, AMB, Cunha, RVD, Pybus, OG, Vandamme, A-M, Alcantara, LCJ & 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, no. 5, e0007231. https://doi.org/10.1371/journal.pntd.0007231
Fonseca, V., Libin, P. J. K., Theys, K., Faria, N. R., Nunes, M. R. T., Restovic, M. I., Freire, M., Giovanetti, M., Cuypers, L., Nowé, A., Abecasis, A., Deforche, K., Santiago, G. A., Siqueira, I. C. D., San, E. J., Machado, K. C. B., Azevedo, V., Filippis, A. M. B., Cunha, R. V. D., ... de Oliveira, T. (2019). A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. PLoS Neglected Tropical Diseases, 13(5), Article e0007231. https://doi.org/10.1371/journal.pntd.0007231
@article{871ae183f2f54f63a2eadc7bbc9f9ebb,
title = "A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes",
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. Available online: http://krisp.org.za/tools.php.",
author = "Vagner Fonseca and Libin, {Pieter J K} and Kristof Theys and Faria, {Nuno R} and Nunes, {Marcio R T} and Restovic, {Maria I} and Murilo Freire and Marta Giovanetti and Lize Cuypers and Ann Now{\'e} and Ana Abecasis and Koen Deforche and Santiago, {Gilberto A} and Siqueira, {Isadora C de} and San, {Emmanuel J} and Machado, {Kaliane C B} and Vasco Azevedo and Filippis, {Ana Maria Bispo-de} and Cunha, {Rivaldo Ven{\^a}ncio da} and Pybus, {Oliver G} and Anne-Mieke Vandamme and Alcantara, {Luiz C J} and {de Oliveira}, Tulio",
year = "2019",
doi = "10.1371/journal.pntd.0007231",
language = "English",
volume = "13",
journal = "PLoS Neglected Tropical Diseases",
issn = "1935-2727",
publisher = "Public Library of Science",
number = "5",
}