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A COMPUTATIONAL METHOD FOR THE IDENTIFICATION OF DENGUE, ZIKA AND CHIKUNGUNYA VIRUS SPECIES AND GENOTYPES
Fonseca, Vagner et al. | Date Issued: 2019
Author
Fonseca, Vagner
Libin, Pieter J. K.
Theys, Kristof
Faria, Nuno Rodrigues
Nunes, Marcio Roberto Teixeira
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 Caldas de Brito
Azevedo, Vasco
Filippis, Ana Maria Bispo de
Cunha, Rivaldo Venâncio da
Pybus, Oliver G.
Vandamme, Anne-Mieke
Alcantara, Luiz Carlos Junior
Oliveira, Tulio de
Affilliation
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil / University of KwaZuluNatal. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.
Vrije Universiteit Brussel. Artificial Intelligence Lab. Department of Computer Science. Brussels, Belgium / KU Leuven-University of Leuven. Rega Institute for Medical Research, Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, Belgium.
KU Leuven-University of Leuven. Rega Institute for Medical Research, Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, Belgium.
University of Oxford. Department of Zoology. Oxford, United Kingdom.
Ministry of Health. Evandro Chagas Institute. Ananindeua, Brazil.
Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Patologia Experimental. Salvador, BA, Brasil.
Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Patologia Experimental. Salvador, BA, Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil.
KU Leuven-University of Leuven. Rega Institute for Medical Research, Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, Belgium.
Vrije Universiteit Brussel. Artificial Intelligence Lab. Department of Computer Science. Brussels, Belgium.
Universidade Nova de Lisboa. Instituto de Higiene e Medicina Tropical. Center for Global Health and Tropical Medicine. Unidade de Microbiologia. Lisbon, Portugal.
EMWEB. Private Company. Herent, Belgium.
Centers for Disease Control and Prevention. Division of Vector-Borne Diseases. San Juan, Puerto Rico, United states of America.
Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Patologia Experimental. Salvador, BA, Brasil.
University of KwaZuluNatal. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa.
Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Patologia Experimental. Salvador, BA, Brasil.
Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil / University of KwaZuluNatal. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.
Fundação Oswaldo Cruz. Coordenação de Vigilância em Saúde e Laboratórios de Referências. Rio de Janeiro, RJ, Brasil.
University of Oxford. Department of Zoology. Oxford, United Kingdom.
KU Leuven-University of Leuven. Rega Institute for Medical Research, Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, Belgium / Universidade Nova de Lisboa. Instituto de Higiene e Medicina Tropical. Center for Global Health and Tropical Medicine. Unidade de Microbiologia. Lisbon, Portugal.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.
University of KwaZuluNatal. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa.
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.
Keywords in Portuguese
Vírus da dengue
Zika virus
Chikungunya
Genótipos
Software
Prevenção
Tratamento
 
Keywords
Dengue virus
Zika virus
Chikungunya
Genotype
Software
Prevention
Treatment
 
Publisher
Public Library of Science
Citation
FONSECA, Vagner et al. A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. PLoS Neglected Tropical Diseases, v. 13, n. 5, p. 1-15, 2019.
DOI
10.1371/journal.pntd.0007231
ISSN
1935-2727