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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Bibliographic Details
Published in:PLoS neglected tropical diseases Vol. 13; no. 5; p. e0007231
Main Authors: 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
Format: Journal Article
Language:English
Published: United States Public Library of Science 01.05.2019
Public Library of Science (PLoS)
Subjects:
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
Online Access:Get full text
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Description
Summary: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.
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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