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A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.
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.
Affiliation
  • Fonseca V; Laboratório de Flavivírus, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
  • Libin PJK; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZuluNatal, Durban, South Africa.
  • Theys K; Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
  • Faria NR; Artificial Intelligence Lab, Department of Computer Science, Vrije Universiteit Brussel, Brussels, Belgium.
  • Nunes MRT; KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.
  • Restovic MI; KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.
  • Freire M; Department of Zoology, University of Oxford, Oxford, United Kingdom.
  • Giovanetti M; Evandro Chagas Institute, Ministry of Health, Ananindeua, Brazil.
  • Cuypers L; Laboratório de Patologia Experimental, Fundação Oswaldo Cruz, Salvador, Brazil.
  • Nowé A; Laboratório de Patologia Experimental, Fundação Oswaldo Cruz, Salvador, Brazil.
  • Abecasis A; Laboratório de Flavivírus, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
  • Deforche K; KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.
  • Santiago GA; Artificial Intelligence Lab, Department of Computer Science, Vrije Universiteit Brussel, Brussels, Belgium.
  • Siqueira IC; Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.
  • San EJ; EMWEB (private company), Herent, Belgium.
  • Machado KCB; Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico, United states of America.
  • Azevedo V; Laboratório de Patologia Experimental, Fundação Oswaldo Cruz, Salvador, Brazil.
  • Filippis AMB; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZuluNatal, Durban, South Africa.
  • Cunha RVD; Laboratório de Patologia Experimental, Fundação Oswaldo Cruz, Salvador, Brazil.
  • Pybus OG; Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
  • Vandamme AM; Laboratório de Flavivírus, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
  • Alcantara LCJ; Coordenação de Vigilância em Saúde e Laboratórios de Referências, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
  • de Oliveira T; Department of Zoology, University of Oxford, Oxford, United Kingdom.
PLoS Negl Trop Dis ; 13(5): e0007231, 2019 05.
Article in En | MEDLINE | ID: mdl-31067235
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Chikungunya virus / Computational Biology / Dengue Virus / Zika Virus Type of study: Diagnostic_studies / Evaluation_studies Language: En Journal: PLoS Negl Trop Dis Journal subject: MEDICINA TROPICAL Year: 2019 Type: Article Affiliation country: Brazil
Fulltext
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PubMed Links
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Chikungunya virus / Computational Biology / Dengue Virus / Zika Virus Type of study: Diagnostic_studies / Evaluation_studies Language: En Journal: PLoS Negl Trop Dis Journal subject: MEDICINA TROPICAL Year: 2019 Type: Article Affiliation country: Brazil