A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2019 |
| Outros Autores: | , , , , , , , , , , , , , , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Digital do Instituto Evandro Chagas (Patuá) |
| DOI: | 10.1371/journal.pntd.0007231 |
| Texto Completo: | https://patua.iec.gov.br/handle/iec/3750 |
Resumo: | 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. |
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Fonseca, VagnerLibin, Pieter J. KTheys, KristofFaria, Nuno RodriguesNunes, Márcio Roberto TeixeiraRestovic, Maria IFreire, MuriloGiovanetti, MartaCuypers, LizeNowé, AnnAbecasis, Ana BarrosoDeforche, KoenSantiago, Gilberto ASiqueira, Isadora C. deSan, Emmanuel JMachado, Kaliane C. BAzevedo, VascoFilippis, Ana Maria Bispo deCunha, Rivaldo Venâncio daPybus, Oliver GVandamme, Anne-MiekeAlcantara, Luiz Carlos JúniorOliveira, Tulio de2019-06-17T13:48:20Z2019-06-17T13:48:20Z2019FONSECA, 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, e0007231, p. 1-15, May 2019. DOI: https://doi.org/0.1371/journal.pntd.0007231. Disponível em: https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0007231&type=printable.1935-2735https://patua.iec.gov.br/handle/iec/37500.1371/journal.pntd.0007231In 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.Supported by a research Flagship grant from the South African Medical Re-search Council (MRC-RFA-UFSP-01-2013/UKZN HIVEPI), a Royal Society Newton Advanced Fellowship (TdO), the VIROGENESIS project receives funding from the European Union’s Horizon 2020 Research and Innovation Programme (under Grant Agreement no. 634650) and the National Institutes of Health Common Fund, grant number U24HG006941. Pieter Libin was supported by a PhD grant of the FWO (Fonds Wetenschappelijk Onderzoek - Vlaanderen). This work was supported by Decit/ SCTIE/MoH and CNPq (440685/2016-8 and 440856/2016-7); by CAPES (88887.130716/2016- 00, 88881.130825/2016-00 and 88887.130823/ 2016-00); and by EU’s Horizon 2020 Programme through ZIKAlliance (PRES-005-FEX-17-4-2-33). Ana Abecasis was supported by Fundac¸a˜o para a Cieˆncia e Tecnologia (FCT) through funds to GHTM-UID/Multi/04413/2013.Fundação Oswaldo Cruz. Instituo Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brazil / University of KwaZulu-Natal. 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, Brazil.Vrije Universiteit Brussel. Department of Computer Science. Artificial Intelligence Lab. Brussels, Belgium / KU Leuven—University of Leuven. Department of Microbiology and Immunology. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Leuven, Belgium.KU Leuven—University of Leuven. Department of Microbiology and Immunology. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Leuven, Belgium.University of Oxford. Department of Zoology. Oxford, United Kingdom.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovações tecnológicas. Ananindeua, PA, Brasil.Fundação Oswaldo Cruz. Laboratório de Patologia Experimental. Salvador, BA, Brazil.Fundação Oswaldo Cruz. Laboratório de Patologia Experimental. Salvador, BA, Brazil.Fundação Oswaldo Cruz. Instituo Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brazil.KU Leuven—University of Leuven. Department of Microbiology and Immunology. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Leuven, Belgium.Vrije Universiteit Brussel. Department of Computer Science. Artificial Intelligence Lab. Brussels, BelgiumUniversidade 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. Laboratório de Patologia Experimental. Salvador, BA, Brazil.University of KwaZulu-Natal. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa.Fundação Oswaldo Cruz. Laboratório de Patologia Experimental. Salvador, BA, Brazil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituo Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Coordenação de Vigilância em Saúde e Laboratórios de Referências. Rio de Janeiro, RJ, Brazil.University of Oxford. Department of Zoology. Oxford, United Kingdom.KU Leuven—University of Leuven. Department of Microbiology and Immunology. Rega Institute for Medical Research. Clinical and Epidemiological Virology. 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. Instituo Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brazil / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brazil.University of KwaZuluNatal. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. 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| dc.title.pt_BR.fl_str_mv |
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes |
| title |
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes |
| spellingShingle |
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes Fonseca, Vagner Arbovirus / classificação Dengue Vírus Chikungunya Zika virus Biologia Computacional / métodos Bases de Dados de Ácidos Nucleicos / utilização Genótipo Técnicas de Genotipagem / métodos Surtos de Doenças Monitoramento Epidemiológico Variação Genética Fonseca, Vagner Arbovirus / classificação Dengue Vírus Chikungunya Zika virus Biologia Computacional / métodos Bases de Dados de Ácidos Nucleicos / utilização Genótipo Técnicas de Genotipagem / métodos Surtos de Doenças Monitoramento Epidemiológico Variação Genética |
| title_short |
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes |
| title_full |
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes |
| title_fullStr |
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes |
| title_full_unstemmed |
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes |
| title_sort |
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes |
| author |
Fonseca, Vagner |
| author_facet |
Fonseca, Vagner Fonseca, Vagner Libin, Pieter J. K Theys, Kristof Faria, Nuno Rodrigues Nunes, Márcio Roberto Teixeira Restovic, Maria I Freire, Murilo Giovanetti, Marta Cuypers, Lize Nowé, Ann Abecasis, Ana Barroso 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 Carlos Júnior Oliveira, Tulio de Libin, Pieter J. K Theys, Kristof Faria, Nuno Rodrigues Nunes, Márcio Roberto Teixeira Restovic, Maria I Freire, Murilo Giovanetti, Marta Cuypers, Lize Nowé, Ann Abecasis, Ana Barroso 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 Carlos Júnior Oliveira, Tulio de |
| author_role |
author |
| author2 |
Libin, Pieter J. K Theys, Kristof Faria, Nuno Rodrigues Nunes, Márcio Roberto Teixeira Restovic, Maria I Freire, Murilo Giovanetti, Marta Cuypers, Lize Nowé, Ann Abecasis, Ana Barroso 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 Carlos Júnior Oliveira, Tulio de |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Fonseca, Vagner Libin, Pieter J. K Theys, Kristof Faria, Nuno Rodrigues Nunes, Márcio Roberto Teixeira Restovic, Maria I Freire, Murilo Giovanetti, Marta Cuypers, Lize Nowé, Ann Abecasis, Ana Barroso 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 Carlos Júnior Oliveira, Tulio de |
| dc.subject.decsPrimary.pt_BR.fl_str_mv |
Arbovirus / classificação Dengue Vírus Chikungunya Zika virus Biologia Computacional / métodos Bases de Dados de Ácidos Nucleicos / utilização Genótipo Técnicas de Genotipagem / métodos Surtos de Doenças Monitoramento Epidemiológico Variação Genética |
| topic |
Arbovirus / classificação Dengue Vírus Chikungunya Zika virus Biologia Computacional / métodos Bases de Dados de Ácidos Nucleicos / utilização Genótipo Técnicas de Genotipagem / métodos Surtos de Doenças Monitoramento Epidemiológico Variação Genética |
| description |
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. |
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2019 |
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2019-06-17T13:48:20Z |
| dc.date.available.fl_str_mv |
2019-06-17T13:48:20Z |
| dc.date.issued.fl_str_mv |
2019 |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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publishedVersion |
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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, e0007231, p. 1-15, May 2019. DOI: https://doi.org/0.1371/journal.pntd.0007231. Disponível em: https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0007231&type=printable. |
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https://patua.iec.gov.br/handle/iec/3750 |
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1935-2735 |
| dc.identifier.doi.pt_BR.fl_str_mv |
0.1371/journal.pntd.0007231 |
| identifier_str_mv |
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, e0007231, p. 1-15, May 2019. DOI: https://doi.org/0.1371/journal.pntd.0007231. Disponível em: https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0007231&type=printable. 1935-2735 0.1371/journal.pntd.0007231 |
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https://patua.iec.gov.br/handle/iec/3750 |
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eng |
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Public Library of Science |
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Public Library of Science |
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