A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
Texto Completo: | https://www.arca.fiocruz.br/handle/icict/33877 |
Resumo: | Funding: 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 Fundação para a Ciência e Tecnologia (FCT) through funds to GHTM-UID/Multi/04413/2013. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: Dr. Koen Deforche is one of the owners of the commercial company, EMWEB. |
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Fonseca, VagnerLibin, Pieter J. K.Theys, KristofFaria, Nuno RodriguesNunes, Marcio Roberto TeixeiraRestovic, Maria I.Freire, MuriloGiovanetti, MartaCuypers, LizeNowé, AnnAbecasis, AnaDeforche, KoenSantiago, Gilberto A.Siqueira, Isadora C. deSan, Emmanuel J.Machado, Kaliane Caldas de BritoAzevedo, VascoFilippis, Ana Maria Bispo deCunha, Rivaldo Venâncio daPybus, Oliver G.Vandamme, Anne-MiekeAlcantara, Luiz Carlos JuniorOliveira, Tulio de2019-07-08T14:05:44Z2019-07-08T14:05:44Z2019FONSECA, 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, 2019.1935-2727https://www.arca.fiocruz.br/handle/icict/3387710.1371/journal.pntd.0007231Funding: 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 Fundação para a Ciência e Tecnologia (FCT) through funds to GHTM-UID/Multi/04413/2013. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: Dr. Koen Deforche is one of the owners of the commercial company, EMWEB.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.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.engPublic Library of ScienceVírus da dengueZika virusChikungunyaGenótiposSoftwarePrevençãoTratamentoDengue virusZika virusChikungunyaGenotypeSoftwarePreventionTreatmentA computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/33877/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALFonseca. V. A computational....pdfFonseca. V. A computational....pdfapplication/pdf1483805https://www.arca.fiocruz.br/bitstream/icict/33877/2/Fonseca.%20V.%20A%20computational....pdf4738d2316b03f620de5499b1275241a4MD52TEXTFonseca. V. A computational....pdf.txtFonseca. V. 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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 Fonseca, Vagner Vírus da dengue Zika virus Chikungunya Genótipos Software Prevenção Tratamento Dengue virus Zika virus Chikungunya Genotype Software Prevention Treatment |
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 |
title_full_unstemmed |
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 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 |
author_role |
author |
author2 |
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 |
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, 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 |
dc.subject.other.pt_BR.fl_str_mv |
Vírus da dengue Zika virus Chikungunya Genótipos Software Prevenção Tratamento |
topic |
Vírus da dengue Zika virus Chikungunya Genótipos Software Prevenção Tratamento Dengue virus Zika virus Chikungunya Genotype Software Prevention Treatment |
dc.subject.en.pt_BR.fl_str_mv |
Dengue virus Zika virus Chikungunya Genotype Software Prevention Treatment |
description |
Funding: 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 Fundação para a Ciência e Tecnologia (FCT) through funds to GHTM-UID/Multi/04413/2013. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: Dr. Koen Deforche is one of the owners of the commercial company, EMWEB. |
publishDate |
2019 |
dc.date.accessioned.fl_str_mv |
2019-07-08T14:05:44Z |
dc.date.available.fl_str_mv |
2019-07-08T14:05:44Z |
dc.date.issued.fl_str_mv |
2019 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.citation.fl_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, p. 1-15, 2019. |
dc.identifier.uri.fl_str_mv |
https://www.arca.fiocruz.br/handle/icict/33877 |
dc.identifier.issn.pt_BR.fl_str_mv |
1935-2727 |
dc.identifier.doi.none.fl_str_mv |
10.1371/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, p. 1-15, 2019. 1935-2727 10.1371/journal.pntd.0007231 |
url |
https://www.arca.fiocruz.br/handle/icict/33877 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Public Library of Science |
publisher.none.fl_str_mv |
Public Library of Science |
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institution |
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