A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes

Detalhes bibliográficos
Autor(a) principal: Fonseca, Vagner
Data de Publicação: 2019
Outros Autores: 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
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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spelling 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. 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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
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/33877/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/33877/2/Fonseca.%20V.%20A%20computational....pdf
https://www.arca.fiocruz.br/bitstream/icict/33877/3/Fonseca.%20V.%20A%20computational....pdf.txt
bitstream.checksum.fl_str_mv 5a560609d32a3863062d77ff32785d58
4738d2316b03f620de5499b1275241a4
1df263542acc6c29eef119a2799d1c85
bitstream.checksumAlgorithm.fl_str_mv MD5
MD5
MD5
repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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