Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon
| Autor(a) principal: | |
|---|---|
| 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/35316 |
Resumo: | Fundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, Brasil. |
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Naveca, Felipe GomesClaro, IngraGiovanetti, MartaJesus, Jaqueline Goes deXavier, JoilsonIani, Felipe Campos de MeloNascimento, Valdinete Alves doSouza, Victor Costa deSilveira, Paola PazLourenço, JoséSantillana, MauricioKraemer, Moritz U. G.Quick, JoshHill, Sarah C.Thézé, JulienCarvalho, Rodrigo Dias de OliveiraAzevedo, VascoSalles, Flavia Cristina da SilvaNunes, Márcio Roberto TeixeiraLemos, Poliana da SilvaCandido, Darlan da SilvaPereira, Glauco de CarvalhoOliveira, Marluce Aparecida AssunçãoMeneses, Cátia Alexandra RibeiroMaito, Rodrigo MeloCunha, Claudeth Rocha Santa BrígidaCampos, Daniela Palha de SousaCastilho, Marcia da CostaSiqueira, Thalita Caroline da SilvaTerra, Tiza MatosMelo, Carlos Frederico Campelo de Albuquerque eCruz, Laura Nogueira daAbreu, Andre Luiz deMartins, Divino ValerioSimoes, Daniele Silva de Moraes VanlumeAguiar, Renato Santana deLuz, Sérgio Luiz BessaLoman, NicholasPybus, Oliver G.Sabino, Ester C.Okumoto, OsneiAlcantara, Luiz Carlos JuniorFaria, Nuno Rodrigues2019-09-03T16:05:13Z2019-09-03T16:05:13Z2019NAVECA, Felipe Gomes et al. Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon. PLoS Neglected Tropical Diseases , v. 13, n. 3, p. 1-21, Mar. 2019.1935-2727https://www.arca.fiocruz.br/handle/icict/3531610.1371/journal.pntd.00070651935-2735engPublic Library of ScienceVírus ChikungunyaBrazilian AmazonVigilância epidemiológicaGenômicaChikungunya virusBrazilian AmazonSurveillanceGenomicEpidemiologicalGenomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazoninfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, Brasil.Universidade de São Paulo. Faculdade de Medicina. Instituto de Medicina Tropical. São Paulo, SP, Brasil.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.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Gonçalo Muniz. Laboratório de Patologia Experimental. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Gonçalo Muniz. 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 / Laboratório Central de Saúde Pública. Instituto Octávio Magalhães. FUNED, Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, Brasil.Fundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, Brasil.Universidade Federal do Rio de Janeiro. Instituto de Biologia. Departamento de Genética. Laboratório de Virologia Molecular. Rio de Janeiro, RJ, Brasil.University of Oxford. Department of Zoology. South Parks Road, Oxford, United Kingdom.Harvard Medical School. Department of Pediatrics. Boston, MA, USA / Boston Children’s Hospital. Computational Health Informatics Program. Boston, MA, USA.University of Oxford. Department of Zoology. South Parks Road, Oxford, United Kingdom / Boston Children’s Hospital. Computational Health Informatics Program. Boston, MA, USA.University of Birmingham. Institute of Microbiology and Infection. Birmingham, United Kingdom.University of Oxford. Department of Zoology. South Parks Road, Oxford, United Kingdom.University of Oxford. Department of Zoology. South Parks Road, Oxford, United Kingdom.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.Universidade de São Paulo. Faculdade de Medicina. Instituto de Medicina Tropical. São Paulo, SP, Brasil.Ministério da Saúde do Brasil. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde do Brasil. Instituto Evandro Chagas. Ananindeua, PA, Brasil.University of Oxford. Department of Zoology. South Parks Road, Oxford, United Kingdom.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.Laboratório Central de Saúde Pública. Boa Vista, RR, Brasil.Laboratório Central de Saúde Pública. Boa Vista, RR, Brasil.Laboratório Central de Saúde Pública. Boa Vista, RR, Brasil.Secretaria Municipal de Saúde de Boa Vista. Superintendência de Vigilância em Saúde. Boa Vista, RR, Brasil.Fundac¸ão de Medicina Tropical Doutor Heitor Vieira Dourado. Departamento de Virologia. Manaus, AM, Brasil.Secretaria Municipal de Saúde de Boa Vista. Superintendência de Vigilância em Saúde. Boa Vista, RR, Brasil.Laboratório Central de Saúde Pública do Amazonas, Manaus, AM, Brasil.Organização Pan-Americana da Saúde/Organização Mundial da Saúde (OPAS-OMS). Brasília, DF, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Brasília, DF, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Brasília, DF, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Brasília, DF, Brasil.Since its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region remains poorly understood despite its importance to better understand the epidemiological spread and public health impact of CHIKV in the country. Methodology/Principal findings: We report a large CHIKV outbreak (5,928 notified cases between August 2014 and August 2018) in Boa vista municipality, capital city of Roraima’s state, located in the Brazilian Amazon region. We generated 20 novel CHIKV-ECSA genomes from the Brazilian Amazon region using MinION portable genome sequencing. Phylogenetic analyses revealed that despite an early introduction of the Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista was caused by an ECSA-lineage most likely introduced from northeastern Brazil. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which translates in an estimated 39 (95% CI: 36 to 45) % of Roraima’s population infected with CHIKV-ECSA. Finally, we find a strong association between Google search activity and the local laboratory-confirmed CHIKV cases in Roraima. Conclusions/Significance: This study highlights the potential of combining traditional surveillance with portable genome sequencing technologies and digital epidemiology to inform public health surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of the Asian genotype by the ECSA genotype in the Amazon region.info: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/35316/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALJoilsonXavier_JaquelineJesus_etal_IOC_2019.pdfJoilsonXavier_JaquelineJesus_etal_IOC_2019.pdfapplication/pdf1374116https://www.arca.fiocruz.br/bitstream/icict/35316/2/JoilsonXavier_JaquelineJesus_etal_IOC_2019.pdf596820f9bb2d117af30343806d661306MD52TEXTJoilsonXavier_JaquelineJesus_etal_IOC_2019.pdf.txtJoilsonXavier_JaquelineJesus_etal_IOC_2019.pdf.txtExtracted 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| dc.title.pt_BR.fl_str_mv |
Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon |
| title |
Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon |
| spellingShingle |
Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon Naveca, Felipe Gomes Vírus Chikungunya Brazilian Amazon Vigilância epidemiológica Genômica Chikungunya virus Brazilian Amazon Surveillance Genomic Epidemiological |
| title_short |
Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon |
| title_full |
Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon |
| title_fullStr |
Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon |
| title_full_unstemmed |
Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon |
| title_sort |
Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon |
| author |
Naveca, Felipe Gomes |
| author_facet |
Naveca, Felipe Gomes Claro, Ingra Giovanetti, Marta Jesus, Jaqueline Goes de Xavier, Joilson Iani, Felipe Campos de Melo Nascimento, Valdinete Alves do Souza, Victor Costa de Silveira, Paola Paz Lourenço, José Santillana, Mauricio Kraemer, Moritz U. G. Quick, Josh Hill, Sarah C. Thézé, Julien Carvalho, Rodrigo Dias de Oliveira Azevedo, Vasco Salles, Flavia Cristina da Silva Nunes, Márcio Roberto Teixeira Lemos, Poliana da Silva Candido, Darlan da Silva Pereira, Glauco de Carvalho Oliveira, Marluce Aparecida Assunção Meneses, Cátia Alexandra Ribeiro Maito, Rodrigo Melo Cunha, Claudeth Rocha Santa Brígida Campos, Daniela Palha de Sousa Castilho, Marcia da Costa Siqueira, Thalita Caroline da Silva Terra, Tiza Matos Melo, Carlos Frederico Campelo de Albuquerque e Cruz, Laura Nogueira da Abreu, Andre Luiz de Martins, Divino Valerio Simoes, Daniele Silva de Moraes Vanlume Aguiar, Renato Santana de Luz, Sérgio Luiz Bessa Loman, Nicholas Pybus, Oliver G. Sabino, Ester C. Okumoto, Osnei Alcantara, Luiz Carlos Junior Faria, Nuno Rodrigues |
| author_role |
author |
| author2 |
Claro, Ingra Giovanetti, Marta Jesus, Jaqueline Goes de Xavier, Joilson Iani, Felipe Campos de Melo Nascimento, Valdinete Alves do Souza, Victor Costa de Silveira, Paola Paz Lourenço, José Santillana, Mauricio Kraemer, Moritz U. G. Quick, Josh Hill, Sarah C. Thézé, Julien Carvalho, Rodrigo Dias de Oliveira Azevedo, Vasco Salles, Flavia Cristina da Silva Nunes, Márcio Roberto Teixeira Lemos, Poliana da Silva Candido, Darlan da Silva Pereira, Glauco de Carvalho Oliveira, Marluce Aparecida Assunção Meneses, Cátia Alexandra Ribeiro Maito, Rodrigo Melo Cunha, Claudeth Rocha Santa Brígida Campos, Daniela Palha de Sousa Castilho, Marcia da Costa Siqueira, Thalita Caroline da Silva Terra, Tiza Matos Melo, Carlos Frederico Campelo de Albuquerque e Cruz, Laura Nogueira da Abreu, Andre Luiz de Martins, Divino Valerio Simoes, Daniele Silva de Moraes Vanlume Aguiar, Renato Santana de Luz, Sérgio Luiz Bessa Loman, Nicholas Pybus, Oliver G. Sabino, Ester C. Okumoto, Osnei Alcantara, Luiz Carlos Junior Faria, Nuno Rodrigues |
| author2_role |
author author author author author author author author author author author author author author author author author author author author 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 |
Naveca, Felipe Gomes Claro, Ingra Giovanetti, Marta Jesus, Jaqueline Goes de Xavier, Joilson Iani, Felipe Campos de Melo Nascimento, Valdinete Alves do Souza, Victor Costa de Silveira, Paola Paz Lourenço, José Santillana, Mauricio Kraemer, Moritz U. G. Quick, Josh Hill, Sarah C. Thézé, Julien Carvalho, Rodrigo Dias de Oliveira Azevedo, Vasco Salles, Flavia Cristina da Silva Nunes, Márcio Roberto Teixeira Lemos, Poliana da Silva Candido, Darlan da Silva Pereira, Glauco de Carvalho Oliveira, Marluce Aparecida Assunção Meneses, Cátia Alexandra Ribeiro Maito, Rodrigo Melo Cunha, Claudeth Rocha Santa Brígida Campos, Daniela Palha de Sousa Castilho, Marcia da Costa Siqueira, Thalita Caroline da Silva Terra, Tiza Matos Melo, Carlos Frederico Campelo de Albuquerque e Cruz, Laura Nogueira da Abreu, Andre Luiz de Martins, Divino Valerio Simoes, Daniele Silva de Moraes Vanlume Aguiar, Renato Santana de Luz, Sérgio Luiz Bessa Loman, Nicholas Pybus, Oliver G. Sabino, Ester C. Okumoto, Osnei Alcantara, Luiz Carlos Junior Faria, Nuno Rodrigues |
| dc.subject.other.pt_BR.fl_str_mv |
Vírus Chikungunya Brazilian Amazon Vigilância epidemiológica Genômica |
| topic |
Vírus Chikungunya Brazilian Amazon Vigilância epidemiológica Genômica Chikungunya virus Brazilian Amazon Surveillance Genomic Epidemiological |
| dc.subject.en.pt_BR.fl_str_mv |
Chikungunya virus Brazilian Amazon Surveillance Genomic Epidemiological |
| description |
Fundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, Brasil. |
| publishDate |
2019 |
| dc.date.accessioned.fl_str_mv |
2019-09-03T16:05:13Z |
| dc.date.available.fl_str_mv |
2019-09-03T16:05:13Z |
| 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 |
NAVECA, Felipe Gomes et al. Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon. PLoS Neglected Tropical Diseases , v. 13, n. 3, p. 1-21, Mar. 2019. |
| dc.identifier.uri.fl_str_mv |
https://www.arca.fiocruz.br/handle/icict/35316 |
| dc.identifier.issn.pt_BR.fl_str_mv |
1935-2727 |
| dc.identifier.doi.none.fl_str_mv |
10.1371/journal.pntd.0007065 |
| dc.identifier.eissn.none.fl_str_mv |
1935-2735 |
| identifier_str_mv |
NAVECA, Felipe Gomes et al. Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon. PLoS Neglected Tropical Diseases , v. 13, n. 3, p. 1-21, Mar. 2019. 1935-2727 10.1371/journal.pntd.0007065 1935-2735 |
| url |
https://www.arca.fiocruz.br/handle/icict/35316 |
| 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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reponame:Repositório Institucional da FIOCRUZ (ARCA) instname:Fundação Oswaldo Cruz (FIOCRUZ) instacron:FIOCRUZ |
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Repositório Institucional da FIOCRUZ (ARCA) |
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Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ) |
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repositorio.arca@fiocruz.br |
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