| Author | Naveca, Felipe Gomes | |
| Author | Claro, Ingra | |
| Author | Giovanetti, Marta | |
| Author | Jesus, Jaqueline Goes de | |
| Author | Xavier, Joilson | |
| Author | Iani, Felipe Campos de Melo | |
| Author | Nascimento, Valdinete Alves do | |
| Author | Souza, Victor Costa de | |
| Author | Silveira, Paola Paz | |
| Author | Lourenço, José | |
| Author | Santillana, Mauricio | |
| Author | Kraemer, Moritz U. G. | |
| Author | Quick, Josh | |
| Author | Hill, Sarah C. | |
| Author | Thézé, Julien | |
| Author | Carvalho, Rodrigo Dias de Oliveira | |
| Author | Azevedo, Vasco | |
| Author | Salles, Flavia Cristina da Silva | |
| Author | Nunes, Márcio Roberto Teixeira | |
| Author | Lemos, Poliana da Silva | |
| Author | Candido, Darlan da Silva | |
| Author | Pereira, Glauco de Carvalho | |
| Author | Oliveira, Marluce Aparecida Assunção | |
| Author | Meneses, Cátia Alexandra Ribeiro | |
| Author | Maito, Rodrigo Melo | |
| Author | Cunha, Claudeth Rocha Santa Brígida | |
| Author | Campos, Daniela Palha de Sousa | |
| Author | Castilho, Marcia da Costa | |
| Author | Siqueira, Thalita Caroline da Silva | |
| Author | Terra, Tiza Matos | |
| Author | Melo, Carlos F. Campelo de Albuquerque | |
| Author | Cruz, Laura Nogueira da | |
| Author | Abreu, André Luiz de | |
| Author | Martins, Divino Valerio | |
| Author | Simoes, Daniele Silva de Moraes Vanlume | |
| Author | Aguiar, Renato Santana de | |
| Author | Luz, Sérgio Luiz Bessa | |
| Author | Loman, Nicholas | |
| Author | Pybus, Oliver G. | |
| Author | Sabino, Ester C. | |
| Author | Okumoto, Osnei | |
| Author | Junior Alcantara, Luiz Carlos | |
| Author | Faria, Nuno Rodrigues | |
| Access date | 2019-09-03T16:05:13Z | |
| Available date | 2019-09-03T16:05:13Z | |
| Document date | 2019 | |
| Citation | 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. | pt_BR |
| ISSN | 1935-2727 | pt_BR |
| URI | https://www.arca.fiocruz.br/handle/icict/35316 | |
| Sponsorship | The ZIBRA-2 project is funded by Conselho Nacional de Desenvolvimento Científico e Tecnológico (grant 440685/2016-8) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (grant 88887.130716/2016-00). FGN is funded by Conselho Nacional de Desenvolvimento Científico e Tecnológico (http://www.cnpq.br, grant 440856/2016–7) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (http://www.capes.gov.br, grants 88881.130825/2016–00 and 88887.130823/2016–00). L.C.J.A. is supported by the EU’s Horizon 2020 Programme through ZIKAlliance (grant PRES-005-FEX-17-4-2-33). N.R.F. is funded by a Royal Society and Wellcome Trust Sir Henry Dale Fellowship (204311/Z/16/Z), internal GCRF grant 005073, and John Fell Research Fund grant 005166. This research received funding from the ERC (grant agreement 614725-PATHPHYLODYN). MS was partially supported by the National Institute of General Medical Sciences of the NIH (USA) under award number R01GM130668. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. | |
| Language | eng | pt_BR |
| Publisher | Public Library of Science | pt_BR |
| Rights | open access | |
| Title | Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon | pt_BR |
| Type | Article | |
| DOI | 10.1371/journal.pntd.0007065 | |
| Abstract | Background: 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. | pt_BR |
| Affilliation | Fundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, Brasil. | pt_BR |
| Affilliation | Universidade de São Paulo. Faculdade de Medicina. Instituto de Medicina Tropical. São Paulo, SP, Brasil. | pt_BR |
| Affilliation | 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. | pt_BR |
| Affilliation | 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. | pt_BR |
| Affilliation | 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. | pt_BR |
| Affilliation | 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. | pt_BR |
| Affilliation | Fundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, Brasil. | pt_BR |
| Affilliation | Fundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, Brasil. | pt_BR |
| Affilliation | Universidade Federal do Rio de Janeiro. Instituto de Biologia. Departamento de Genética. Laboratório de Virologia Molecular. Rio de Janeiro, RJ, Brasil. | pt_BR |
| Affilliation | University of Oxford. Department of Zoology. South Parks Road, Oxford, United Kingdom. | pt_BR |
| Affilliation | Harvard Medical School. Department of Pediatrics. Boston, MA, USA / Boston Children’s Hospital. Computational Health Informatics Program. Boston, MA, USA. | pt_BR |
| Affilliation | University of Oxford. Department of Zoology. South Parks Road, Oxford, United Kingdom / Boston Children’s Hospital. Computational Health Informatics Program. Boston, MA, USA. | pt_BR |
| Affilliation | University of Birmingham. Institute of Microbiology and Infection. Birmingham, United Kingdom. | pt_BR |
| Affilliation | University of Oxford. Department of Zoology. South Parks Road, Oxford, United Kingdom. | pt_BR |
| Affilliation | University of Oxford. Department of Zoology. South Parks Road, Oxford, United Kingdom. | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil. | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil. | pt_BR |
| Affilliation | Universidade de São Paulo. Faculdade de Medicina. Instituto de Medicina Tropical. São Paulo, SP, Brasil. | pt_BR |
| Affilliation | Instituto Evandro Chagas. Ananindeua, PA, Brasil. | pt_BR |
| Affilliation | Instituto Evandro Chagas. Ananindeua, PA, Brasil. | pt_BR |
| Affilliation | University of Oxford. Department of Zoology. South Parks Road, Oxford, United Kingdom. | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil. | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil. | pt_BR |
| Affilliation | Laboratório Central de Saúde Pública. Boa Vista, RR, Brasil. | pt_BR |
| Affilliation | Laboratório Central de Saúde Pública. Boa Vista, RR, Brasil. | pt_BR |
| Affilliation | Laboratório Central de Saúde Pública. Boa Vista, RR, Brasil. | pt_BR |
| Affilliation | Secretaria Municipal de Saúde de Boa Vista. Superintendência de Vigilância em Saúde. Boa Vista, RR, Brasil. | pt_BR |
| Affilliation | Fundac¸ão de Medicina Tropical Doutor Heitor Vieira Dourado. Departamento de Virologia. Manaus, AM, Brasil. | pt_BR |
| Affilliation | Secretaria Municipal de Saúde de Boa Vista. Superintendência de Vigilância em Saúde. Boa Vista, RR, Brasil. | pt_BR |
| Affilliation | Laboratório Central de Saúde Pública do Amazonas, Manaus, AM, Brasil. | pt_BR |
| Affilliation | Organização Pan-Americana da Saúde. Organização Mundial da Saúde. Brasília, DF, Brasil. | pt_BR |
| Affilliation | Ministério da Saúde. Secretaria de Vigilância em Saúde. Brasília, DF, Brasil. | pt_BR |
| Affilliation | Ministério da Saúde. Secretaria de Vigilância em Saúde. Brasília, DF, Brasil. | pt_BR |
| Affilliation | Ministério da Saúde. Secretaria de Vigilância em Saúde. Brasília, DF, Brasil. | pt_BR |
| Subject | Chikungunya Virus | pt_BR |
| Subject | Brazilian Amazon | pt_BR |
| Subject | Surveillance | pt_BR |
| Subject | Genomic | pt_BR |
| Subject | Epidemiological | pt_BR |
| e-ISSN | 1935-2735 | |
