TY - JOUR
T1 - Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon
AU - Naveca, Felipe Gomes
AU - Claro, Ingra
AU - Giovanetti, Marta
AU - de Jesus, Jaqueline Goes
AU - Xavier, Joilson
AU - Iani, Felipe Campos de Melo
AU - do Nascimento, Valdinete Alves
AU - de Souza, Victor Costa
AU - Silveira, Paola Paz
AU - Lourenço, José
AU - Santillana, Mauricio
AU - Kraemer, Moritz U.G.
AU - Quick, Josh
AU - Hill, Sarah C.
AU - Thézé, Julien
AU - Carvalho, Rodrigo Dias de Oliveira
AU - Azevedo, Vasco
AU - Salles, Flavia Cristina da Silva
AU - Nunes, Márcio Roberto Teixeira
AU - Lemos, Poliana da Silva
AU - Candido, Darlan da Silva
AU - Pereira, Glauco de Carvalho
AU - Oliveira, Marluce Aparecida Assunção
AU - Meneses, Cátia Alexandra Ribeiro
AU - Maito, Rodrigo Melo
AU - Cunha, Claudeth Rocha Santa Brígida
AU - Campos, Daniela Palha de Sousa
AU - Castilho, Marcia da Costa
AU - Siqueira, Thalita Caroline da Silva
AU - Terra, Tiza Matos
AU - Albuquerque, Carlos F.Campelo de
AU - Cruz, Laura Nogueira da
AU - Abreu, André Luis de
AU - Martins, Divino Valerio
AU - Simoes, Daniele Silva de Moraes Vanlume
AU - Aguiar, Renato Santana de
AU - Luz, Sérgio Luiz Bessa
AU - Loman, Nicholas
AU - Pybus, Oliver G.
AU - Sabino, Ester C.
AU - Okumoto, Osnei
AU - Alcantara, Luiz Carlos Junior
AU - Faria, Nuno Rodrigues
N1 - Funding Information:
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. We are thankful to all personnel from Secretaria de Vigilância em Saúde SVS/MS, PAHO/Brazil, Roraima and Boa Vista Health Surveillance System that coordinated surveillance and helped with data collection and assembly. We thank Oxford Nanopore Technologies for the support to the ZIBRA-2 (Zika in Brazil Real time Analyses-second round) project with additional flowcells and corresponding reagents, and also thank QIAGEN for donation of consumables.
Publisher Copyright:
© 2019 Naveca et al.
PY - 2018/3
Y1 - 2018/3
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85063279072&partnerID=8YFLogxK
U2 - 10.1371/journal.pntd.0007065
DO - 10.1371/journal.pntd.0007065
M3 - Article
C2 - 30845267
AN - SCOPUS:85063279072
SN - 1935-2727
VL - 13
JO - PLoS Neglected Tropical Diseases
JF - PLoS Neglected Tropical Diseases
IS - 3
M1 - e0007065
ER -
