Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage
Naveca, Felipe Gomes; Claro, Ingra Morales; 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; Sales, 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, Catia 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; Albuquerque, Carlos Frederico Campelo de; Cruz, Laura Nogueira da; Abreu, André Luiz de; Martins, Divino Valerio; Simoes, Daniele Silva de Moraes Vanlume; Aguiar, Renato Santana de; Luz, Sergio Luiz Bessa; Loman, Nicholas; Pybus, Oliver G; Sabino, Ester Cerdeira; Okumoto, Osnei; Alcantara, Luiz Carlos Júnior; Faria, Nuno Rodrigues.
NAVECA, Felipe Gomes et al. Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage. bioRxiv, e492595, p. 1-41, 2018. DOI: https://doi.org/10.1101/492595. Disponível em: https://www.biorxiv.org/content/10.1101/492595v1.full.pdf.
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| IED | ID: ied-3648
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. In just 48 hours, 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.
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