Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage
Authors: Naveca Felipe Gomes , Claro Ingra , Giovanetti Marta , de Jesus Jaqueline Goes , Xavier Joilson , Iani Felipe Campos de Melo , do Nascimento Valdinete Alves , de Souza Victor Costa , Silveira Paola Paz , Lourenço José , Santillana Mauricio , Kraemer Moritz U. G. , Quick Josh , Hill Sarah C. , Theze 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 F. Campelo de , Cruz Laura Nogueira da , Abreu André Luis de , Martins Divino Valerio , Simoes Daniele Silva de Moraes Vanlume , Aguiar Renato Santana , Luz Sergio Luiz Bessa , Loman Nicholas , Pybus Oliver G. , Sabino Ester Cerdeira , Okumoto Osnei , Alcantara Luiz Carlos Junior , Faria Nuno Rodrigues 
Published: December 2018

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.