Abstract
BackgroundSince 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 findingsWe 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/SignificanceThis 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.
Highlights
In August 2014, local transmission of chikungunya virus (CHIKV) was detected in Brazil for the first time, with cases being reported nearly simultaneously in Oiapoque (Amapastate, north Brazil) and Feira de Santana (Bahia state, northeast Brazil), two municipalities separatedChikungunya virus outbreak in the Amazon region by >2000 km distance
Until the end of 2017, Brazil notified the highest number of infections caused by chikungunya virus (CHIKV) in the Americas
We investigated a large CHIKV outbreak in Boa vista municipality in the Brazilian Amazon region
Summary
In August 2014, local transmission of chikungunya virus (CHIKV) was detected in Brazil for the first time, with cases being reported nearly simultaneously in Oiapoque (Amapastate, north Brazil) and Feira de Santana (Bahia state, northeast Brazil), two municipalities separatedChikungunya virus outbreak in the Amazon region by >2000 km distance. In August 2014, local transmission of chikungunya virus (CHIKV) was detected in Brazil for the first time, with cases being reported nearly simultaneously in Oiapoque (Amapastate, north Brazil) and Feira de Santana (Bahia state, northeast Brazil), two municipalities separated. Since 2014 and until the end of September 2018, a total of 697,564 CHIKV cases have been notified in Brazil (including 94,672 laboratory-confirmed cases). This is the largest number recorded in any of the 51 countries or territories reporting local CHIKV transmission in the Americas [2]. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript
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