Genome sequencing reveals coinfection by multiple chikungunya virus genotypes in a recent outbreak in Brazil

Chikungunya virus (CHIKV) is an RNA virus from the Togaviridae family transmitted by mosquitoes in both sylvatic and urban cycles. In humans, CHIKV infection leads to a febrile illness, denominated Chikungunya fever (CHIKF), commonly associated with more intense and debilitating outcomes. CHIKV arrived in Brazil in 2014 through two independent introductions: the Asian/Caribbean genotype entered through the North region and the African ECSA genotype was imported through the Northeast region. Following their initial introduction, both genotypes established their urban cycle among large naive human populations causing several outbreaks in the Americas. Here, we sequenced CHIKV genomes from a recent outbreak in the Northeast region of Brazil, employing an in-house developed Next-Generation Sequencing (NGS) protocol capable of directly detecting multiple known CHIKV genotypes from clinical positive samples. Our results demonstrate that both Asian/Caribbean and ECSA genotypes expanded their ranges, reaching cocirculation in the Northeast region of Brazil. In addition, our NGS data supports the findings of simultaneous infection by these two genotypes, suggesting that coinfection might be more common than previously thought in highly endemic areas. Future efforts to understand CHIKV epidemiology should thus take into consideration the possibility of coinfection by different genotypes in the human population.