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 directly from clinical samples with different disease symptoms, first demonstrating that both Asian/Caribbean and African ECSA genotypes expanded their ranges reaching cocirculation in the same region (Northeast Brazil). We also found that coinfection by the two genotypes occurred mostly in patients with CHIKF severe manifestations. Our results suggests that a higher genomic variability owed to co infection might be associated to disease severity and call for a deeper evaluation of the possible link between coinfection and CHIKF severe symptoms.