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. Author summary Human infection by different arthropod borne viruses such as Chikungunya, Dengue and Zika causes a continuous and extensive health burden mainly in tropical regions of the world. Most of the CHIKV infections result in only mild symptoms, however more extreme manifestations can occur, occasionally leading to death. Different CHIKV genotypes have been circulating in almost all continent around the globe but so far human outbreaks were reported only for single CHIKV genotypes. In Brazil two CHIKV genotypes arrived in the North and Northeast region: the Asian/Caribbean and African ECSA respectively. Here, through viral genome sequencing, we showed that some samples were coinfected by both Asian/Caribbean and ECSA CHIKV genotypes, indicating that these two genotypes expanded their ranges and currently co-circulate in some areas of Brazil. In summary, such findings call for improved surveillance in order to detect co-circulation of different viral genotypes and further evaluate the impact of co-infection in disease epidemiology.