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

Abstract

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.

Natural Infection of Aedes aegypti by Chikungunya and Dengue type 2 Virus in a Transition Area of North-Northeast Brazil

“…The co-circulation of ECSA and Asian/Caribbean genotypes in Northeast Brazil has also been recently reported, including cases of simultaneous infection in clinical samples [96]. It can be inferred by our results, and those records in the literature in human samples, that the ECSA genotype is still prevalent in the country.…”

Chikungunya virus Detection in Aedes aegypti and Culex quinquefasciatus during an Outbreak in the Amazon Region

“…However, the circulation of the ECSA genotype in the North may be troublesome, as the Asian genotype already circulated in the region since its first introduction in the country, in Oiapoque, Amapá [9]. Surprisingly, their co-infection has already been reported in a recent study in human individuals naturally infected in the Northeast region [55]. It has been shown that both the Asian and ECSA genotypes could spread and co-circulate in the country, considering the vector species suitability [9].…”

Vector competence of Aedes albopictus populations for chikungunya virus is shaped by their demographic history

“…The first detection of CHIKV in the Americas was recorded in the Caribbean in late 2013, followed by a dramatic spread of the virus throughout the continent. It has been stated that CHIKV arrived in Brazil through two independent introductions: the Asian genotype from the Caribbean entered through the northern region, while the African ECSA genotype was imported through the north-east region 64 . Following their initial introduction, both genotypes established and expanded their range with CHIKV-ASIA being the prevalent genotype causing several outbreaks in relation to the presence of Ae.…”