Short report: Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas

Abstract

Since introduction into Brazil in 2014, chikungunya virus (CHIKV) has presented sustained transmission, although much is unknown about its circulation in the midwestern states. Here, we analyze 24 novel partial and near complete CHIKV genomes from Cuiaba, an urban metropolis located in the Brazilian midwestern state of Mato Grosso (MT). Nanopore technology was used for sequencing CHIKV complete genomes. Phylogenetic and epidemiological approaches were used to explore the recent spatio-temporal evolution and spread of the CHIKV-ECSA genotype in Midwest Brazil as well as in the Americas. Epidemiological data revealed a reduction in the number of reported cases over 2018-2020, likely as a consequence of a gradual accumulation of herd-immunity. Phylogeographic reconstructions revealed that at least two independent introductions of the ECSA lineage occurred in MT from a dispersion event originating in the northeastern region and suggest that the midwestern Brazilian region appears to have acted as a source of virus transmission towards Paraguay, a bordering South American country. Our results show a complex dynamic of transmission between epidemic seasons and suggest a possible role of Brazil as a source for international dispersion of the CHIKV-ECSA genotype to other countries in the Americas.

Fig 1. CHIKV transmission dynamics in Brazil (2014–2019).

(A) Map of Brazil and Americas showing sampling location of the CHIKV genomes from this study (white circles). (B) Weekly notified chikungunya cases normalized per 100K individuals per Brazilian region in 2015–2020 (until EW06). Incidence (cases per 100K population) is presented in log10 for visual purposes. Epidemic curves are coloured according to geographical macro region: SE = Southeast, NE = Northeast, MW = Midwest, N = North, S = South. (C) Time-scaled phylogeographic tree of 120 complete and near-complete CHIKV genome sequences from the ECSA genotype sampled in Brazil and Americas. Colours represent different sampling locations according to the legend on the left of the tree. Tip circles (white) represent the genome sequences generated in this study. Skyline plot (black and gray lines) is superimposed. Relative genetic diversity is represented here as a surrogate for the product of effective population size and generation time. The solid black line represents the mean relative genetic diversity and the light gray area around the line represents the 95% HPD interval of the estimates.