Emergence and persistence of the Chikungunya virus East-Central-South-African genotype in Northeast Brazil

Abstract

SummaryWe investigate an outbreak of exanthematous illness in Maceió, Alagoas, using molecular surveillance. Of 273 samples, 76% tested RT-qPCR positive for Chikungunya virus. Phylogenetic analysis reveals that the outbreak was caused by the East-Central-South-African genotype, and that this lineage has likely persisted since mid-2014 in Northeast Brazil.Article summary lineTransmission of the Chikungunya virus East-Central-South-African genotype has been ongoing in the Northeast region of Brazil since mid-2014.

Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil

“…In this study, we increased the number of CHIKV genomes deposited in the NCBI by generating 422 genomes that cover 12 Brazilian states over the years 2021-2022. By combining genomic and demographic data this effort has provided a comprehensive overview of CHIKV ECSA phylogeny in Brazil which summarizes and updates previous phylogenies from other studies of localized outbreaks 10,12,14,26,27 . The updated and metadataenriched dataset allowed us not only to describe the genetic diversity of circulating CHIKV variants but also to describe branching patterns observed in the updated phylogeny and infer the divergence time and likely location of emerging distinct subclades from the Brazilian lineage.…”

“…Recurring CHIKF epidemics, as indicated by the seasonal peak patterns displayed in the case time-series plot, are evidence that the virus is endemic in Brazil. Human mobility, population immunity, vector suitability, vegetation coverage, site socioeconomic status, and viral sequence variation are factors considered to mediate the dispersal of CHIKV in Brazil 26,58,59 .…”

“…Following the arrival of ECSA lineage in the Northeast region, a number of other studies have predicted and reported the establishment and spread of this lineage to the rest of the country [10][11][12]14,17,[26][27][28][29] . The Bayesian phylogeographic approach employed in this study has revealed the main routes of dispersion of CHIKV in the country.…”