Chikungunya viruses containing the A226V mutation detected retrospectively in Cameroon form a new geographical subclade

Abstract

Background: Chikungunya virus (CHIKV) is a re-emerging arbovirus associated with sporadic outbreaks in Cameroon since 2006. Viral whole genomes were generated to analyze the origins of evolutionary lin- eages, the potential of emergence/re-emergence, and to infer transmission dynamics of recent Cameroon CHIKV outbreak strains. Methods: Samples collected between 2016 and 2019 during CHIKV outbreaks in Cameroon were screened for CHIKV using reverse transcription PCR (RT-PCR), followed by whole genome sequencing of positive samples. Results: Three coding-complete CHIKV genomes were obtained from samples, which belong to an emerg- ing sub-lineage of the East/Central/South African genotype and formed a monophyletic taxon with pre- vious Central African strains. This clade, which we have named the new Central African clade, appears to be evolving at 3.0 ×10 −4 nucleotide substitutions per site per year (95% highest posterior density (HPD) interval of 1.94 ×10 −4 to 4.1 ×10 −4 ). Notably, mutations in the envelope proteins (E1-A226V, E2- L210Q, and E2-I211T), which are known to enhance CHIKV adaptability and infectious potential in Aedes albopictus , were present in all strains and mapped to established high-density Ae. albopictus populations. Conclusions: These new CHIKV strains constitute a conserved genomic pool of an emerging sub-lineage, reflecting a putative vector host adaptation to Ae. albopictus , which has practically displaced Aedes aegypti from select regions of Cameroon.