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

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 x 10(-4) nucleotide substitutions per site per year (95% highest posterior density (HPD) interval of 1.94 x 10(-4) to 4.1 x 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. (C) 2021 The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.

Automated summary

By sequencing the whole genomes of CHIKV strains in Cameroon, a new Central African clade was identified with mutations enhancing adaptability and infectious potential in Ae. albopictus. These new CHIKV strains demonstrate putative vector host adaptation to Ae. albopictus.