Phylogeny and homologous recombination in Chikungunya viruses.

The periodic and recent outbreaks of endemic Chikungunya virus (CHIKV) infection have jeopardized the public health in wider geographical regions. Particularly, full genome-based phylogenetic analyses and recombination of CHIKV have rarely been reported. In this study, phylogenetic and recombination analyses were performed on 122 complete CHIKV genomes. Three major phylogroups were identified which included West African genotype (group I); Asian genotype (group II) as well as ESCA and Indian Ocean genotype (group III). The latter was divided into three subgroups: East/South/Central African subgroup (IIIa and b) and Indian Ocean and Asian subgroup (IIIc). Re-emerging of the CHIKV in Asian countries gave rise to a novel subgroup. Two potential recombination events were found; nevertheless, neither of both was supported by further phylogenetic and statistical analyses. These data refine the phylogeny of the currently available CHIKVs and homologous recombination did not contribute to the genetic diversity of these viruses.