Maximum likelihood phylogenetic analysis of partial CHIKV E1 gene sequences.

A phylogeny of 420 CHIKV strains with an O’nyong-nyong strain used as an outgroup (not shown) built using the General Time Reversible substitution model with a gamma distributed rate variation among sites. Statistical support for major tree nodes is shown as aLRT scores. Epidemic linages are shown in grey and a statistically supported cluster of 6 Mexican strains is marked with an asterisk. The scale bar represents nucleotide substitutions per site. ECSA, East-Central-South Africa; IOL, Indian Ocean Lineage; WAf, West African.