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Input: Supplementary Figure 1. Phylogenetic tree for complete genomes of 91 representative IOL CHIKV strains constructed using the maximum likelihood method. Bootstrap values and sl1-4-specific substitutions are indicated. The SL07 strain used as a genetic background for all in vivo experiments is highlighted with an asterisk. The purple arrow highlights strain LK(EH)CH18608 with the E2-K233E substitution. The blue diamond highlights the Thailand-2009_CK11/53 strain of sl1 used in competition experiment (see Supplementary Fig. 2) . The bar indicates 0.2% nucleotide sequence divergence. (a) Schematic representation of the experimental design. Table shows genetic differences between the competing viruses. A 1:1 ratio (based on pfu) of wt (SL07-226V_Apa) and mut (contains one of the sl2-specific mutations) viruses was presented to Thai colony A.

Supplementary information