Fig. 4

Phylogenetic analysis of CHIKV genomes from Kenya. BEAST MCC tree of 123 ECSA genomes collected across the world, including 24 from Kenya is shown in the left panel. On the right panel is an extraction highlighting the CHIKV sequences generated in this study. The tips are coloured according to geographic location or child identity (as in Fig. 3, for those with paired index-recurrent episode sequence pairs), with posterior probability support shown for select nodes with probability > 0.8. Sample MT526800 was from a child with a single CHIKF episode whose RT-PCR cycle threshold (Ct) value was low (Ct = 19). The same and more detailed MCC tree can be found in Figure S3 in Supplementary Material