Evolution history and lineage-specific structures of the CHIKV 3′UTR.

<p>On the left is the MCC (Maximum Clade Credibility) tree based on the complete ORF sequences, with the branches in each lineage collapsed. The estimated year of the most recent common ancestor (MRCA: mean and the 95% HPD values) of each clade is labeled left to the node. The 3′UTR structures, based on sequence alignment, are shown next to each lineage. Direct repeats are illustrated by different colored blocks, each of the four colors represents a different homologous sequence region. Sequence gaps in the alignment are indicated by white blocks. In the Asian lineage, two distinct derived differences are observed: 1) duplication of DR3, and duplication the of DR(1+2) region. The detailed alignment can be found in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003591#ppat.1003591.s002" target="_blank">Fig. S2</a>.