Figure 2. Phylogeny of chikungunya virus (CHIKV). (Upper panel) All 188 nearly-full or full genome CHIKV sequences available in the National Center for Biotechnology Information nucleotide database as of March 2015, including the 3 new genomes from Puerto Rico recovered in this study (red boldface) were aligned by using the multiple alignment fast Fourier transform (MAFFT) algorithm, and phylogenetic trees were constructed by using the MrBayes algorithm in the Geneious software package (12). Branch lengths are drawn proportionally to the number of nucleotide substitutions per position, and support values are shown for each node. (Lower panel) Molecular clock analysis of the Southeast Asian/Pacific branch containing the Caribbean sublineage (pink) was performed by using BEAST software (13). Branch lengths are drawn proportionally to the number of years before January 1, 2015, and the number of years is shown for each node. The 3 major lineages and Caribbean-associated sublineage are shown in different colors, and the nodes corresponding to the Caribbean (orange) and Puerto Rico (red) offshoots are highlighted.