Figure 1.

Phylogenetic analysis of Nicaraguan chikungunya viruses (CHIKV). (A) Nicaraguan CHIKV belongs to the Caribbean clade of the Asian genotype. Phylogenetic analysis included 37 full-length genomic nucleotide sequences (one Nicaraguan strain and 36 reference strains), with the format of country/strain/GenBank no./year. The three major genotypes and two clades are labeled. Bootstrap values are shown on major branches. (B) Mutations in the E1 gene of Nicaraguan CHIKV. This analysis included E1 gene sequences of 19 representative monthly Nicaraguan CHIKV strains, with the format of country/strain/GenBank no./year month, and E1 sequences of seven reference strains in the format of country/strain/GenBank no./year. For simplicity, each month only one sample identical to and all the samples different from the BritishVirginIslands/99659/KJ451624/2014 strain were included in the subtree, resulting in elimination of 14 duplicate identical Nicaraguan CHIKV sequences from the subtree. The relevant mutations are indicated at each branch point. Both trees are drawn to scale, with branch lengths measured in the number of substitutions per site. Bootstrap values are shown on major branches. All positions containing gaps and missing data were eliminated. Phylogenetic analyses were conducted in MEGA6.¹⁵