FIG 3.

Phylogenetic analysis of EV-A71 genotypes B and C. Neighbor-joining phylogenetic analysis of EV-A71 genotypes B and C was based on their P2-P3 genome region, rooted by the coxsackievirus (CV) A16 prototype strain G10 (isolated in 1951). The subtrees show mixed clusters of evolutionary intra- and intertypic recombination events of analyzed EV-A71 sequences (n = 182). EV-A71 subgenotypes and genotypes are depicted in different colors. The subgenotype B5 (orange arrow) is located within the genotype B cluster, showing a ladder-like evolutionary scale. In contrast to other subgenotypes of genotype C, the subgenotype C4 (labeled in green) forms an outgroup of genotype C, close to other recombinogenic EV-A71 strains (e.g., B3 and C2-like) and the prototype CV-A16 sequence. The probabilities of replicate trees in which associated taxa clustered together in the bootstrapped data (1,000 replicates) are shown next to the branches. The phylogenetic tree is drawn to scale, with branch lengths representing the numbers of base substitutions per site.