Table 1.
Primer sets used for coxsackievirus A24 variant.
Fig 1.
Comparison of coxsackievirus A24v strains in (A–C) 305 codon sites of 111 VP1 sequences and in (D–F) 230 codon sites of 44 3Dpol sequences. (A, D) Secondary structure guide (PDB ID codes 4Q4V for VP1, 2IJD for 3Dpol products). (B, E) Consensus residues graphically depicted by Weblogo. (C, F) Entropy-based variability plotted by DEMBA.
Fig 2.
Maximum clade credibility phylogeny of 111 VP1 sequences of coxsackievirus A24v without outgroup.
Blue bars at nodes indicate 95% HPDs of TMRCAs. Branch color indicates the likely location, and branch thickness indicates posterior probability from Bayesian inference (PP-BMCMC). Support values are also shown for major nodes and are indicated as BS-NJ/BS-ML/PP-BMCMC, where BS is the bootstrap value, NJ indicates the neighbor-joining method, and ML indicates the maximum likelihood method. The VP1 genotypes are shown on the right and are distinguished by color. Within-genotype nucleotide and amino acid similarities are also shown on the right. For comparison, the 3Dpol genotypes are distinguished by shading (GA: purple, GB: green, GC: yellow, GD: orange, and GE: blue). The branch length indicates the evolution time, and the scale bar at the bottom indicates the calendar time.
Fig 3.
Bayesian skyline plots of (A) 111 VP1 sequences, (B) 11 VP1 sequences of genotype III strains, and (C) 99 VP1 sequences genotype IV strains. The x-axis is the time scale (years), and the y-axis is the logarithmic Neτ scale (where Ne is the effective population size and τ is the generation time). The thick solid line indicates the median estimates, and the shaded area indicates the 95% highest posterior density.
Fig 4.
Maximum clade credibility phylogeny of 111 VP1 sequences of coxsackievirus A24v with outgroups.
Branch thickness indicates support value (posterior probability, PP), and branch color indicates the most probable location. Support values for major nodes are also shown. The right side of the figure shows within-genotype nucleotide/amino acid similarities. The VP1 genotypes for each strain are distinguished by color (Genotype I: purple, Genotype III: orange, and Genotype IV: blue). The 3Dpol genotypes for each strain are distinguished by shading. Evolution time is indicated by branch length (see scale bar).