Evolutionary and Genetic Recombination Analyses of Coxsackievirus A6 Variants Associated with Hand, Foot, and Mouth Disease Outbreaks in Thailand between 2019 and 2022

Figure 1. Temporal distribution of enteroviral infections, by epidemiological month, Thailand, 2019–2022 (n = 755).

Figure 2. Phylogenetic comparisons of sequences from partial VP1 and 3Dpol. Phylogenetic comparisons of sequences from (A) partial VP1 (nt positions 2630–3286, 657 bp) and (B) partial 3Dpol (nt positions 6188–7388, 1200 bp) using samples and sequences of other coxsackievirus (CV)-A6 variants obtained from GenBank. Maximum-likelihood trees were reconstructed using 1000 bootstrap re-samples to demonstrate the robustness of groupings; values ≥ 70% are shown.

Figure 3. Unrooted phylogenetic trees of coxsackievirus (CV)-A6 strains based on different genomic regions. Maximum-likelihood trees were constructed based on the 5′-UTR and the P1, P2, and 3Dpol regions. Sequences are numbered according to the numbering of the Gdula prototype strain (GenBank accession number AY421764) and previously referenced sequences. Bootstrap values at key nodes are shown as percentages of 1000 replicates. The nearly complete genome sequences of the 20 CV-A6/TH strains, obtained in this study, are highlighted using colored dots. The scale bars represent the number of substitutions per site.

Figure 4. Time-scaled phylogenetic tree of VP1 sequences of coxsackievirus (CV)-A6 variants. The phylogenetic tree was generated using CV-A6 VP1 sequences characterized in this study (red) and previously published sequences. A maximum clade credibility tree was constructed from 10,000 trees, sampled from the posterior distribution with mean node ages. Clades described in previous studies (A, B, C, D1, D2, and D3) are shown. Several subclades were associated with severe hand, foot, and mouth outbreaks in Thailand; posterior probability support is provided. Branch colors denote different countries.

Figure 5. (A) Schematic diagram of the enteroviral (EV) genome structure. (B) Recombination analysis of putative recombinant coxsackievirus (CV)-A6 strains. SimPlot analysis of the recombinant strain CVA6-CU3494. The vertical axis represents the nucleotide sequence similarity (%) between the putative recombinant strain and other EV-A lineages, constructed using SimPlot v3.5.1 with a window size of 200 nt and a step size of 20 nt. (C) Bootscan plot of recombination events between the daughter strain EVA71-CU3494 and major (CV-A6) or minor (CV-A10) parental strains. The bootstrapping support value was computed using the RDP4 program with a window size of 200 nt, a step size of 10 nt, and 1000 bootstrap replicates. (D) Amino acid changes between the CV-A6 subclade and the D3/A and D3/Y strains.