Phylogenetic molecular evolution and recombination analysis of complete genome of human parechovirus in Thailand

Figures

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  Figure 1. Phylogenetic tree of the complete genome of HPeV. The tree was constructed using the BEAST program under the relaxed clock-uncorrelated exponential with 10 million chains, and was run in the Genetic Testing Registry (GTR) with a gamma distribution substitution model. Each branch is labeled as GenBank accession number/genotype/strain name/origin country/year of collection. The genotype was classified based on the cluster on the VP3/VP1 gene. The samples from this study are indicated with a darkened circle. The most recent common ancestors (tMRCAs) are defined at the tree node, and the highest posterior density (HPD) is indicated at each tree branch.

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  Figure 2. Phylogenetic tree of the P1 (A), P2 (B), and P3 (C) of HPeV. The tree was constructed using the BEAST program under the relaxed clock-uncorrelated exponential with 10 million chains, and was run in the Genetic Testing Registry (GTR) with a gamma distribution substitution model. Each branch is labeled as GenBank accession number/genotype/strain name/origin country/year of collection. The samples from this study are indicated with a darkened circle. The most recent common ancestors (tMRCAs) are defined at the tree node, and the highest posterior density (HPD) is indicated at each tree branch.

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  Figure 3. The matrix revealed a recombination event and genetic diversity of the human parechovirus (HPeV) genome. The hot spectrum of recombination region count matrix (upper part of A) indicated discordance of inheritance along the entire genome. High genetic diversity has been typically found in the virus's structural protein (hot spectrum of the lower part of A). The breakpoint hotspots for recombination in this study appeared in the junctions between VP3 and VP1, and between 2C and 3A (upper matrix of B). In comparison, the breakpoint hotspots in the reference sequences that are published in the database are shown between VP1 and 2A (lower matrix of B).

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  Figure 4. Recombination analysis of B1091/HPeV14/TH/2011. The Bootscan analysis (A) was performed using the RDP4 recombination detection program with a sliding window of 200 nucleotides. The result indicated two breakpoints (BPs) between the junctions of VP3 and VP1, and between VP1 and 2A region of the viral genome. These two BPs were confirmed using direct Sanger sequencing (B).