Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Sapovirus GI.1 and GI.2

Figures

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  Figure 1. Time-scaled phylogenetic tree of the HuSaV GI.1 constructed by the Bayesian MCMC method: RdRp region (A); and VP1 gene (B). Time-scaled phylogenetic tree of the HuSaV GI.2 constructed by the Bayesian MCMC method: RdRp region (C); and VP1 gene (D). The horizontal axis represents time (years). Blue bars indicate the 95% HPD for a branched year.

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  Figure 2. Evolutionary rates of each sequence in the HuSaV of RdRp region and VP1 gene. The y-axis represents the evolutionary rate (substitutions/site/year), and the x-axis indicates each genotype and cluster. The black circles indicate the mean and the bars indicate the intervals of 95% HPD. The detailed evolutionary rates are shown in Supplementary Table S3.

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  Figure 3. Phylodynamics of the RdRp region and VP1 genes in HuSaV GI.1 and GI.2 determined using BSP analysis. The y-axis represents the effective population size on the logarithmic scale and the x-axis indicates the time in years. The thick line (blue) shows the median value over time. The intervals with the HPDs (95%) are shown by thin lines (blue).

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  Figure 4. Phylogenetic distances of the RdRp region (A); and VP1 gene (B) in HuSaV GI.1 and GI.2, illustrated by violin plots. The width of the violin plot represents the kernel density, indicating the distribution shape of the data. Total HuSaV GI.1, GI.1 Cluster A, GI.1 Cluster B, and HuSaV GI.2 are illustrated in light blue, red, green, and gold. The central box plot (black) and white dots represent the interquartile range and the median, respectively. The whiskers from the box plots represent the data intervals. The detailed statistical data are shown below the violin plots. There were significant differences in all combinations of genotypes and clusters (unpaired t test; p < 0.0001).

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  Figure 5. Similarity plot analysis of the VP1 gene in HuSaV GI.1. Nucleotide similarity to the prototype strain (GenBank accession no. MN794208, collected in 1977) was calculated using SimPlot analysis. Total HuSaV GI.1, GI.1 Cluster A, and GI.1 Cluster B are illustrated in black, red, and blue. Nucleotide position numbers correspond to the VP1 gene in the prototype strain. The positions of each subunit are shown below the graph [1].

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  Figure 6. Structural models of the RdRp dimer proteins and mapping of predicted conformational epitopes. Chains A and B are colored by gray and light gray, respectively. The predicted conformational epitopes are shown in blue. The strains are as follows: (A) GI.1 prototype strain collected in 1977 (MN794208); (B) GI.1 strain belonging to Cluster A collected in 2020 (LC671561); (C) GI.1 strain belonging to Cluster B collected in 2020 (OP654153); (D) GI.2 prototype strain collected in 1978 (MN794205); (E) GI.2 strain collected in 2018 (MN510438); and (F) the sites and the number of methods predicted as epitopes and visualized in heat maps. Amino acid residues predicted as conformational B-cell epitopes by 0, 1, 2, 3, 4, and 5 of the five methods are shown in dark blue, blue, dark green, green, yellow, and white.

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  Figure 7. Structural models of the VP1 trimer proteins and mapping of predicted conformational epitopes. Chains A, B, and C are colored in dark gray, light gray, and white, respectively. The predicted conformational epitopes are shown in blue. The strains are as follows: (A) GI.1 prototype strain collected in 1977 (MN794208); (B) GI.1 strain belonging to Cluster A collected in 2020 (LC671561); (C) GI.1 strain belonging to Cluster B collected in 2020 (OP654153); (D) GI.2 prototype strain collected in 1978 (MN794205); (E) GI.2 strain collected in 2018 (MN510438); and (F) the sites and the number of methods predicted as epitopes and visualized in heat maps. Amino acid residues predicted as conformational B-cell epitopes by 0, 1, 2, 3, 4, and 5 of the five methods are shown in dark blue, blue, dark green, green, yellow, and white.