Genetic Characterizations and Molecular Evolution of VP7 Gene in Human Group A Rotavirus G1

Figures

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  Figure 1. Phylogenetic relationship of RVA G1 strains based on the complete genome of the VP7 gene using maximum likelihood method. Red and light purple dots indicate Rotarix and RotaTeq vaccine reference strains, respectively.

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  Figure 2. Distribution of nucleotide pairwise distances of RVA G1 VP7 strains: (a) all analyzed strains, (b) lineage I, (c) lineage II.

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  Figure 3. (a) Shannon entropy comparison between two lineages with significant differences colored in red. (b) Amino acid alignment between two lineages with significant specific amino acid residues labeled with asterisks.

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  Figure 4. Root-to-tip divergence plots of the RVA G1 VP7 gene: (a) all analyzed strains, (b) lineage I, (c) lineage II. The Y-axis indicates the root-to-tip divergence based on the maximum likelihood tree, and the X-axis indicates the collection year. Each strain is represented by a circle, and the dashed line indicates a locally weighted scatterplot smoothing (LOWESS) line.

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  Figure 5. Accumulation plots of amino acid over time of the RVA G1 VP7 gene: (a) Lineage I, (b) lineage II. The X-axis indicates the timespan of collection, and the Y-axis shows the mean amino acid difference. The dashed line indicates a linear regression line.

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  Figure 6. Time-scaled phylogenetic tree of RVA G1 VP7 gene by using the Bayesian Markov Chain Monte Carlo method. Branches are scaled in time and strains are colored according to sub-lineages. Node bars indicate 95% highest posterior densities of the most recent common ancestor.

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  Figure 7. Bayesian skyline plots of RVA G1 VP7 gene: (a) all analyzed strains, (b) lineage I, (c) lineage II. The Y-axis indicates the effective population size. Mean effective population is shown as a black line. The 95% highest posterior densities are shown as light blue lines.