Extended analyses of rotavirus C (RVC) G-types and P-types reveal new cut-off value for the G-types and reclassification of strains

Figures

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  Fig 1. Phylogenetic analyses and pairwise identity frequency distribution graph for the G-type (VP7). (A) Phylogenetic tree based on the ORF nucleotide sequences of the VP7 gene (G-type) of RVC strains. The dendrogram was constructed in MegaX using Maximum Likelihood with General Time Reversible Model + G + I and 1,000 bootstrap replicates. Genotypes are represented by compressed clusters and designated on the right; the accession number of the respective reference strain is shown in brackets. The determined cut-off value of 82% is shown by the vertical line. (B) Nucleotide pairwise identity frequency graph of 295 complete VP7 ORF sequences. The proposed 82% nucleotide cut-off value is shown by the vertical line. (C) Phylogenetic tree based on the ORF nucleotide sequences of the VP7 gene (G-type) of RVC strains. The dendrogram was constructed in MegaX using Maximum Likelihood with General Time Reversible Model + G + I and 1,000 bootstrap replicates. The visualization of the tree was conducted using iTOL (58). Symbols (filled dots) indicate the sequences (n = 138) obtained in this study. Genotypes are specified with colored branches and associated designation outside of the tree.

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  Fig 2. Phylogenetic analyses and pairwise identity frequency distribution graph for the P-type (VP4). (A) Phylogenetic tree based on the ORF nucleotide sequences of the VP4 gene (P-type) of RVC strains. The dendrogram was constructed in MegaX using Maximum Likelihood with General Time Reversible Model + G + I and 1,000 bootstrap replicates. Genotypes are represented by compressed clusters and designated on the right; the accession number of the respective reference strain is shown in brackets. The current cut-off value of 85% is shown by the vertical line. (B) Nucleotide pairwise identity frequency graph of 165 complete VP4 ORF sequences. The current 85% nucleotide cut-off value is shown by the vertical line. (C) Phylogenetic tree based on the ORF nucleotide sequences of the VP4 gene (P-type) of RVC strains. The dendrogram was constructed in MegaX using Maximum Likelihood with General Time Reversible Model + G + I and 1,000 bootstrap replicates. The visualization of the tree was conducted using iTOL (58). Symbols (filled dots) indicate the sequences (n = 97) obtained in this study. Genotypes are specified with colored branches and associated designation outside of the tree.

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  Fig 3. Subtree of cluster G1 displayed separately from the detailed phylogenetic tree of VP7 (Fig. S1). The dendrogram was constructed in MegaX using Maximum Likelihood with General Time Reversible Model + G + I and 1,000 bootstrap replicates. Symbols (filled dots) indicate the sequences obtained in this study. Subtypes are specified with brackets and associated designation on the right.

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  Fig 4. Subtree of cluster G5 displayed separately from the detailed phylogenetic tree of VP7 (Fig. S1). The dendrogram was constructed in MegaX using Maximum Likelihood with General Time Reversible Model + G + I and 1,000 bootstrap replicates. Symbols (filled dots) indicate the sequences obtained in this study. Subtypes are specified with brackets and associated designation on the right.

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  Fig 5. Subtree with compressed subclusters of cluster G6 displayed separately from the detailed phylogenetic tree of VP7 (Fig. S1). The dendrogram was constructed in MegaX using Maximum Likelihood with General Time Reversible Model + G + I and 1,000 bootstrap replicates. Subtypes are designated on the right.

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  Fig 6. Nucleotide pairwise identity frequency graph of 102 complete VP4 ORF sequences without the genotype P21. The current 85% nucleotide cut-off value is shown by the vertical line.