Article Figures & Data
Figures
- FIG 1
Evolutionary dynamics of the major capsid protein of GII.2 noroviruses. (a) Maximum likelihood phylogenetic tree of VP1-encoding (nt) sequences from GII.2 strains. The numbers on the ancestral nodes of the clusters represent the node support value calculated by the approximate likelihood-ratio test using PhyML. (b) Root-to-tip divergence plot of VP1 nt sequences of GII.2 strains. The x axis indicates isolation year, and the y axis shows the root-to-tip divergence on the maximum likelihood phylogenetic tree. The black line indicates a linear regression line of the root-to-tip divergence and isolation year. A total of 151 sequences were included for both analyses. Each strain is represented by a circle and colored according to its polymerase genotype. Strains whose polymerase genotype was not available are indicated in black. The genomic region used in the analyses spanned nt 5085 to 6419 relative to Snow Mountain virus (GenBank accession number AY134748 ). (c) The kernel density plot indicates the posterior estimates of substitution rate (substitutions/site/year) of VP1 nt sequences. To calculate the substitution rate of the VP1 associated with different polymerases, strains were clustered using the VP1 phylogenetic tree. Thus, the P2 cluster is shaded in red, the P16 cluster in green, and the P2-P16 mix in yellow. The overall rate is indicated by black shading.
- FIG 2
Amino acid diversification of the major capsid protein of GII.2 noroviruses. (a) Heat map indicating the accumulation of aa mutations in the partial VP1 sequences of GII.2 strains (445 amino acids) over time. The x axis indicates the pairwise aa mutations, and the y axis indicates isolation year. The number of pairwise comparisons is represented by the color gradient in the heat map. (b) The plot indicates the substitution rates (substitutions/site/year) of VP1 nucleotide sequences at each codon position. The mean and the 95% highest posterior density intervals are indicated. The substitution rates were calculated using the same sequence matrix and groups as those represented in Fig. 1.
- FIG 3
Positive evolution of the major capsid protein of GII.2 noroviruses. Maximum likelihood trees of VP1 nucleotide (nt) sequences of GII.2 indicate the branches under possible positive selection. The branches with evidence of positive selection (empirical Bayes factor of >10, P < 0.05; estimated using the mixed-effect model of evolution [MEME] method) at codon positions 344 (a), 345 (b), 384 (c), and 385 (d) are represented by red branch lines. The color shade indicates the phylogenetic clustering based on the polymerase genotype as indicated in Fig. 1. Reemerging GII.P16-GII.2 strains are indicated in blue.
- FIG 4
Evolutionary dynamics of the GII.2 polymerase. (a) Maximum likelihood trees of RdRp-encoding (nt) sequences of strains GII.P2 (n = 72) and GII.P16 (n = 131). Phylogenetic clusters based on VP1 nt sequences (Fig. 1) are shown here; the P2 cluster is represented in red, the P16 cluster in green, and the P2-P16 mix cluster in yellow. Reemerging GII.P16 strains, including GII.P16-GII.2 and GII.P16-GII.4, are indicated in blue. Each strain is represented by a circle, with different colors according to the associated capsid genotypes; GII.P2-GII.2 and GII.P16-GII.2 strains are indicated by red and green, respectively. The numbers on the ancestral nodes of the clusters represent the node support value calculated by the approximate likelihood-ratio test using PhyML. (b) The root-to-tip divergence plot of RdRp-encoding (nt) sequences of GII.P2 and GII.P16 strains. The x axis indicates isolation year, and the y axis shows the root-to-tip divergence on the maximum likelihood phylogenetic tree. The black lines indicate a linear regression line of the root-to-tip divergence and isolation year. Each strain is colored according to its capsid genotype. The genomic regions used spanned nt 4385 to 5104 relative to Snow Mountain virus (GenBank accession number AY134748 ). (c) The kernel density plot indicates the posterior estimates of substitution rate (substitutions/site/year) among GII.P2, GII.P16, and GII.P16 without reemerging strains. (d) Structural mapping of the amino acid (aa) substitutions in the reemerging GII.P16-GII.2 strains. Conservative mutations in the RdRp aa sequence from the reemerging GII.P16 strains compared to pre-2016 GII.P16 strains (P16 cluster and P2-P16 mix cluster) are mapped on the structural model of a GII.P4 RdRp (PDB number 4QPX ). The molecular model was visualized using Chimera v.1.11. aa substitutions are indicated in blue. Residue 291, a residue that was shown by Bull et al. (46) to alter the incorporation rate of GII.4 polymerases, is indicated in red.
Tables
- TABLE 1
Amino acid substitution observed in the consensus VP1 sequence among phylogenetic clusters
Strain or cluster No. of sequences Amino acid substitution at codon: 71 130 303 335 344 354 364 386 400 Reemerging GII.P16-GII.2 (2016) 27 A V V I (1 V)a S (1G)a G A N E P2-P16 mix clusterb (2005–2015) (without reemerging strains) 9 A V V I (2 V)a S G A N E P16 clusterb (2008–2014) 38 S V V V T (1 I, 2 A)a A A N D (2 E)a P2 clusterb (2007–2010) 29 A I (4 V)a I (1 V)a I S G A S E P2 clusterb (2004–2006) 18 A V V V S G S (1P)a N E - TABLE 2
Codon position of VP1 sequences (1,337 nucleotides) with positive selection
Positively selected site Method(s) (P value) Domain 24 MEMEa (0.015) N terminus 78 iFELb (0.015) Shell 275 MEME (0.016) P1 344 MEME (0.039) P2 (surface) 345 iFEL (0.01), MEME (0.020) P2 (surface) 384 MEME (0.01) P2 (surface) 385 MEME (0.024) P2 (surface) 397 iFEL (0.045) P2 (surface)
FIG S1
Histogram of the pairwise p-distance of VP1 nucleotide (nt) sequences among GII.2 strains (n = 151). The pairwise distance data for three strains from the GII.P21 cluster (including two strains with unknown polymerase genotypes [KC998960 and AY660568 ] and JQ320072 ) and three from the GII.P22 cluster (DQ366347 , AB279554 , and AB279556 ) are indicated in black. The genomic region used spanned nt 5085 to 6713 of Snow Mountain virus (GenBank accession number AY134748 ). Download FIG S1, TIF file, 1 MB.
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FIG S2
Evolutionary dynamics of the major capsid protein of GII.2 noroviruses. Evolutionary dynamics of VP1 was analyzed by using full-length VP1-encoding (nt) sequences. (a) Maximum likelihood phylogenetic tree of VP1 nt sequences from GII.2 strains. The numbers on the ancestral nodes of the clusters represent the node support values calculated by the approximate likelihood-ratio test using PhyML. (b) Root-to-tip divergence plot of VP1 nt sequences of GII.2 strains. The x axis indicates isolation year, and the y axis shows the root-to-tip divergence on the maximum likelihood phylogenetic tree. The black line indicates a linear regression line of the root-to-tip divergence and isolation year. A total of 134 sequences are included for both analyses. Each strain is colored according to its polymerase genotype. Strains whose polymerase genotype was not available are indicated in black. The genomic region used in the analyses spanned nt 5085 to 6713 relative to Snow Mountain virus (GenBank accession number AY134748 ). (c) The kernel density plot indicates the posterior estimates of substitution rates (substitutions/site/year) of VP1 nt sequences. To calculate the substitution rate of the VP1 protein associated with different polymerases, strains were clustered using the VP1 phylogenetic tree. Thus, the P2 cluster is shaded in red, the P16 cluster in green, and the P2-P16 mix in yellow. The overall rate is indicated by black shading. Download FIG S2, TIF file, 1.9 MB.
Copyright © 2017 Tohma et al.
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TABLE S1
Data set. Download TABLE S1, PDF file, 0.04 MB.
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FIG S3
Amino acid diversification of the major capsid protein of GII.2 noroviruses. The heat map indicates the accumulation of aa mutations in the complete VP1 of GII.2 strains (543 amino acids) over time. The x axis indicates the pairwise aa mutations, and the y axis indicates isolation year. The number of pairwise comparisons is represented by the color gradient in the heat map. Download FIG S3, TIF file, 0.3 MB.
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FIG S4
Maximum likelihood phylogenetic tree of VP1 amino acid sequences of GII.2 strains. Each strain is colored according to its polymerase genotype. Strains whose polymerase genotype was not available are indicated in black. A total of 151 sequences were included in the analysis. The genomic region used spanned nt 5085 to 6419 relative to Snow Mountain virus (GenBank accession number AY134748 ). The numbers on the ancestral nodes of the clusters represent the node support value calculated by the approximate likelihood-ratio test using PhyML. The color shade indicates the phylogenetic clustering based on the polymerase genotype as indicated in Fig. 1. Download FIG S4, TIF file, 1.1 MB.
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TABLE S2
Codon position of complete VP1 sequences (1,629 nt) with positive selection. Download TABLE S2, PDF file, 0.03 MB.
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FIG S5
Maximum likelihood trees of the RdRp amino acid sequences. Trees were built using GII.P2 (n = 72) (a) and GII.P16 (n = 131) (b) strains. Phylogenetic clusters based on VP1 nt sequences (Fig. 1) are shown here; the P2 cluster is represented in red, the P16 cluster in green, and the P2-P16 mix cluster in yellow. Reemerging GII.P16 strains, including GII.P16-GII.2 and GII.P16-GII.4, are indicated in blue. Each strain is represented by a circle, with different colors according to the associated capsid genotypes; GII.P2-GII.2 and GII.P16-GII.2 strains are indicated by red and green, respectively. The numbers on the ancestral nodes of the clusters represent the node support value calculated by the approximate likelihood-ratio test using PhyML. Download FIG S5, TIF file, 1.5 MB.
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TABLE S3
Amino acid substitution observed in the RdRp sequence of reemerging GII.P16 strains. Download TABLE S3, PDF file, 0.03 MB.
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FIG S6
Maximum clade credibility (MCC) tree of GII.2 strains. VP1-encoding sequences of GII.2 strains (n = 151) (a), RdRp-encoding sequences from GII.P2 strains (n = 72) (b), and GII.P16 strains (n = 131) (c) were used for tree reconstructions. Each strain in the VP1 MCC tree is colored according to its polymerase genotype (a), and each strain in the RdRp MCC trees is colored by its capsid genotype (b and c). Strains whose polymerase genotype was not available are indicated in black. Reemerging GII.P16-GII.2 strains are indicated by blue shading. Arrows indicate the means and 95% highest posterior density intervals of the time of the most recent common ancestor. Phylogenetic clustering is indicated by color as described for Fig. 1. The numbers on the ancestral nodes of the clusters represent the posterior probability values of the nodes. The x axis and branch length represent the year. Estimated divergence time is indicated on the node of common ancestors of phylogenetic clustering. Download FIG S6, TIF file, 2.3 MB.
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TABLE S4
Evolutionary models used in BEAST analyses. Download TABLE S4, PDF file, 0.03 MB.
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