Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains

Figures

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  Fig 1. Lineage constellation of representative G2P[4] and representative genotype 2 reassortant strains. Lineage colours for I-V, VII and VII (for VP3 and NSP4) were adapted from Doan et al.’s [39] G2P[4] lineage designation.

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  Fig 2. Host distribution/isolation source of genotype 2 genes retrieved from the GenBank using the virus variation rotavirus resource.

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  Fig 3. Reference phylogenetic lineage designation for the VP1-R2 genotype of RVA strains of human and animal host species origin. Phylogenetic tree was constructed using the maximum likelihood method with 1000 bootstrap replicate trials. The tree was rooted using the VP1-R1 gene of the genotype 1 prototype strain Wa. “Hybrid lineages” containing a mixture of human and animal RVA sequences are indicated with § in addition to the lineage number. Representative unusual emerging reassortant strains whose lineage constellations were determined in this study using the newly established phylogenetic framework are indicated in red font. Scale bar at the bottom of the tree represents genetic distance expressed as nucleotide substitutions/site.

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  Fig 4. Reference phylogenetic lineage designation for the VP2-C2 genotype of RVA strains of human and animal host species origin. Phylogenetic tree was constructed using the maximum likelihood method with 1000 bootstrap replicate trials. The tree was rooted using the VP2-C1 gene of the genotype 1 prototype strain Wa. “Hybrid lineages” containing a mixture of human and animal RVA sequences are indicated with § in addition to the lineage number. Representative unusual emerging reassortant strains whose lineage constellations were determined in this study using the newly established phylogenetic framework are indicated in red font. Scale bar at the bottom of the tree represents genetic distance expressed as nucleotide substitutions/site.

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  Fig 5. Reference phylogenetic lineage designation for the VP3-M2 genotype of RVA strains of human and animal host species origin. Phylogenetic tree was constructed using the maximum likelihood method with 1000 bootstrap replicate trials. The tree was rooted using the VP3-M1 gene of the genotype 1 prototype strain Wa. “Hybrid lineages” containing a mixture of human and animal RVA sequences are indicated with § in addition to the lineage number. Representative unusual emerging reassortant strains whose lineage constellations were determined in this study using the newly established phylogenetic framework are indicated in red font. Scale bar at the bottom of the tree represents genetic distance expressed as nucleotide substitutions/site.

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  Fig 6. Reference phylogenetic lineage designation for the VP6-I2 genotype of RVA strains of human and animal host species origin. Phylogenetic tree was constructed using the maximum likelihood method with 1000 bootstrap replicate trials. The tree was rooted using the VP6-I1 gene of the genotype 1 prototype strain Wa. “Hybrid lineages” containing a mixture of human and animal RVA sequences are indicated with § in addition to the lineage number. Representative unusual emerging reassortant strains whose lineage constellations were determined in this study using the newly established phylogenetic framework are indicated in red font. Scale bar at the bottom of the tree represents genetic distance expressed as nucleotide substitutions/site.

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  Fig 7. Reference phylogenetic lineage designation for the NSP1-A2 genotype of RVA strains. Phylogenetic tree was constructed using the maximum likelihood method with 1000 bootstrap replicate trials. The tree was rooted using the NSP1-A1 gene of the genotype 1 prototype strain Wa. Representative unusual emerging reassortant strains whose lineage constellations were determined in this study using the newly established phylogenetic framework are indicated in red font. Scale bar at the bottom of the tree represents genetic distance expressed as nucleotide substitutions/site.

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  Fig 8. Reference phylogenetic lineage designation for the NSP2-N2 genotype of RVA strains of human and animal host species origin. Phylogenetic tree was constructed using the maximum likelihood method with 1000 bootstrap replicate trials. The tree was rooted using the NSP2-N1 gene of the genotype 1 prototype strain Wa. “Hybrid lineages” containing a mixture of human and animal RVA sequences are indicated with § in addition to the lineage number. Representative unusual emerging reassortant strains whose lineage constellations were determined in this study using the newly established phylogenetic framework are indicated in red font. Scale bar at the bottom of the tree represents genetic distance expressed as nucleotide substitutions/site.

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  Fig 9. Reference phylogenetic lineage designation for the NSP3-T2 genotype of RVA strains. Phylogenetic tree was constructed using the maximum likelihood method with 1000 bootstrap replicate trials. The tree was rooted using the NSP3-T1 gene of the genotype 1 prototype strain Wa. Representative unusual emerging reassortant strains whose lineage constellations were determined in this study using the newly established phylogenetic framework are indicated in red font. Scale bar at the bottom of the tree represents genetic distance expressed as nucleotide substitutions/site.

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  Fig 10. Reference phylogenetic lineage designation for the NSP4-E2 genotype of RVA strains of human and animal host species origin. Phylogenetic tree was constructed using the maximum likelihood method with 1000 bootstrap replicate trials. The tree was rooted using the NSP4-A1 gene of the genotype 1 prototype strain Wa. “Hybrid lineages” containing a mixture of human and animal RVA sequences are indicated with § in addition to the lineage number. Representative unusual emerging reassortant strains whose lineage constellations were determined in this study using the newly established phylogenetic framework are indicated in red font. Scale bar at the bottom of the tree represents genetic distance expressed as nucleotide substitutions/site.

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  Fig 11. Reference phylogenetic lineage designation for the NSP5-H2 genotype of RVA strains. Phylogenetic tree was constructed using the maximum likelihood method with 1000 bootstrap replicate trials. The tree was rooted using the NSP5-A3 gene of the genotype 3 prototype strain AU-1. Representative unusual emerging reassortant strains whose lineage constellations were determined in this study using the newly established phylogenetic framework are indicated in red font. Scale bar at the bottom of the tree represents genetic distance expressed as nucleotide substitutions/site.