Phylogenetic Investigation of Norovirus Transmission between Humans and Animals

Figures

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  Figure 1. Genetic characterization of GII.4 sequences found in animals. A maximum-likelihood tree based on 223 bp GII.4 sequences was inferred with PhyML v3.0 software using the general time reversible nucleotide substitution model (GTR + G). Sequences that were found in animals (red) were aligned with most closely related human sequences (black) and the reference sequences from the noronet typing tool (blue, black circle). The animal in which norovirus was found as well as the date and country of collection are indicated next to the sequence. The scale bar indicates nucleotide substitutions per site.

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  Figure 2. Genetic characterization of non-GII.4 GII sequences found in animals. A maximum-likelihood tree based on 180 bp GII sequences was inferred with PhyML v3.0 software using the general time reversible nucleotide substitution model (GTR + G). Sequences that were found in animals (red) were aligned with most closely related human sequences (black) and the reference sequences from the noronet typing tool (blue, black circle). The animal in which norovirus was found as well as the date and country of collection are indicated next to the sequence. The scale bar indicates nucleotide substitutions per site.

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  Figure 3. Genetic characterization of GI sequences found in animals. A maximum-likelihood tree based on 271 bp GI sequences was inferred with PhyML v3.0 software using the general time reversible nucleotide substitution model (GTR + G). Sequences that were found in animals (red) were aligned with most closely related human sequences (black) and the reference sequences from the noronet typing tool (blue, black circle). The animal in which norovirus was found as well as the date and country of collection are indicated next to the sequence. The scale bar indicates nucleotide substitutions per site.

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  Figure 4. Molecular clock phylogeny of the complete VP1 gene sequences for GII.7 (A) and GII.17 (Kawasaki308 cluster) (B) constructed by the Bayesian Markov chain Monte Carlo (MCMC) method. Sequences in red indicate sequences from animal origin. Node bars indicate the 95% HPDs of the time of the most common recent ancestor. Numbers in the nodes show the posterior densities (only values > 0.7 are shown). The expanded GII.17 tree is shown in Supplementary Figure S1.

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  Figure 5. Mapping of amino acid differences between human strains found in animals versus humans onto p-dimers (the two subunits are shown in two shades of grey, top-view). Amino acid changes exclusively found in the strains detected in animals are colored in turquoise. Predicted HBGA binding sites are marked in red, and the epitopes A-G in color. Changes were mapped onto the p-domain GII.7 3D structure predicted by SWISS-MODEL on the basis of the crystal structure of the p-domain of a GII.17 strain (PDB number 5f4o.1) for GII.7 (KT943504 and KT943505) (A) and GII.17 Kawasaki (5LKG) for GII.17 (KX356908) (B). The alignment was performed with MEGA ClustalW and shows the amino acids defining the antigenic sites [17] that differ between strains found in animals and humans (C). Amino acid numbering was based on GII.4 2004. Putative binding sites were taken from reference [37].