Epochal Evolution of GGII.4 Norovirus Capsid Proteins from 1995 to 2006

Neighbor-joining tree for complete capsid amino acid sequences. Type strains from GenBank were used in order to emphasize and confirm the groupings. Branch lengths are drawn to scale. Bootstrap values are percentages of 1,000 iterations.

Fixed amino acid changes (informative sites) in capsid sequences of GGII.4 outbreak strains collected between 1995 and 2006. The informative sites throughout the protein are listed from left to right. Amino acid numbering is indicated at the top, and outbreak dates (month-year of isolation, e.g., 01-95 is January 1995) and names are given on the left. From top to bottom, the same color indicates identical amino acids, and different colors are distinct amino acids. Colors were assigned by frequency; amino acids that occurred most are shown in green, followed by red, blue, and yellow (diminishing frequencies). The amino acids circled in magenta are part of the additional RGD motif present in the 2002 variant and the earliest strain. The arrow at the top indicates where an amino acid insertion occurred. The orange bars at the bottom indicate the locations of insertions in GGII.4 compared to NV and correspond to insertions 1 to 3 in Fig. 5A. Asterisks indicate hypervariable sites (with more than one mutation), and the arrows below the sequences indicate the sites where an amino acid mutation occurs at each variant change (not including 2006a). Domains are indicated in the bar below the figure.

Graph showing the prevalence of GGII.4 variant types in The Netherlands between January 1995 and February 2007. Genotype and variant type assignments were done based on partial polymerase sequence data (region A) available from the Dutch norovirus surveillance database.

Informative sites mapped on 3D model of GGII.4 capsid proteins. Sites with two distinct amino acid changes over the 12-year period are depicted in green, and sites with three or more amino acid changes are shown in red. The conserved RGD motif is shown in blue. (A) Dimeric subunit of two capsids, with one in gray and one in light blue. The extra RGD motif is indicated in yellow. The locations of the insertions compared to the NV capsid, which have not been modeled, are indicated by orange arrows 1 to 4. The brackets on the right indicate the different domains. The shell domain is indicated in grey, the P1 domain is shown in green, and the P2 domain is shown in blue. (B) Three capsid proteins, including a dimer with one-half of a neighboring dimer. The gray and light blue areas form one dimer, and the yellow capsid belongs to another dimer. The inserted RGD motif is indicated by the blue arrows.