Figure 1 The structure of the calicivirus capsid exemplified by cryo-image reconstruction of recombinant Norwalk virus (NV)-like particles (rNV VLPs) (Left). X-ray structure of the Norwalk virus capsid (Right) with the Shell, Protruding 1, and Protruding 2 domains colored in blue, red and yellow, respectively.
(Courtesy of B.V. Prasad.)
Figure 2 Reading frame usage and gene order in the Caliciviridae. Caliciviruses have a positive-strand RNA genome (7.4–8.3 kb), depicted by the horizontal black lines, which carry a protein (VPg) covalently linked to the 5′-terminus. The genome also contains a characteristic, short repeated sequence (█) at the 5′-terminus and at the start of the VP1 gene. The genome (of each genus as indicated) is organized into at least two or three major ORFs as indicated. Structural genes are shown as pink (VP1) and blue (VP2) and the VPg gene is shown as green. In all genera, the structural proteins VP1 and VP2 are produced during replication from an abundant subgenomic RNA transcript that is co-terminal with the 3′-terminus of the genome. The ORF1 cleavage events mediated by the viral cysteine protease vary among the genera, but the gene order of the nonstructural proteins is conserved. Conserved cleavage sites are indicated with a solid vertical line; cleavage sites that vary in usage among genera are indicated with a broken vertical line.
(Re-designed by Rachel Skilton.)
Figure 3 Phylogenetic relationships in the family Caliciviridae. The noroviruses are highlighted in red, lagoviruses in light blue, neboviruses in yellow, vesiviruses in green and sapoviruses in blue. Two prototype viruses were included to represent each genogroup, For some genera, additional strains were included to demonstrate circulation in different species (e.g., Po/Sw917 in norovirus GII). Genera are defined by amino acid p-distance of up to 0.7, genera cut-offs were expanded to include all representative genogroups within a genus. The amino acids of full length VP1 capsid sequences were aligned in SeaView 4.2 using MUSCLE with a gap cost of −5 and neighbor-joining clustering method for the 1st and 2nd iterations. Bayesian phylogenetic analysis was run on BEAST without a molecular clock for 106 iterations using the WAG amino acid substitution and Yule speciation tree model. Parameters and length of the run was verified by using Tracer, part of the BEAST suite of programs. All genera are supported by posterior distribution value of 1.0 (100% of sampled trees). The scale bar represents amino acid substitutions per site.
(Courtesy of Everardo Vega.)