Genetic heterogeneity and recombination in canine noroviruses

Abstract

Alphatronlike (genogroup IV [GIV]) noroviruses (NoVs) have been recently identified in carnivores. By screening a collection of 183 fecal samples collected during 2007 from dogs with enteric signs, the overall NoV prevalence was found to be 2.2% (4/183). A unique strain, Bari/91/07/ITA, resembled GIV.2 NoVs in its ORF1 (polymerase complex), while it was genetically unrelated in its full-length ORF2 (capsid gene) to GIV animal and human NoVs (54.0 to 54.4% amino acid identity) and to any other NoV genogroup (<54.7% amino acid identity). It displayed the highest identity (58.1% amino acid identity) to unclassified human strain Chiba/040502/04/Jp. Interestingly, the very 5' end of ORF2 of the canine virus matched short noroviral sequences (88.9% nucleotide identity and 98.9% amino acid identity) identified from oysters in Japan, indicating that similar viruses may be common environmental contaminants.

FIG. 1.

Genome organization of the canine NoV Bari/91/07/ITA. A nucleotide identity plot of the genome of the canine NoV Bari/91/07/ITA (from the 3′ end of ORF1 to the poly[A] tail) was compared with those for the canine strain GIV.2/Bari/170/07-4/ITA (EU224456), the lion strain GIV.2/Pistoia/387/06/ITA (EF450827), and the human GIV.1 NoVs Fort Lauderdale/560/98/US (AF414426) and Saint Cloud/624/US (AF414426). The sequences were analyzed with Simplot (26) using a window size of 200 and step size of 20, with gap strip off and Hamming correction on. The arrow indicates the crossover site at the ORF1-ORF2 junction region. NTR, nontranslating region.

FIG. 2.

Phylogenetic tree constructed on the 268-aa sequence of the COOH terminus of the polymerase complex. The tree was constructed using a selection of NoV strains representative of GI to GV. Strain designations follow the outlines of Wang et al. (46) and Zheng et al. (47). Abbreviations: Bo, bovine; Mu, murine.

FIG. 3.

Phylogenetic tree constructed on the full-length amino acid sequence of the capsid protein. The tree was constructed using a selection of NoV strains representative of GI to GV. Strain designations follow the outlines of Wang et al. (46) and Zheng et al. (47). Abbreviations: Bo, bovine; Po, porcine; NA, not assigned. In the box, a subtree displaying the homology between the canine strain Bari/91/07/ITA and NoV strains identified in oysters in Japan is shown. The tree was constructed based on a 93-aa fragment at the NH₃ terminus of the capsid protein.