Frequent detection of noroviruses and sapoviruses in swine and high genetic diversity of porcine sapovirus in Japan during Fiscal Year 2008

Abstract

A molecular biological survey on porcine norovirus (NoV) and sapovirus (SaV) was conducted in Toyama Prefecture, Japan, during fiscal year 2008. Both NoV and SaV were detected from swine fecal samples throughout the surveillance period, indicating that these viruses were circulating in this region. NoV strains detected in this study belonged to three genotypes that are known as typical swine NoVs. Although human NoVs were occasionally detected, it was unclear whether they replicated in pigs. As for SaV, genogroup VII (GVII) and other divergent genogroups were identified in addition to the dominant genogroup, GIII, which is the prototypic porcine SaV. In addition, 3 strains genetically related to human SaV were detected. Two of these 3 strains were closely related to human SaV GV. Our study showed that genetic diversification of porcine SaV is currently progressing in the swine population.

FIG. 1.

Neighbor-joining phylogenetic tree based on partial capsid genes of NoV GII strains. DDBJ accession numbers of all reference strains are shown in parentheses. More than 80% bootstrap values are shown on the branches. Newly sequenced representative strains are shown in italics.

FIG. 2.

Neighbor-joining phylogenetic tree based on partial RdRp genes of SaV strains. DDBJ accession numbers of all reference strains are shown in parentheses. More than 80% bootstrap values are shown on the branches. Asterisks indicate strains detected by the p290/p289 primer pair. Representative strains of newly sequenced strains are shown in italics.

FIG. 3.

Neighbor-joining phylogenetic tree based on partial capsid genes of SaV strains. DDBJ accession numbers of all reference strains are shown in parentheses. More than 80% bootstrap values are shown on the branches. Two strains genetically similar to human SaV are shown in italics.

FIG. 4.

Sequence alignments of the RdRp gene-capsid gene junction regions of SaVs. Boxed nucleotides represent the deduced genomic and subgenomic conserved motifs, and shaded nucleotides represent the putative start codon for the capsid gene. Dots indicate residues identical to those in the sequence of the first line (GI/1 Hu/Sapporo/82/JP). The two newly sequenced porcine SaV strains are in boldface.