Prevalence of porcine noroviruses, molecular characterization of emerging porcine sapoviruses from finisher swine in the United States, and unified classification scheme for sapoviruses

Abstract

Noroviruses (NoVs) and sapoviruses (SaVs) are important human pathogens. Although the involvement of porcine NoVs in disease in pigs is unclear, they are genetically and antigenically closely related to human NoVs. Human NoV-like strains have been detected in pigs, raising public health concerns of potential interspecies transmission. Porcine SaVs are highly diverse and emerging in swine populations. Recently, at least three new genogroups of porcine SaVs have been proposed. In this study, we tested 413 pooled fecal samples collected from apparently healthy finisher pigs in North Carolina swine farms during 2009. Reverse transcription (RT)-PCR coupled hybridization assays were performed to detect known porcine NoVs. The overall prevalence of porcine NoVs determined was 18.9% based on this method. Samples were then tested by RT-PCR targeting the 5' end of the capsid region for genogroup II (GII) NoVs, a group which includes human NoVs, followed by sequence analysis. All NoVs identified belonged to typical porcine NoV genotypes, and no human NoV-like strains were detected in specimens from these pigs. Porcine NoV-negative samples (n = 335) were subsequently screened using universal calicivirus primers, and 17 SaV strains were confirmed by sequencing. Based on the partial RNA-dependent RNA polymerase (RdRp) region, they clustered with GIII, GVII, and GVIII and with currently unclassified SaVs. According to analysis of the complete capsid sequences, 7 representative strains clustered with GVII, GVIII, and GIX? SaVs. We tentatively classified SaVs into 14 genogroups based on the complete capsid protein VP1. In summary, porcine NoVs and highly divergent SaVs were present in North Carolina finisher pigs.

Fig 1

Maximum-likelihood phylogenetic tree of sapoviruses based on complete capsid deduced amino acid sequences using MEGA5 (40). Strains from this study are in boldface. Three genetic clusters within GVII are boxed. The scale represents the number of aa substitutions per site. GenBank accession numbers are in parentheses. Hu, human strains; Po, porcine strains.

Fig 2

Pairwise distance (p-distance) distribution of 95 SaV strains determined using the deduced complete capsid amino acid (aa) sequences and MEGA5 (40). The arrow indicates the genogroup cutoff (≥60% aa identity) used in this study.

Fig 3

Nucleotide alignment of the polymerase-capsid junction region of SaVs. The conserved motif is indicated by the box. Asterisks indicate residues identical to those in the top sequence (Sapporo). The start codon for the capsid protein is underlined. The porcine strains determined in this study are in boldface. A superscript italic a indicates that only the capsid sequence was available for those strains.