Characterization and Prevalence of a New Porcine Calicivirus in Swine, United States Qiuhong Wang, Kelly Scheuer, Zhenwen Zhang, Wondwossen A. Gebreyes, Bayleyegn Z. Molla, Armando E. Hoet, and Linda J. Saif Real-time reverse transcription PCR revealed that new St-Valerien–like porcine caliciviruses are prevalent (2.6%– 80%; 23.8% overall) in finisher pigs in North Carolina. One strain, NC-WGP93C, shares 89.3%–89.7% genomic nucleotide identity with Canadian strains. Whether these viruses cause disease in pigs or humans or are of food safety concern requires further investigation. V iruses in the family Caliciviridae are nonenveloped, polyadenylated, single-stranded, positive-sense RNA viruses (1). They have been classified into 5 genera (Norovirus, Sapovirus, Vesivirus, Lagovirus, and Nebovirus) since 2009 (www.ictvonline.org). Later, the nonhuman primate Tulane virus (2) and the porcine St- Valerien–like viruses (3) were characterized as potential new genera in the Caliciviridae family. The Study Recently, we identified a St-Valerien–like virus, NC- WGP93C strain, from a healthy finisher pig in the United States by reverse transcription PCR (RT-PCR) with calicivirus universal primers p290/110 (4,5), followed by direct sequencing and nucleotide BLAST search (www. ncbi.nlm.nih.gov). We further sequenced the genome of NC-WGP93C strain by using primer walking, 3′ and 5′ rapid amplification of cDNA ends (RACE) methods (3,6,7). The NC-WGP93C strain was closely related genetically to the Canadian St-Valerien–like viruses, AB90, AB104, and F15–10 strains (3), sharing 89.3%– 89.7% nt identity, without insertions or deletions, and similar genomic organization. Complete genomes of strains representing different Caliciviridae genera were selected for a phylogenetic tree (Figure 1). The NC-WGP93C strain grouped with the Canadian St-Valerien–like viruses to form a potentially new genus within the Caliciviridae family. Next, we developed a real-time quantitative RT- PCR (RT-qPCR) for detection of St-Valerien–like viruses with primers (WGP93-polF1, 5′-TCTAAAG CGTGCACTCTGGGTCAT-3′; WGP93-polR1, 5′-ACC CTTTCTCCACCAGGAACTTCT-3′) and probe (WGP93- polP1, FAM-ACGAGTTTGTGGACTTCCTCTCGCA- BHQ) that targeted the RNA-dependent RNA polymerase (RdRp). The assay was performed by using the OneStep RT- PCR Kit (QIAGEN, Valencia, CA, USA) and a real-time thermocycler (RealPlex, Eppendorf, Germany). A plasmid DNA carrying the p290/110 amplicon of the NC-WGP93C strain was used to generate a standard curve. The detection limit was 10 genomic equivalents (GE) per 20-μL reaction (cycle threshold 37.71), corresponding to 4 × 10 4 GE/g of fecal sample (cut-off cycle threshold 38.00). No other porcine enteric caliciviruses, including sapoviruses (GIII/ Cowden, GVI/JJ681, GVII/LL26 strains) and noroviruses (GII.11/QW48, GII.18/QW101, and GII.19/QW170 strains) (8,9), were detected. This RT-qPCR is sensitive and specific for the detection of St-Valerien–like caliciviruses. Using the above RT-qPCR, we performed a prevalence study of St-Valerien–like viruses. Pig fecal samples (n = 1,567) were collected during May–November 2009 from a study of Salmonella infections in apparently healthy finisher pigs from 3 different swine production systems (3 farms per system, and 4 barns per farm, except for farm RW [3 barns]) located in North Carolina (Table 1) (10). Each barn was treated with 1 of 3 biocides—Biosentry (Biosentry, Inc., Stone Mountain, GA, USA), Synergize (Preserve International, Reno, NV, USA), or VirkonS (Dupont Animal Health Solutions, Sudbury, UK)—or with pressurized water as control (11). One pig per pen Emerging Infectious Diseases  www.cdc.gov/eid  Vol. 17, No. 6, June 2011 1103 Author affiliations: The Ohio State University, Wooster, Ohio, USA (Q. Wang, K. Scheuer, Z. Zhang, L.J. Saif); and The Ohio State University, Columbus, Ohio, USA (W.A. Gebreyes, B.Z. Molla, A.E. Hoet) DOI: 10.3201/eid1706.101756 Figure 1. Neighbor-joining phylogenetic tree of caliciviruses based on the complete genomes (nucleotide). The newly identified St-Valerien–like virus NC-WGP93C strain is in boldface. The GenBank accession number of each strain is within parentheses. Bootstrap values are shown near branches. Human Poliovirus Sabin 1 was an outgroup control. Scale bar indicates nucleotide substitutions per site.