Detection and molecular characterization of zoonotic viruses in swine fecal samples in Italian pig herds

Gastrointestinal disease is frequent in pigs, and among the different etiological agents involved, viruses are considered the leading cause of infection in this animal species. Furthermore, about half of the newly identified swine pathogens are viruses, many of which may be transmitted to humans by direct contact or by indirect transmission pathways. In this study, the prevalence of astrovirus (AstV), group A rotavirus (RVA), norovirus (NoV) and hepatitis E virus (HEV) infections in pigs was investigated. During 2012-2014, 242 fecal samples were collected from pigs at different production stages (5 to 220 days old) on eight swine farms located in northern, central and southern Italy. Seven out of eight farms analyzed were positive for AstV, which was detected in 163 out of 242 (67.4 %) samples and was the most prevalent virus; 61 of the 163 AstV-positive animals (37.4 %) had diarrhea. HEV was detected on six farms and in 45 (18.6 %) of the 242 samples analyzed. Twenty-three HEV-infected pigs had diarrhea (51.1 %). A lower prevalence was observed for RVA, which was found in 10 of the 242 samples (4.1 %) from three positive farms, and diarrhea was present only in six infected pigs (60.0 %). No swine samples were found to be positive for NoV. Genetic diversity and phylogenetic relationships of some strains representative of the different viruses detected were investigated, confirming a wide heterogeneity of viral strains circulating among pigs.