Detection and molecular characterization of swine hepatitis E virus in North Carolina swine herds and their faecal wastes

Julie A. Kase (corresponding author) Microbial Methods Development Branch Division of Microbiology, Office of Regulatory Sciences Center for Food Safety and Applied Nutrition, US Food and Drug Administration 5100, Paint Branch Parkway, Rm 3E-017, HFS-711, College Park, MD 20740, USA Tel.: 301.436.2571 Fax: 301.436.2644 E-mail: [email protected] Mark D. Sobsey Department of Environmental Sciences and Engineering, The School of Public Health, University of North Carolina, 4114A McGavran-Greenberg Hall, Chapel Hill, North Carolina 27599-7400, USA Maria T. Correa Department of Farm Animal Health and Resource Management, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USA Recent findings of almost genetically indistinguishable swine and human strains, have suggested swine play a role in the transmission of hepatitis E virus (HEV). The extent to which HEV may be present and persist in the faecal waste generated from intensive swine operations is largely unknown. The fate of swine waste liquid is often land application, possibly resulting in unintentional seepage into groundwater or run-off into surface waters, hence validating concerns of human exposure risks. Freshly passed swine faeces, barn flush liquid waste, and lagoon liquid from production sites in North Carolina were surveyed periodically for HEV using RT-PCR primers located in ORF2. On three farms where HEV RNA was detected in swine faeces, it was also found in stored liquid waste on several occasions. HEV presence was related to swine age but not to animal management and waste management procedures, which varied amongst the farms. Seasonal patterns of HEV prevalence could not be established as viral RNA was isolated at all time points from two farms. Phylogenetic analysis of 212 bases of the genomic RNA indicated that isolates resembled the known US swine and human strains (percentage nucleic acid homology 91 to 94%), with one amino acid substitution.