Detection and characterization of potentially zoonotic viruses in faeces of pigs at slaughter in Germany

Pigs can harbour a variety of viruses in their gastrointestinal tract. Some of them are closely related to human viruses and are therefore suspected to have a zoonotic potential. Only little is known about the presence of those viruses in pigs at slaughter. However, by contamination of meat with zoonotic viruses during the slaughtering process, food-borne transmission to humans may be possible. Here we analyzed 120 faecal samples of pigs at slaughter from 3 different geographical regions of Germany for the presence of astrovirus (AstV), encephalomyocarditis virus (EMCV), hepatitis E virus (HEV), norovirus genogroup II (NoV GII) and group A rotavirus (GARV). Using real-time RT-PCR, the most frequently detected virus was AstV, which was present in 20.8% of the samples, followed by NoV GII with a detection rate of 14.2%. EMCV, HEV and GARV were found only occasionally with detection rates of 4.2%, 2.5% and 0.8%, respectively. Analyses of partial genome sequences of the viruses indicated that the detected AstV and NoV GII mainly represented typical pig virus strains, which have not been detected in humans so far. However, the GARV and HEV strains were more closely related to human strains. The results indicate that enteric viruses, some of them with zoonotic potential, are present in pig faeces at slaughter. Application of good hygiene practice is necessary to minimize the risk of introducing these viruses into the food and to prevent virus transmission to highly exposed persons such as slaughterers and veterinarians