Caractérisation du virome entérique porcin et évaluation de son implication dans la diarrhée néonatale

Canada is a major pork exporter around the world and the province of Quebec alone accounts for 6% of this trade. To maintain the province’s competitiveness and the excellence of its products, a comprehensive understanding of the infectious agents circulating in herds is essential. Several pathogens have been intensively studied, while others have yet to be investigated even though they have been reported in pigs all around the world. This study evaluated the prevalence of porcine astroviruses, calicivirus, porcine kobuvirus, rotavirus, torque teno sus virus and hepatitis E virus, monitored in a pig production network, from the nursing farms to the end of the fattening farms to portray the excretion patterns of these viruses through the different life stages of pigs. The sampling of healthy piglets alongside piglets with diarrhea in the nursing farms allowed to determine which viruses, or co-infections of viruses were factors of diarrhea at this life stage. The intestinal virome, the viral part of the microbiome, was characterized and viral diversity of porcine enteric viruses at different life stages, as well as between healthy and diarrheic piglets were evaluated. Moreover, the dissemination of the hepatitis E virus in the farm environment, as well as the possible sources of contamination were described, from the indoor and outdoor environment of fattening farms, the slaughterhouse yard and animal transporters.  The results obtained in this study described the temporal excretion dynamics of these porcine enteric viruses according to the life stages of the pigs, demonstrating the difference in the excretion of the studied viruses according to the life stage. The calicivirus, as well as the porcine astrovirus groups 3 and 5 were found to be risk factors for diarrhea in the nursing farms. For the first time in Canada, the detection and characterization of porcine kobuvirus strains were evaluated and provided a better understanding of their diversity and the persistence of these strains in the network. The porcine enteric virome diversity was analyzed on a MiSeq sequencing platform and this diversity was different between healthy and diarrheic piglets, as well as between the different life stages. However, the different enzymatic treatments used as pretreatments for fecal samples altered the ability to detect certain single-stranded RNA viruses. Similar strains of the hepatitis E virus were present in the indoor and outdoor environment of the fattening farms, as well as in common places of high circulation from the various stakeholders in the pig production network. The activities in the slaughterhouse yard could therefore be involved in the spread of this virus.  This study shed light on enteric viruses infecting pigs. In addition, some of the infections from enteric viruses studied were risk factors for diarrhea in co-infections and will need to be studied in more details to understand their mechanisms, in relation to neonatal diarrhea. More specific interventions during outbreaks of porcine diarrhea of unknown etiology could be carried out, as well as the development of more adapted biosecurity measures according to the life stage of the pigs.

Keyphrases: astrovirus, calicivirus, kobuvirus, rotavirus, torque teno sus virus, virome, co-infections, hepatitis E virus, piglets, pigs, neonatal diarrhea, environment