Caractérisation de l’importance clinique des rotavirus A et C dans la diarrhée des porcelets et leur excrétion jusqu’à l’âge adulte

Rotaviruses (RVs) are a major global cause of neonatal diarrhea in a variety of animal species as well as humans. Among the nine officially recognized RV serogroups (RVA to RVI), RVA is considered to be the most important group due to their high prevalence and pathogenicity in humans and their zoonotic potential due to numerous evidence of reassortment events between human and animal strains, including swine. However, in Quebec, no recent information is available concerning the circulating strains of porcine RVA. Furthermore, RVC have been recently investigated in several countries across the world, revealing a potential involvement of these enteric viruses in swine diarrhea. Currently, in Quebec, data on prevalence of RVC in swine are lacking and characterisation of their strains has not been conducted.  The present study evaluated the prevalence and epidemiology of RVA and RVC in swine from two integrated production systems in Quebec over a 29 month period. In a first system, the clinical importance of RVs in farrowing farms was investigated and dynamics of fecal excretion up to pre-slaughter age was described. For the second production system, the presence and characterization of RVs in fattening sites was first evaluated. Then, the dynamics of enteric viral contamination from this pre-slaughter system was investigated to identify potential vectors and reservoirs of viral transmission using porcine RVA as markers. Molecular analysis based on RT-PCR as well as Sanger and high-throughput sequencing were conducted to detect the presence of RVs and to characterize partial and/or complete viral genomes enabling classification of strains. Results revealed the presence of RVs throughout all stages of production on farm, with a predominance of these viruses surrounding the weaning period. In farrowing farms, RVC was found to be significantly associated to the clinical portrait of diarrhea (p=0.02) at the batch level, which was not the case for RVA. Statistical evaluations revealed an overall prevalence of 45.4% and 27.4% for RVA and RVC in piglets, respectively. Phylogenetic analysis of strains showed a frequent shift of predominant RV strains between production stages. In the pre-slaughter production system, the results revealed frequent contamination of fattening farms, livestock transportation vehicles and the abattoir yard by RVA. Although a large genetic diversity has been described throughout the different environmental sites collected, identical strains of RVA were identified from farm samples, the slaughter yard and the livestock transport vehicle. Overall, this study enabled the assessment of the current prevalence of porcine RVA and RVC in Quebec as well as the characterization of circulating strains. The results confirm the importance of RVC as a causative agent of diarrhea in piglets and describe, for the first time, complete porcine RVC genomes in Canada. Analysis from the pre-slaughter production system suggest a potential role for slaughterhouses and livestock transporters as reservoirs and vectors for enteric viruses, which may lead to the spread of viral contamination within an animal production system or even between different production systems.

Keyphrases: rotavirus, Swine, Production systems, Diarrhea, Viral strains, Viral indicators, Fecal contamination