A matched case-control study of porcine group A and C rotaviruses in a swine farrowing production system.

Group A rotaviruses (RVA) and group C rotaviruses (RVC) are important enteric pathogens in swine. Comprehensive studies investigating porcine rotaviruses in Canada are necessary to enhance understanding of the frequency, impacts, and dynamics of these infections in swine herds. This study aims to estimate the prevalence of RVA and RVC, describe circulating strains, and assess the association of rotaviruses with diarrhea at the piglet, litter, and batch levels in Canadian farrowing swine productions. A matched case-control study was conducted on farrowing farms within an integrated production system experiencing a diarrheic episode. Rectal swabs from 94 diarrheic piglets and 127 healthy piglets were collected and subjected to VP7 and VP4 gene amplification of RVA and RVC using RT-PCR. Results indicated a 45.4 % and 27.4 % prevalence for RVA and RVC in piglets, respectively. A significant association between RVC and diarrhea (odds ratio = 7.1; p = 0.02) was identified at the batch level, while RVA detection did not show a significant relationship with diarrhea. Molecular characterization of various RVA and RVC strains detected in this study described at least four different RVA strains and three different RVC strains circulating on farms within the integrated production system. This study estimates the prevalence of RVA and RVC and describes the main viral strains in swine herds experiencing an episode of neonatal diarrhea. While it also highlights the importance of RVC in piglet diarrhea when detected in a batch, results from his study warrant the implementation of additional prevention measures and regular surveillance for the control of both RVA and RVC in swine herds.