Assessment of individual and population-based sampling for detection of Influenza A virus RNA in breeding swine herds

This study compared the probability of IAV RNA detection between selected individual and population-based samples. A 3500-sow breeding herd was sampled for matched sets (n = 57) of FOF, udder wipes, sow nasal wipes, individual piglet nasal wipes, and drinker wipes and tested by RT-rtPCR for IAV RNA detection. Overall, 57.9% (33/57) of FOF samples, 49.1% (28/57) of udder wipes, 28.1% (16/57) of sow nasal wipes, 15.8% (9/57) of drinker wipes and 66.6% (38/57) of the individual piglet nasal wipes tested positive for IAV RNA. FOF had a Kappa value of 0.81, a near-perfect agreement compared to individual piglet nasal wipes. Udder wipes revealed a Kappa value of 0.65, a substantial agreement with individual piglet nasal wipes. The other sample types had a fair agreement with individual piglet nasal wipes (Kappa values <0.28). These results validate FOF as an efficient alternative population-based sample type for IAV surveillance in the breeding herd. The proportion of positive piglets within litter by room A had 91% positivity (20/22), room B had 70% (17/24), and room C had 9% (1/11) positivity. The findings also highlight the importance of testing different farrowing rooms in the same breeding herd to strengthen IAV surveillance.