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

Sample types currently used for Influenza A virus (IAV) surveillance in swine farms vary in sensitivity, convenience of collection, and herd representativeness. Family oral fluids are an effective population-based sample type for detecting porcine reproductive and respiratory syndrome virus (PRRSV) (ribonucleic acid) RNA by real-time reverse transcription-polymerase chain reaction (RT-rtPCR) in breeding herds. However, little is known about the efficacy of family oral fluids samples for detecting IAV RNA in these herds. This study compared the probability of IAV RNA detection among individual and population-based samples. A 3,500-sow breeding herd was sampled for matched sets (n = 57) of family oral fluids, udder wipes, sow nasal wipes, individual piglet nasal wipes, and drinker wipes, tested by RT-rtPCR for IAV RNA. Overall, 57.9 % (33/57) of family oral fluids, 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 individual piglet nasal wipes were positive. Family oral fluids showed a Kappa value of 0.81, indicating near-perfect agreement with individual piglet nasal wipes, while udder wipes had a substantial agreement (Kappa = 0.65). Other sample types showed fair agreement (Kappa < 0.28). These results validate family oral fluids as an efficient alternative population-based sample for IAV surveillance in breeding herds. The proportion of positive piglets within litters by room was 91 % in room A (20/22), 70 % in room B (17/24), and 9 % in room C (1/11). This study also highlights the importance of sampling different farrowing rooms within the same breeding herd to enhance IAV surveillance.