Litter-Level Agreement of RT-qPCR Results for Influenza A Virus Between Oropharyngeal Swab, Udder Wipe, and Nasal Wipe Samples Collected in Chilean Swine Breeding Herds

This study evaluated the use of udder wipes and aggregated nasal wipes as group sampling methods to detect influenza A virus (IAV) in swine breeding herds. Five breeding herds were selected and sampled from 2022 to 2024. At each sampling, six pigs in five due-to-wean litters were selected and sampled using oropharyngeal swabs (one per pig) and nasal wipes (one nasal wipe for three pigs). Additionally, an udder wipe sample was collected for each litter. Overall, 26.1% (89/341) of the oropharyngeal samples were IAV RT-qPCR positive. At the litter level, 43.9% (25/57) had at least one positive oropharyngeal swab, 33.3% (19/57) had a positive udder wipe, and 26.7% (12/45) had at least one positive nasal wipe. When compared to the oropharyngeal litter-level classification, the sensitivity and specificity of udder wipes were estimated at 68.0% (46.5–85.1%) and 93.8% (79.2–99.2%), respectively. For nasal wipes, the estimated values were 75.0% (47.6–92.7%) and 100.0% (88.1–100.0%), respectively. Udder wipes and nasal wipes can be used for IAV monitoring in breeding herds. However, false-negative results may be of concern at the litter level. These estimates can be used to implement a sampling strategy that maximizes the room- and herd-level sensitivity.