Background: Influenza A virus (IAV) is an important pathogen in pigs that affects productivity and has important\npublic health implications because of its zoonotic nature. Surveillance is central to the control of influenza, however,\ndetection of IAV infections can be challenging in endemically infected herds with low prevalence of infection.\nMethods: In groups of suckling (18-21 days of age) and growing (35-45 days of age) pigs, we compared various\nsampling approaches to detect, isolate and sequence IAV using individual (nasal swabs, nasal wipes and oropharyngeal\nswabs), group (oral fluids, surface wipes and sow udder skin wipes) and environmental (airborne particles deposited on\nsurfaces and air samples) sampling approaches. All samples were tested by IAV rRT-PCR and a subset was used for virus\nisolation and direct sequencing.\nResults: In general, environmental and group samples resulted in higher odd ratios (range = 3.87-16.5, p-value < 0.05)\nof detecting a positive sample by rRT-PCR compared to individual pooled samples, except for oropharyngeal swabs\n(OR = 8.07, p-value < 0.05). In contrast, individual samples were most likely to yield a viral isolate by cell\nculture. Oropharyngeal swabs in suckling pigs (78.4%), and nasal swabs (47.6%) or nasal wipes (45%) in\ngrowing pigs, and udder wipes in lactating sows (75%) were the preferred samples to obtain an isolate.\nConclusions: Our findings indicate that group and environmental sampling strategies should be considered\nin influenza surveillance programs in particular if the goal is just to detect infection. This study provides\nnew information on sampling approaches to conduct effective influenza surveillance in pigs and identifies\nudder wipes from lactating sows as a novel sample type that offers a convenient, cheap and sensitive\nmanner to monitor IAV in litters prior to weaning.
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