Ten Years Later: Molecular Detection and Circulation of Enteric Viruses in Italian Pig Herds

Enteric viral infections remain a major challenge for the swine industry, particularly in young animals, and represent a potential source of zoonotic risk. Ten years after a previous survey conducted in Italy, we performed a cross-sectional study investigating mostly the same viruses to evaluate the persistence and circulation of different enteric viruses in Italian pig farms. A total of 240 pooled swine fecal samples from asymptomatic swine, collected from 12 pig farms in Northern and Central Italy, were analyzed for hepatitis E virus (HEV), porcine astrovirus (PAstV), porcine kobuvirus (PKoV), rotavirus A (RVA), caliciviruses (norovirus; NoV and sapovirus; SaV), and coronaviruses (CoVs). Overall, frequent circulation of enteric viruses was confirmed, with common codetection of multiple viruses within the same samples. PAstV and PKoV were each detected in 10 of 12 farms, followed by RVA in 9 farms, HEV in 6 farms, and caliciviruses in 1 farm; no CoV RNA was detected. PAstV, PKoV, HEV, RVA, and calicivirus RNA were detected in 70.0%, 51.2%, 27.1%, 19.6%, and 1.3% of pooled fecal samples, respectively, and 61.7% of pools contained RNA from two or more viruses. Caliciviruses were rarely detected, while no CoVs were identified, indicating either a limited circulation in the investigated farms or in fecal samples, being mostly associated with respiratory diseases. Associations between viral detection and pig age, supply-chain affiliation, and herd size were assessed using generalized estimating equation (GEE) models accounting for within-farm clustering. Although crude pool-level detection frequencies differed among categories, no statistically significant associations were identified. Although comparison with previous studies should be interpreted cautiously because the sampled farms and some diagnostic assays were not identical, this study demonstrates the continued circulation of several enteric viruses in Italian pig farms. The result highlights the importance of molecular surveillance to safeguard animal health and assess risks of interspecies transmission.