The role of the rural poultry sector in viral circulation and evolution: evaluation of infectious bronchitis virus and avian metapneumovirus dynamics in an Italian dealer farm

Although the steady growth of poultry production is primarily driven by intensive systems, rural farming is still present even in developed countries. Despite representing a small niche of the overall production, some of its features, such as lower managerial and biosecurity levels and the frequent exchanges of live animals among different establishments, make the rural sector a potential hotspot for the maintenance, spread and evolution of infectious agents. Nonetheless, this sector appears often underinvestigated compared to its industrial counterpart. The present longitudinal study was conducted in a multi-age, multi-species, two-site rural dealer farm in Northeast Italy, using molecular assays to assess the introduction, circulation, and genetic variability of two endemic viral pathogens, infectious bronchitis virus (IBV) and avian metapneumovirus (aMPV). During the 5-month-long study period, 43 flocks of different species were periodically sampled, obtaining 130 pools of respiratory swabs. IBV was found in 58 samples from 23 chicken flocks, and aMPV in 35 samples from 22 flocks of chickens, ducks and guinea fowls, proving their extensive circulation in both farm sites. The detected IBVs, either of field or vaccine origin, belonged to 5 different IBV lineages (GI-1, GI-13, GI-16, GI-19, and GVIII-2), also including two recombinant strains. All aMPV strains belonged to subtype B, except for a single aMPV/A detection. Most were field aMPVs, but some seemingly vaccine strains were detected, although no aMPV vaccine was reportedly administered. Despite a continuous viral circulation, clinical manifestations appeared limited both in frequency and severity, which could be partially attributed to the lower population density and environmental stress compared to intensive farms. Nonetheless, the evolution of multiple genetic types without proper monitoring nor control may still favor the emergence and spread of pathogenic variants, causing detriment not only to the interested farm but to the entire poultry sector.