Molecular detection of infectious bronchitis and avian metapneumoviruses in Oman backyard poultry

•First IBV and aMPV epidemiological study in backyard poultry in Oman.•IBV M41, D274, 793/B, IS/885/00 and IS/1494/06 were identified in backyard chickens.•First detection of IBV 793/B in duck and turkey backyard flocks.•Avian metapneumovirus subtype B detected in some backyard chicken flocks.•Disease risk to backyard and industrial poultry flocks discussed. Infectious bronchitis virus (IBV) and avian metapneumovirus (aMPV) are economically important viral pathogens infecting chickens globally. Identification of endemic IBV and aMPV strains promotes better control of both diseases and prevents production losses. Orophrayngeal swab samples were taken from 2317 birds within 243 different backyard flocks in Oman. Swabs from each flock were examined by RT-PCR using part-S1 and G gene primers for IBV and aMPV respectively. Thirty-nine chicken flocks were positive for IBV. Thirty two of these were genotyped and they were closely related to 793/B, M41, D274, IS/1494/06 and IS/885/00. 793/B-like IBV was also found in one turkey and one duck flock. Five flocks were positive for aMPV subtype B. Though no disease was witnessed at the time of sampling, identified viruses including variant IBV strains, may still pose a threat for both backyard and commercial poultry in Oman.