Molecular detection and associated risk factors of infectious bronchitis virus (IBV) isolated from poultry in Khyber Pakhtunkhwa, Pakistan.

Infectious bronchitis, caused by the infectious bronchitis virus (IBV), is a highly contagious multisystem disease affecting poultry of all ages and leading to significant economic losses worldwide. IBV exhibits considerable genetic variability, with numerous genotypes and lineages associated with respiratory, reproductive and kidney issues. This study aimed to investigate the molecular epidemiology of IBV in poultry-dense areas of Khyber Pakhtunkhwa, Pakistan. An outbreak-driven sampling method was used to collect a total of 425 clinical samples, including tracheal swabs and tissue specimens, from suspected flocks across different districts. Specifically, 100 samples were collected from Abbottabad and Mansehra, 90 from Mardan and Peshawar, and 45 from Malakand Division, proportionate to regional poultry populations. Viral RNA was extracted and tested using RT-PCR targeting the IBV S1 gene. Selected positive samples underwent Sanger sequencing. Sequence analysis was carried out using ClustalW in MEGA 12, and phylogenetic relationships were inferred via the Maximum Likelihood method based on the T92+G Tamura 3-parameter model with gamma distribution. The overall IBV prevalence was 29.6%. The highest prevalence was observed in Mansehra (39%), whereas Malakand Division had the lowest prevalence (7.7%). IBV detection was more frequent in young birds (35.2%) and layer flocks (33.7%) compared to broilers (30.7%). Phylogenetic analysis revealed that most circulating IBV strains belong to genotype GI-1, indicating ongoing circulation of classical IBV strains in the area. These findings highlight the importance of ongoing molecular surveillance and the development of region-specific vaccines. Implementing improved biosecurity measures, such as enhanced ventilation, thorough disinfection between production cycles, and all-in-all-out flock management, is essential to reduce IBV outbreaks and improve poultry health and productivity in Khyber Pakhtunkhwa.