A comprehensive molecular investigation and evolution of the infectious bronchitis virus in India reveals the region-specific mutations in the receptor-binding domain of S1 gene.

Infectious Bronchitis (IB) is an acute contagious disease of poultry caused by the infectious bronchitis virus (IBV), genus Gammacoronavirus of the family Coronaviridae. The objective of this study was to characterize the genotypic and pathological features of IBV circulating in chickens in major poultry-producing states of India from 2022 to 2024. A total of 1685 representative carcasses from 272 IB-suspected flocks were examined with the help of conventional and advanced diagnostic techniques. All the flocks under study were vaccinated with live/inactivated IB vaccines. A total of 33 flocks (12.2%) out of 272 showed PCR positivity for IBV. A total of 22 field isolates were successfully adapted in embryonated chicken eggs. Clinical signs, gross and histopathological lesions relevant to a respiratory/renal/reproductive system ailment were apparent in all IB cases. Thirty selected S1 gene PCR products were sequenced, and phylogenetic analysis revealed that all the study sequences were clustered with the Genotype I-1 (GI-1). Three consistent mutations were identified in the S1 protein from Northern India isolates: Ile131Leu, Asn306Asp, and Gly376Arg. Similarly, all the IBV isolates from Southern India had a consistent Glu179Ala substitution. S1 epitope analysis predicted one amino acid variation in a potential linear B-cell epitope in the IBV 376Arg variant, located within HVR3, alters the local charge, which may potentially influence antigenicity and vaccine efficacy, however confirmation will require neutralization assays and reverse-genetics experiments. This comprehensive study provides valuable insights into IBV evolution and its implications for disease control in the Indian poultry sector.