Phylogenetic and antigenic analysis of infectious bronchitis virus isolated from commercial and backyard chickens in Pakistan, 2015–2018

Infectious bronchitis virus (IBV) is a rapidly evolving virus affecting both vaccinated and unvaccinated poultry flocks and is responsible for significant economic losses globally; hence, it is imperative to obtain a deeper understanding of this pathogen. In this study, seven IBV strains were isolated from commercial and backyard poultry flocks during 2015-2018. We obtained full-length IBV genomes of two viruses using the Illumina sequencing method, while five additional viruses were genetically characterized through full-length spike (S1) gene sequencing. Phylogenetic and distance analysis based on complete S1 gene and full-length genome sequences revealed that one IBV isolate belonged to genotype GI-1 and six viruses were clustered within genotype GI-13. Deduced amino acid sequences of GI-13 strains exhibited 31.8-37.2 % divergence with the commonly used classic vaccine strains (M41) and 2.7-12.6 % with variant vaccine strains (4/91) in Pakistan. High evolutionary distances suggest that the IBV viruses circulating in Pakistan are under continuous evolutionary pressure. Moreover, ch/IBV/Pak/AW-2/2017 was found to have originated from an intra-genotypic recombination event between the variant group (GI-23 lineage as a major parent) and variant vaccine strain (4/91-like as a minor parent) and is the first example of recombination within genotype GI-13 in Pakistan. Together, these findings provide genetic and evolutionary insights into the currently circulating IBV genotypes in Pakistan, which could help to better understand the origin, spread and evolution of IBVs, and to ascertain the importance of disease monitoring as well as re-evaluation forof currently used vaccines and vaccination programmes.