Abstract
Infectious bronchitis virus (IBV) is a highly contagious pathogen in poultry that causes significant economic losses worldwide. In this study, two novel IBV isolates, CK/CH/MY/24053 of the GI-19 lineage and CK/CH/SC/25605 of the GI-22 lineage, were isolated and analyzed through whole-genome sequencing, recombination mapping, pathogenicity assessment in SPF chickens, and S1 protein structural comparison. Whole-genome analysis revealed that CK/CH/SC/25605 underwent recombination across different genotypes involving multiple parental lineages, whereas CK/CH/MY/24053 exhibited recombination within the same genotype. Pathogenicity assessment in specific-pathogen-free chickens showed that CK/CH/MY/24053 primarily exhibited kidney tropism, resulting in pronounced renal lesions and high viral loads in the kidneys, whereas CK/CH/SC/25605 predominantly targeted the respiratory tract, causing severe tracheal and pulmonary lesions and a higher mortality rate compared with typical QX strains. Viral shedding occurred in both the trachea and intestines, indicating active replication. Structural analysis of the S1 protein revealed only subtle differences within the hypervariable regions between the two isolates. Notably, both strains were isolated from flocks vaccinated with the QXL87 vaccine, and recombination analysis identified QX-derived genomic segments in each isolate. Although these structural differences alone do not provide direct evidence of antigenic variation or vaccine escape, they may reflect potential alterations in antigenicity under vaccine-induced immune pressure and therefore warrant further investigation. Overall, these findings demonstrate cross-genotype recombination, distinct tissue tropism, and subtle S1 structural variations, underscoring the importance of continued surveillance of recombination events in circulating IBV strains and their possible implications for vaccine effectiveness.