Pathogenicity and Bioinformatics Analysis of Two GI-13 Infectious Bronchitis Virus Strains in China

Despite long-term vaccination and control efforts, infectious bronchitis virus (IBV) remains a major threat to the global poultry industry, largely due to its high prevalence and extensive genetic diversity. This study aimed to characterize two novel GI-13 (4/91-like) IBV field strains, CK/CH/JS/2302 and CK/CH/AH/2307, isolated from H120-vaccinated broiler flocks in China, in order to elucidate their pathogenicity, genomic characteristics, and evolutionary relationships. Although both isolates belonged to the GI-13 genotype but exhibited divergent pathogenic profiles and evolutionary patterns. CK/CH/JS/2302 exhibited higher virulence, severe respiratory symptoms, tracheal hemorrhage, kidney lesions, and 10% mortality, while CK/CH/AH/2307 induced only mild respiratory signs and slight renal swelling. Phylogenetic analysis revealed that CK/CH/JS/2302 displayed a recombinant genome involving GX-YL5 and IBV/India/ck/01/23, in which the S1 gene was clustered within GI-13 genotype, whereas other genes showed high similarity to domestic GI-7, GI-19, and GI-22 genotypes. In contrast, CK/CH/AH/2307 showed high genomic similarity to the 4/91 vaccine strain without evidence of recombination but still impaired tracheal ciliary activity. Sequence and structural modeling of the S1 protein revealed that amino acid substitutions within hypervariable regions (HVRs) may affect receptor binding and antigenicity, potentially reducing cross-protection from current vaccines. These findings demonstrate the coexistence of a virulent recombinant strain (CK/CH/JS/2302) and a low-pathogenic variant (CK/CH/AH/2307) within the same lineage in China, underscoring the role of recombination and immune selection in IBV evolution. Overall, these findings emphasize the necessity for continuous molecular surveillance and genotype-specific vaccine development to improve protection against emerging 4/91-like IBV variants and reduce the economic losses caused by infectious bronchitis in poultry production.