The GI-19 dominant genotype of infectious bronchitis virus in chickens from 2021 to 2023 in Sichuan province is frequently involved in recombination events

Infectious bronchitis virus (IBV), the etiological agent of infectious bronchitis (IB) in chickens, is a highly contagious respiratory disease that poses significant economic burdens on the global poultry industry. Comprehensive knowledge of the epidemiological patterns and genetic variations of IBV is crucial for effective prevention and control strategies. In this study, we collected 684 suspected samples from Sichuan province between 2021 and 2023. PCR testing revealed a total positivity rate of 26.9 %, with the Guangyuan region exhibiting the highest positivity rate at 37.2 %. Subsequently, we obtained 21 complete IBV S1 gene sequences and the phylogenetic analysis identified the GI-19 type as the predominant strain. Comparing nucleic acid similarity among the 21 isolated strains, we observed a range of 66.48 %–99.69 % nucleotide similarity (56.22 %–99.45 % in amino acids). The QXL87 vaccine strain exhibited higher similarity to the isolated strains. Amino acid variations in the three hypervariable regions (HVRs) showed the highest variability in HVR I. The GVI type strain differed in amino acid composition from QXL87 in HVR I, resulting in reduced N-glycosylation sites on the S1 gene. Furthermore, all isolated strains displayed varying reductions in N-glycosylation sites on the S1 gene compared to the QXL87 vaccine strain. Ultimately, recombination analysis revealed frequent involvement of the GI-19 and GI-22 strains in gene recombination. The majority of recombined strains were derived from partial segments of the GI-19 strain, with no recombination observed in any of the isolated GI-19 strains. In summary, our findings elucidate the prevalence of IBV in Sichuan province and highlight the pivotal role of the GI-19 strain in IBV recombination, thereby offering valuable data support for IBV control.