Genetic and pathogenic characteristics of a novel recombinant GI-19 infectious bronchitis virus strain isolated from northeastern China

Since the 1980s, despite vaccination, the infectious bronchitis virus (IBV) infection rate in commercial broilers and layers in China has continued to rise significantly, causing substantial economic losses to the poultry industry. In this study, an IBV strain was isolated from a layer farm in northeast China and named CK/CH/LN/2302. The whole genome sequence analysis revealed that CK/CH/LN/2302 shared a high level of homology (96.41 %) with the GI-19 strain SC/SDL/19. The phylogenetic tree based on the S1 gene indicates that CK/CH/LN/2302 belongs to the GI-19 lineage. Notably, recombination analysis using RDP5 and SimPlot software suggested that the GI-19 strain and a 4/91-like strain likely contributed to four recombination events in the CK/CH/LN/2302 genome. Phylogenetic analysis of these four regions further supported this conclusion. Protein structure analysis revealed that most of the nonstructural protein 2 (nsp2), main protease (M^pro), S1, and 5a protein regions were replaced by sequences from the 4/91-like strain. After infecting 1-day-old SPF chickens, CK/CH/LN/2302 presented a mortality rate as high as 60 %. Higher viral loads were detected in tissues such as the larynx, trachea, lungs, duodenum, jejunum and kidneys, indicating the multitissue tropism of this strain. Neutralization assay results revealed that the serum from 28-day-old commercial chickens immunized with the H120 vaccine was unable to effectively neutralize CK/CH/LN/2302. Compared with the S1 subunit of H120, CK/CH/LN/2302 demonstrated conformational changes, particularly in the hypervariable regions (HVRs), which may facilitate immune evasion. The genetic characteristics and pathogenicity of CK/CH/LN/2302 highlight the ongoing evolution of GI-19 IBV strains in China, emphasizing the urgent need for appropriate control strategies.