Abstract
Infectious bronchitis remains one of the most economically significant viral diseases in commercial poultry farming, despite the widespread implementation of vaccination programs. The high genetic variability of the infectious bronchitis virus (IBV) leads to the emergence of genetically and antigenically diverse variants, including vaccine-related and field variants detected in vaccinated flocks. This study presents a molecular genetic analysis of an IBV variant detected in 2025 at a poultry farm in the Almaty region of Kazakhstan. Samples were collected from seven 35-day-old deceased chickens during an episode of mortality. The reported clinical presentation included diarrhea and signs described as hepatitis, without pronounced respiratory manifestations. Initial molecular screening followed by amplicon sequencing confirmed the presence of IBV RNA in these clinical samples. For detailed genotyping and assessment of genetic variability, an 858-nucleotide fragment of the S1 gene was analyzed. Phylogenetic analysis showed that the detected virus belongs to genotype GI-13 and clusters with the 4/91 vaccine lineage while possessing distinct nucleotide substitutions. Comparison with the 4/91 reference strain identified 17 variable nucleotide positions, including two synonymous and 15 non-synonymous changes, corresponding to 10 unique amino acid substitutions. Broader molecular screening also detected avian leukosis virus (ALV) genotype E and fowl adenovirus type 5 (FAdV-5), whereas the other tested pathogens were not detected. These findings demonstrate the genetic distinctness of the detected GI-13 virus from the 4/91 vaccine reference; however, the available data cannot establish its origin, pathogenic significance, persistence, or sustained circulation. The findings underscore the value of continued molecular surveillance and sequence-based characterization of IBV in vaccinated poultry.