# First Molecular Characterization and Comprehensive Bioinformatic Analysis of Avian Infectious Bronchitis Virus from Uzbekistan Reveals GI-1, GI-13, and GI-23 Genotypes in Broilers

## TL;DR

This study identifies and analyzes three types of Avian Infectious Bronchitis Virus in Uzbekistan, revealing genetic differences that could affect vaccine effectiveness.

## Contribution

The first molecular characterization and bioinformatic analysis of IBV in Uzbekistan, revealing new insights into regional genetic diversity.

## Key findings

- Three IBV strains in Uzbekistan were classified as GI-1, GI-13, and GI-23 genotypes.
- Uzbek isolates showed distinct nucleotide and amino acid substitutions compared to global reference strains.
- Genotype-specific changes in spike proteins suggest potential impacts on vaccine cross-protection.

## Abstract

Avian Infectious Bronchitis Virus (IBV) is a highly contagious Gammacoronavirus that poses a significant threat to the global poultry industry. Despite its worldwide prevalence, a critical knowledge gap exists regarding the genetic diversity of IBV in Central Asia, particularly in Uzbekistan. This study is the first comprehensive molecular characterization of IBV in Uzbekistan. This study also provides a unique and informative bioinformatic analysis of the detected strains. Three IBV strains were isolated and identified from chickens suspected of IBV infection. The isolates were identified and subjected to S1 gene sequencing, phylogenetic analysis, recombination screening, selective pressure mapping, and in silico structural and antigenic profiling. Phylogenetic inference revealed that the isolates clustered within the established genotypes GI-1, GI-13, and GI-23. Comparative alignments revealed distinct nucleotide and amino acid substitutions relative to global reference strains. The evolutionary patterns are consistent with a predominantly clonal mode of evolution. Structural modeling and B-cell epitope prediction revealed pronounced antigenic and topological divergence among the Uzbek isolates. Genotype-specific substitutions, particularly in solvent-exposed regions of the spike protein, were associated with altered epitope profiles, implying potential impacts on vaccine cross-protection. These findings contribute to current knowledge of IBV molecular characterization and provide the first reference framework for the Central Asian region. The study highlights the importance of continuous molecular surveillance, region-specific vaccination strategies, and integrated genomic monitoring for novel IBV variants.