# Characterization of the Genomics and Antigenicity of a Naturally Attenuated Gammacoronavirus Infectious Bronchitis Virus Strain in the Genotype GVI-1 Lineage

## TL;DR

Researchers studied a naturally weakened strain of a chicken coronavirus, finding unique genetic and immune properties that could help improve vaccines.

## Contribution

The study reveals unique genomic and antigenic features of a naturally attenuated IBV strain in the GVI-1 lineage.

## Key findings

- YC_GVI-1 shares 98.2% nucleotide similarity with CK/CH/FJ/202005 and likely originated from a genetic recombination event.
- YC_GVI-1's S protein has ten unique amino acid substitutions, with one substitution (M485V) affecting local protein structure.
- Vaccination with YC_GVI-1 provided 100% protection against a different strain (JS96_GI-19) and strong antibody responses.

## Abstract

Infectious bronchitis virus (IBV) causes a highly contagious disease in chickens. The prevalence of GVI-1 is increasing; however, the genomic characteristics and antigenic properties of this genotype strain remain insufficiently characterized. In this study, the genome characteristics and antigenic properties of a naturally attenuated CK/CH/SC/YC_GVI-1-DK/LMB20210104 (abbreviated as YC_GVI-1) strain were systematically analyzed. YC_GVI-1 occupies a distinct phylogenetic lineage and shares a similarity of 98.2%, the highest nucleotide sequence homology, with the reference strain CK/CH/FJ/202005 (accession number: MW791835.1). This strain was likely originated through a genetic recombination event between two major parental strains, CK/CH/FJ/202005 and CK/CH/GX/HX (accession number: PP817796.1). However, its S protein harbors ten unique amino acid substitutions, compared to the same protein in the other two virulent strains in the same genotype. AlphaFold3-based structural prediction reveals that one of these substitutions, methionine 485 to valine substitution, may induce a conformational change in the adjacent phenylalanine residue at position 431, resulting in a shift in the local secondary structure from β-sheet to random coil. Characterization of its antigenicity showed that this strain induces a strong humoral immune response, with neutralizing antibody titers of 26.40 against homologous strain YC_GVI-1 and 24.00 against heterologous strain JS96_GI-19. Furthermore, vaccination of chickens with this strain conferred complete protection (100%) against JS96_GI-19. The findings provide novel insights into the molecular evolution and antigenicity of YC_GVI-1, offering key information for improving IBV surveillance and vaccine development.