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

Figures

• 

  Figure 1. Phylogenetic classification of the first Avian Infectious Bronchitis Virus (IBV) strains identified in Uzbekistan. (a) A schematic diagram of the IBV spike (S) protein. The diagram illustrates the functional S1 and S2 subunits, the S1/S2 cleavage site, the hypervariable regions (HVR I, II, and III), and the N-linked glycosylation sites. The peach-colored region represents the fragment of the S1 gene amplified by PCR, while the binding sites for the primers (SX1+, SX3+, SX2−, and SX4−) used for amplification are indicated below the schematic. (b) A Maximum Likelihood phylogenetic tree based on the S1 gene nucleotide sequence. This tree demonstrates the genetic relationships of the three Uzbek isolates to consensus sequences from established IBV genotypes. The findings show the isolates cluster into three separate, globally recognized lineages: UZB-IBV-1 clusters with GI-1 (a common vaccine genotype), UZB-IBV-2 clusters with GI-23, and UZB-IBV-3 clusters with GI-13. (c) A parallel phylogenetic tree was constructed from the deduced S1 amino acid sequences. The topology is congruent with the nucleotide tree, providing strong corroboration for classifying the three Uzbek strains into…

• 

  Figure 2. Analysis of genetic variability and selective pressure on the S1 gene of Uzbek IBV isolates. This panel shows site-specific analysis of nucleotide entropy (a measure of genetic variability, blue line) and the ratio of non-synonymous to synonymous substitutions (ω = dN/dS, red line) for each of the three identified genotypes. (a) The plot for the GI-1 isolate (UZB-IBV-1). (b) The plot for the GI-23 isolate (UZB-IBV-2). (c) The plot for the GI-13 isolate (UZB-IBV-3). Peaks in the red line (ω) highlight specific nucleotide positions evolving under positive (diversifying) selection, which are key sites for viral adaptation. Specific nucleotide substitutions are annotated above each plot. The heatmaps below each plot show the frequency of different amino acids at key variable positions, illustrating the unique mutational signatures for each genotype. The color intensity represents the relative frequency of each amino acid (from 0 to 1) based on the reference sequence. Crosses (×) mark the amino acid present at each site in the vaccine strain, and filled circles (●) indicate substitutions detected in the new strain.

• 

  Figure 3. Comparative structural and antigenic analysis of the three Uzbek IBV genotypes. (a,c,e) Predicted linear B-cell epitope profiles for the S1 protein of the GI-1 (a), GI-23 (c), and GI-13 (e) isolates, respectively. Peaks above the dotted line indicate regions predicted to be targeted by the host immune system. The differing profiles suggest the strains are antigenically distinct. (b,d,f) Corresponding 3D homology models of the S1 protein. Unique amino acid substitutions (e.g., 355E > Q in GI-1, 254E > R in GI-23) are mapped onto the surface of the protein. This analysis provides a structural basis for the predicted antigenic differences, showing how genetic changes alter the physical shape and properties of surface-exposed regions.