Chicken anemia virus is a significant immunosuppressive pathogen of poultry that causes anemia, lymphoid atrophy, and increased susceptibility to secondary infections, leading to significant economic losses. The current study aimed to investigate the genetic diversity and structural characteristics of indigenous CAV isolates. VP1 gene sequences of indigenous CAV isolates OP11 - OP19 were amplified, sequenced, and comparatively analyzed with reference and vaccine strains using bioinformatics tools. Multiple sequence alignment and phylogenetic analysis were performed using MEGA 11. Alignment revealed amino acid substitutions at various positions of VP-1 Protein, indicating genetic variability among circulating isolates. Phylogenetic analysis showed that OP11 - OP17 clustered with international strains such as Egy-4-CAV and Arg728, whereas OP18 and OP19 were more closely related to the vaccine strain Del-Ross. Selected isolates OP12 and OP14 were further analyzed for structural and immunological studies. Three-dimensional structures predicted using AlphaFold2 showed conserved folding patterns, while epitope prediction identified surface-exposed antigenic regions. Docking Analysis of VP-1 protein with Toll-like receptor 3 indicated variations in binding patterns. Overall, the study highlights the genetic diversity and structural characteristics of circulating CAV isolates.
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