Antigenic Drift and Immune Escape of Infectious Bursal Disease Viruses in Egypt: Molecular, Phylogenetic and Field Insights

Infectious bursal disease virus (IBDV) remains a major constraint to poultry production due to its continuous evolution and impact on vaccine efficacy. This study investigated the molecular characteristics of circulating IBDV strains in Egypt and assessed their relationship with field vaccination outcomes. Bursa samples were collected from clinically IBD suspected broiler flocks (n = 50) across five Egyptian governorates. Real-time RT-PCR identified 34 positive samples, of which five representative isolates were selected based on geographic distribution and age (≤23 days). Genotyping revealed the co-circulation of three novel variants (A2dB1b), one very virulent strain (A3B2), and one classical virulent strain (A1B1a). Molecular characterization of both VP2 and VP1 genes demonstrated marked diversity from standard vaccine backbones. VP2 analysis identified multiple amino acid substitutions within key neutralizing epitopes in the novel variants, including a consistent substitution at residue 321, suggesting a potential molecular marker. The very virulent isolate exhibited a distinct VP2 hypervariable profile featuring a substitution at residue 222 alongside mutations at positions 254 and 324. VP1 analysis further identified variations associated with viral replication efficiency. Sequence comparison indicated considerable genetic divergence from commercial vaccines, while sharing key amino acid features with recombinant HVT-VP2-based and immune complex vaccine strategies. Field observations strongly supported these molecular findings, as their use, particularly in combination with live vaccines, reduced IBDV detection rates to 28.5% and 40%, respectively, while reaching 93–100% with intermediate live vaccines. Overall, these findings highlight the critical need for continuous VP2-HVR molecular surveillance to optimize vaccine matching under field conditions.