Molecular Inspection of Avian Influenza HA1 Gene through Protein Homology Modeling and Prediction of Antibody-Binding Epitopes

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Abstract The study analyzed avian influenza in seven bird species including wild and Domestic birds: Eurasian Coot, Eurasian Teal, Common Moorhen, Northern Pintail, Tufted Duck, domestic duck and domestic chickens - by collecting tissue samples from dead birds, and nasal and cloaca swabs from some living birds ducks and local domestic chickens. This comprehensive approach respected the birds' well-being while providing valuable insights into the virus's prevalence. Highly contagious avian influenza virus (AIV) threatens Egypt's poultry industry, prompting a deep dive into its molecular and epidemiological landscape. Focusing on H5 and H9 subtypes in both domestic and wild birds across five provinces, researchers uncovered a diverse array of circulating strains. H5N8 AIV detected in 4 flocks, mixed H5N1 AIV and NDV infections in 3, and H9N2 AIV in 22. One flock harbored both H9N2 and H5N1, raising concerns about co-circulation and reassortment. Vaccine mismatch, Genetic analysis revealed significant divergence between circulating strains and commercially used vaccines, particularly for H5N8 and H9N2, suggesting potential ineffectiveness. Predicted antibody-binding epitopes further corroborated this, showing higher similarity to a specific older vaccinal strain than currently used ones. A critical gap exists between vaccines and circulating AIV strains in Egypt. Updated vaccines based on prevalent viruses are urgently needed. This study highlights the importance of integrating molecular and epidemiological approaches for developing informed vaccine strategies and improving avian influenza control.

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