Relationship between some H5 commercial vaccines and the highly pathogenic H5N8 avian influenza virus that is recently circulating in Egypt

The prevalence of avian influenza viruses (AIVs) in Egypt has had a devastating effect on the poultry sector. Here, we isolated two HPAI (H5N8) viruses from broiler poultry farms in Menoufia and Dakahlia governorates during the period from November 2020 to December 2021. The phylogenetic profiling of the two isolates showed a relationship to clade 2.3.4.4b viruses. The percentage of identity between the sequences of nucleotides of the haemagglutinin gene (HA) between our two isolates and the two commercial vaccinogenic viruses; A/chicken/Egypt/18-H/2009/H5N1 that belongs to clade 2.2.1.1, and A/duck/postdam/1402/1986 (H5N2) that belongs to classical strains, is 84% and 87%, respectively, while the percentage of amino acid similarity is 88% and 86%, respectively. In addition, we compared the 3D protein structure of the HA gene from our recently isolated H5N8 viruses with the identical commercial vaccines previously mentioned, and we found that the newly emerging H5N8 viruses have some mutations in antigenic sites A, C, D, and E that are not found in the commercial vaccines. This antigenic mismatching leads to the vaccinal failure of avian influenza and the appearance of escape mutant strains.