Avian influenza virus A (AIV) is found in most instances in birds, and rarely in humans. Since 1997, there have been isolated occurrences of the H5N1 subtype in humans. In the current investigation, the emerged highly pathogenic avian influenza subtype H5N1 was isolated from infected birds from different governorates (Kaliobya, Sharkyia, Mansora and Gharbia) over a
five year period from 2010 to 2015.birds was suffering acute infection and showed high mortality rate and molecularly assessed by PCR amplification of the cleavage site and full Haemagglutinin gene then sequencing. Sequence analysis discovered some variation across various isolates from various years. Analysis of the multi-basic amino acid sequence of the
isolated virus revealed the presence of the characteristic cleavage motif of the highly pathogenic H5N1 (PQ↓ (G/R) EKRRKKR↓GLF) while some strains having differences in the (G>R) a single amino acid within the cleavage site motif. The deduced amino acid sequence analysis of the isolated nine strains of HPAI (H5N1 subtype) revealed a high degree of homology.