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Abstract
In this study, we have approached the epidemiological situation of avian influenza in duck species during the period between February 2013 to October 2014 collected from the delta region governorates especially in domestic ducks which maintain the viruses in close proximity to other species and have been implicated in the spread of both LPAI and HPAI viruses to domestic poultry and terrestrial birds. We have pursue HA gene evolution by sequencing of selected 6 isolates from 17 positively confirmed by real time RT - PCR which revealed that 5 isolates were H5 subtype and its phylogenetic analysis belong to clade 2.2.1while one isolate was H9 subtype and its phylogenetic analysis showed that it is related to G1 like viruses. The sequence analysis of H5 nucleotides and predicted sequence amino acid revealed that all study isolates are closely related to each other while identity percentage from the first avian influenza isolate in Egypt was (95.4 to 98.5%) while H9 isolate show slightly different (96.7%) identity from the first H9N2 avian influenza isolated in Egypt. Although mutational rate differ between H5N1 isolates but all H5 isolates showed deletion of AA residue 129 and D43N substitution mutation while H9N2 isolate show S5P and S16N indicating continuous genetic evolution of avian influenza virus