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Abstract
In this work, an active surveillance was applied on 216 live bird markets (LBMs) from eight different Egyptian governorates, where 34 out of 467 samples (7.3%) were positive for AIV subtype H5N1 but negative for the H7, H9 genes using RRT-PCR. The high detection rate was found in waterfowl (7.86%) and the infections were higher in winter season. The positive samples were isolated in ECE and 8 isolates were genetically characterized for the H5 gene and 4 out of the 8 for the N1 gene. The results showed that they retain the reported most of H5N1 AIV sequence properties relevant to virus virulence and were closely related to each other based on (HA, NA) sequencing . Mutations at various positions of the HA gene were reported and they were more identitical to the household AIV isolated in Egypt. N1 genes of the 4 isolated strains have no mutations in the amino acids responsible for oseltamivir resistance. Interestingly, we found that the current circulating strains isolated in 2009 show the low similarity to strains used for poultry vaccination in Egypt.