Genetic characterization of highly pathogenic H5N1 avian influenza viruses isolated from poultry farms in Egypt

Twenty-four avian influenza viruses were collected from poultry farms in three different governorates in Egypt during the years 2006–2009 and genetically characterized. All the isolates were confirmed to be type A and subtype H5 influenza virus by chromatographic strip test and hemagglutination inhibition assay. The sequence and phylogenetic data revealed that all Egyptian isolates cluster together and belong to subclade 2.2.1 of the H5N1 virus of Eurasian origin. Within the clade, Egyptian isolates were classified into three major groups (A, B, and C) based on genetic similarity and chronology of the isolation. The majority of the recent isolates belonged to subgroup A. Interestingly, four strains, which were isolated from the same farm with two of the samples collected on the same day, were located in separate subgroups. In addition, the difference in topology between HA and NS phylogenetic trees, which indicates possible difference in dynamics of genetic evolution in two genes, was observed. Genetic characterization data of H5N1 isolates obtained from farms with different vaccination histories indicate the vaccines currently being used in Egypt do not provide adequate level of protection. Our study provides additional evidence for the need for updated vaccine and warrants continuous monitoring of H5N1 influenza virus in Egypt.