الفهرس 
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Abstract
The poultry industry in Egypt has been severely affected by continuous outbreaks of Avian influenza H5N1, resulting in severe losses to investors in the field of poultry and death of human beings who come in contact with infected birds. Many efforts to control highly pathogenic H5N1 avian influenza virus in poultry and in humans have failed despite increased biosecurity, quarantine and vaccination, therefore in this study 75 representative samples from broiler, layer, breeder and duck flocks suspected to be suffering from AI disease were collected from Alexandria, El-Behera, Cairo, El-Fayoum, Giza, Gharbia and Dakahlia governorates and examined for epidemiological survey and the spread of AI virus in these provinces.
75 poultry flocks including 49 broiler, 17 layer, 4 breeder and 5 duck flocks were collected from governorates mentioned above and tested through isolation and identification of HPAI H5N1 virus via SPFegg inoculation, HA, HI, RT-PCR, immunochromatography and Sequencing H5 gene to determine mutation incidence and Phylogenetic analysis of some local AIV isolates.
The total incidence in all tested flocks by HI test was 44% recording a high incidence in layers followed by breeders, ducks then broilers as the following:
AI virus was detected among broiler flocks in Alexandria, El-Behera, El-Fayoum, Gharbia and Giza at a percentage of 26.1%, 34.8%, 100%, zero% and 100% respectively in examined flocks with a total incidence of 32.7%.
The detection of AI virus among layer flocks in Alexandria, EL-Behera, Cairo, Gharbia and Giza was 57.14%, 100%, 50%, 100% and 100% respectively in examined flocks with a total incidence of 76.5%.
The incidence of AI virus among breeder flocks in Alexandria and Dakahlia was at a percentage of 33.3% and 100% respectively in examined flocks with a total incidence of 50%.
AI virus was detected among duck flocks in Alexandria and El-Behera at a percentage of 33.3% and 50% respectively in examined flocks with a total incidence of 40%.
In the attempt to compare the specificity and sensitivity of polymerase chain reaction (RT-PCR) and HI, 28 samples were tested with both tests; the sensitivity and specificity of RT-PCR was 100%.
In the attempt to compare the specificity and sensitivity of immunochromatography and HI, 33 samples were tested with both tests, the sensitivity and specificity of immunochromatography was 100%.
In the attempt to compare the specificity and sensitivity of immunochromatography and polymerase chain reaction (RT-PCR), 22 samples were tested with both tests, both sensitivity and specificity of immunochromatography were 100%.
Sequencing and phylogenetic tree of hemagglutinin (HA) gene of six positive AIV H5N1 isolates from different flocks (broiler, layer and breeder) of different governorates (El-Behera , Dakahlia and Gharbia) during 2010 were done and the results were as the following:
Phylogenetic tree showed that all HA gene sequences belonged to highly diverse clade 2.2.1 viruses according to WHO/FAO/OIE nomenclature and the isolates analyzed grouped separately in two distinct sublineages (clade A and clade B) Some viruses clustered together and with Egyptian viruses isolated in 2009-2010 (clade A), while the isolates belonged to distinct sublineage (clade B) with viruses isolated in 2008-2010.
Analysis of amino acid sequences of HA glycoprotein revealed some mutations at the receptor binding site of the HA molecule.