الفهرس 
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Abstract
In Egypt the poultry industry has been severely affected by continuous outbreaks of Avian influenza H5N1 and H9N2 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 have failed despite increased biosecurity, quarantine and vaccination, therefore in this study 90 samples from symptoms like broiler, layer, breeder and duck flocks suspected to be suffering from AI disease were collected from Alexandria, El-Behera, Gharbia and Kafr El-Sheikh governorates and examined for epidemiological survey and the spread of AI virus in these provinces.
Ninety poultry flocks including 60 broiler, 5 layer, 5 breeder and 20 duck flocks were collected from governorates mentioned and tested through isolation and identification of AI via RT-PCR ,SPF inoculation , HA tests and sequencing of H5 and H9 gene determine mutation incidence and Phylogenetic analysis of some local AIV isolates.
The total incidence in all tested flocks by RT-PCR test was 42.2% recording a high incidence in broilers (48.3%) then ducks (35%) later equal incidence in layer and breeder (20%) as the following:
AI virus was detected among broiler flocks in Alexandria, El-Behera, Gharbia and Kafr El-Sheikh at a percentage of 20%, 60.53%, 37.50%, and 20% respectively in examined broiler flocks with a n incidence of 48.3%.
The detection of AI virus among layer flocks in Alexandria was 33.33% and negative in EL-Behera in examined flocks with a total incidence of 20%.
The incidence of AI virus among breeder flocks in EL-Behera was 25% and negative in Gharbia in examined flocks with a total incidence of 20%.
AI virus was detected among duck flocks in El-Behera and Gharbia at a percentage of 20% and 50% respectively and negative in Alexandria , in examined flocks with a total incidence of 35%.
Sequencing and phylogenetic tree of hemagglutinin (HA) gene of three positive AIV two of them for H5N1 isolates from duck flocks of Gharbia at 2011and El-Behera at 2013 and one of broiler flock of EL-Behera governorate at 2013 .
One sample was sequenced for H9N2 isolate from broiler flock of EL-Behera governorate during 2012 were done and the results were as the following:
Phylogenetic tree showed that all HA gene sequences of three H5N1 samples was belonging to highly diverse clade 2.2.1 viruses Phylogenetic tree of one H9N2 sample was relted to the isolate are G1- like HA lineage present in the Middle East.