Molecular characterization of the avian influenza virus in Egypt

Epidemiological studies on AI virus in different governorates in Egypt [Alexandria, Bohera, Gharbia, Kafr El Sheikh, Fayoum and Menofia] during 2007 to 2009 were carried out. These studies included broiler, layer and breeder flocks in addition to duck flocks and pigeon samples. Using the RT-PCR and Chromatography test, the data revealed the following: A total of 29 out of 59, 5 out of 11 and 2 out of 5 broiler, layer and breeder examined flocks were positive with a percentage of 49.2%, 45.5% and 40% respectively. Regard to duck flocks, 10 examined flocks were negative but 2 birds out of 82 pigeon samples were positive with a percentage of 2.4%. The data clearly indicated that the highest outbreaks with AI virus were recorded in broiler flocks followed by layer and breeder flocks, then pigeon samples. The data also, indicated that the chromatography test is a highly sensitive test used for detection of the avian influenza virus. The phylogenetic analysis of the full length genome sequences of the eight viral segments from virus isolates from chicken revealed that the clustering of our samples was within clade 2.2. The isolates had the multiple basic sequences in the heamagglutinin gene at cleavage site indicating a highly pathogenic phenotype. Sequence analysis of the eight gene segments showed nucleotide as well as amino acid substitutions