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Abstract This study documents surveillance and trials for virus isolation of avian influenza from broiler, broiler breeders and commercial chicken layer flocks among different governorates of Egypt. The study recorded the recent incidence of AIV infection in Egypt during fall, winter, spring and summer of 2012-2013. 2960 samples from 148 commercial chicken farms from 13 governorates showed that 5 flocks were positive for type A AIV infection. Subtype specific (RT-PCR) results revealed 3 positive H5N1 flocks (2%) and 2 positive H9N2 flocks (1.35%) and negative for H7 subtypes. Multiplex PCR showed an accurate sensitive tool for simultaneous detection of different AIV subtypes. The phylogenetic analysis of avian influenza isolates demonstrated that these isolates clustered with reference isolates reported recently from Egypt in the period from 2011 to 2012 and the Egyptian AI viruses continue to evolve giving possibility for variant group formation. |