In this study, the incidence of avian influenza (AI) was investigated in commercial and native chicken and duck farms in West Delta region in Egypt during 2011 to 2013. There were ninety flocks (60 broilers, 5 layers, 5 breeder and 20 duck flocks) showing respiratory manifestation and mortalities. Tracheal swab samples were collected and tested for AIV by real-time RT-PCR. The results of real-time RT-PCR test used for detection of matrix gene of AI was positive for a percentage of 48.3%, 20%, 20% and 35% in broilers, layers, breeders and duck flocks respectively. The highest incidence was recorded in broiler flocks followed by duck flocks then layers and broiler breeder flocks with a total incidence of 42.22% in all chicken sectors.
Subtyping using real-time RT-PCR for H5 and H9 subtypes has been done. The results were positive for H5 by percentage of 13.33%and for H9 by percentage of 28.88%for chickens and duck farms.
Sequencing of HA gene from four AIV (3 from H5 and one from H9) viruses isolated during 2011 and 2013 and the phylogenetic trees were constructed. Phylogenetic tree showed that all HA gene sequences belonged to the Egyptian subclade 2.2.1 according to WHO/FAO/OIE nomenclature and the H9 isolate of 2012 was belong to G1- like lineage of H9N2 circulating the Middle East.
Key words: Polymerase chain reaction;
Avian influenza virus;
West Delta Egypt.