Genetic analysis of avian influenza viruses (H5N1) isolated from backyard flocks in Egypt
2012
Ahmed, M. S.
The incidence of HPAI H5N1 virus in backyard birds was investigated in this study which covered different provinces of Egypt during the period of 1/2007 to 12/2010 using Real-time PCR, the samples were collected from different species of domestic poultry (chickens, turkeys, ducks and geese). The highly pathogenic avian influenza H5N1 virus was detected in (26.8%) of examined backyard birds, (13.5%), (20%) and (26%) in 2007, 2008, 2009 and 2010 respectively. it is noted that a higher numbers of positive flocks reared in mixed system. The vaccination status of positive backyard flocks, was recorded in (14.5 %), (38%), (14.6%) and (3.8%) in 2007, 2008, 2009 and 2010 respectively. The Nile Delta region was the highest recorded area and the circulation of the virus was higher in cooler temperatures. Full hemagglutinin (HA) gene sequencing was carried out to 95 AI H5N1 strains were isolated from different bird species. Analysis of the amino acid sequences revealed a pattern typical of HPAI, all Egyptian strains were very closely related and belonging to subclade 2.2. Six subgroups within the main Egyptian cluster were identified on the phylogenetic tree from A to F. Analyses of the amino acid sequence showed many substitution mutations appeared in comparison to Egyptian viruses isolated primarily in 2006.
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