Thesis (M.Sc.) - Cairo University - Faculty of Pharmacy - Department of Microbiology and Immunology

In Egypt, HPAI (H5N1) virus was first detected in poultry in February 2006; and in March 2006, the first human infection was detected. A total of 173 cases with 63 deaths were reported since March 2006 till 30 June 2013. Increases in the annual number of human infections and accompanying decreases in case-fatality ratios in Egypt during 2009-2011 compared with those in 2006-2008, led to the hypothesis that the circulating viruses may have acquired distinct properties. To address this issue, we studied the genetic and antigenic diversity of subtype H5N1 viruses isolated from humans in Egypt during 2007-2011.Oropharyngeal swabs from patients with suspected HPAI (H5N1) infection were received in the US Naval Medical Research Unit No. 3 (NAMRU-3) as the WHO Influenza Reference Laboratory from the Central Public Health Laboratory (CPHL) operated by the Egyptian Ministry of Health and Population for confirmation. Samples were tested by molecular methods for the presence of Influenza A subtype (H5N1) genes. Positive samples were sequenced and inoculated in SPF eggs to isolate the virus. All analyzed viruses evolved from the lineage of subtype H5N1 viruses introduced into Egypt in 2006; we found minimal evidence of reassortment and no exotic introductions. The hemagglutinin genes of the viruses from 2011 formed a monophyletic group within clade 2.2.1 that also included human viruses from 2009 and 2010 and contemporary viruses from poultry; this finding is consistent with zoonotic transmission

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