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Avian influenza virus of H5N1 subtype, clade 2.2.1, was introduced into Egypt by wild birds In February 2006. Since then, these viruses caused significant losses in the poultry industry and posed a public health threat. Surveillance and monitoring of wild birds and domestic poultry described in this dissertation revealed important aspects in the epidemiology of AIV, particularly H5N1, in Egypt. In 2007, isolation of H7 from wild birds in an artificial wetland in Egypt incited us to carry out surveillance on household poultry on the border of the lake. None of the surveyed birds was positive for H7 viruses but few birds had antibodies against H5 (chapter 2).
In chapter 3, we conducted a national surveillance in domestic poultry in 2009 and wild birds in 2009-2010. In domestic poultry, the prevalence of the virus was very high in birds in the backyards and LBMs compared to the commercial enterprises. Prevalence of the virus was significantly high in households and LBMs that kept ducks. Infections of H5-vaccinated birds were not uncommon. Also, the virus was detected all over the year and from different provinces particularly in the Nile Delta region. We showed that the Egyptian H5N1 viruses are genetically diverse where two major groups are co-circulating since 2008: an antigenicdrift variant group in the vaccinated commercial poultry and a classic group in the backyard birds and human. Both genotypes developed powerful strategies to continue to evolve in different evolutionary pathways. Meanwhile, the viruses accumulated several point mutations in the HA immunogenic epitopes resulting in antigenic drift and the establishment of infections in vaccinated poultry. The classic viruses acquired mutations thought to improve the dual receptor binding affinity in avians and mammals. None of the samples tested from wild birds was positive for H5N1 virus.
In chapter 4, we described in details the vaccination failure of a layer chickens flock infected with a classic 2.2.1/C virus. The flock was vaccinated three times with a homologous H5N1 vaccine but morbidity, mortality and reduced egg production were reported. Breach in the biosecurity and/or poor vaccination was probably the main reasons for the infection. In chapter 5, we recorded for the first time the isolation of H9N2 from asymptomatic H5-vaccinated commercial bobwhite quails. The Egyptian G1-like virus was closely related to the viruses circulating in the neighbouring countries which may indicate a possible epidemiological link.
Based on the findings of this study we provided several recommendations to control the disease in poultry in Egypt. Although there are accumulating data from surveillance on the Egyptian H5N1 and H9N2 viruses in the last few years, many key knowledge gaps regarding the epidemiology and evolution of these viruses in poultry should be investigated.