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Freie Universität Berlin (2020)

Avian influenza infections in poultry farms in Egypt, a continuous challenge : Current problems related to pathogenesis, epidemiology and diagnosis

Hassan, Kareem

Titre : Avian influenza infections in poultry farms in Egypt, a continuous challenge : Current problems related to pathogenesis, epidemiology and diagnosis

Aviäre Influenza-Infektionen in Geflügelfarmen in Ägypten, eine ständige Herausforderung : Aktuelle Probleme im Zusammenhang mit Pathogenese, Epidemiologie und Diagnose

Auteur : Hassan, Kareem

Université de soutenance : Freie Universität Berlin

Grade : Doktors der Veterinärmedizin 2020

Résumé partiel
Since 2006, Egypt is facing huge challenges related to the spread of avian influenza viruses. This is partly due to the very high death toll of HPAI in poultry populations causing huge economic losses. The ability of some AI viruses to cross species barriers and invoke severe and often fatal illness in human beings causes further alert. Sequential introduction of new viruses and enzootic co-circulation of different AI subtypes and clades as well as presence of further avian respiratory pathogens, such as IBV and NDV, are at the basis of these problems. All previous efforts to eradicate and control AI in Egypt were unsuccessful. The main objectives of this study aim at providing an update of the epidemiological situation regarding AIV including molecular characterization, and genotyping and reassortment analysis of AIV subtypes circulating in poultry in Egypt between 2017 and 2019. In addition, an assessment was attempted of the role of co-infections with different AIV subtypes and/or other respiratory viruses such as IBV and NDV. As a prerequisite for such work, improved diagnostic tools were developed and evaluated for AIV detection. In Chapter 2.1, various combinations of co-infections in poultry flocks with three different AIV subtypes and other respiratory pathogens such as IBV and NDV were detected in 32 out of 39 farms examined. The percentage of AIV H9N2‐positive samples was high (27/39), and co‐presence of HPAIV H5N8 was detected most often (22/39). The previously dominating HPAIV subtype H5N1 was only infrequently detected. Sequence and phylogenetic analyses of the hemagglutinin gene showed that both H5 and H9 viruses were located at the tips of the respective cluster branches indicating ongoing genetic drift. Several coding mutations in the neuraminidase N2 hemadsorption site suggested some adaptation to mammalian hosts. Sensitive detection of H9N2 viruses by RT-qPCRs required an update of diagnostic tools. Examination of further Egyptian poultry samples collected in early 2019 from 11 commercial broiler chicken farms revealed the presence and circulation of new reassortant AI viruses (Chapter 2.2). This affected HPAIV H5N8 of which two different reassortants were characterized that had not been reported in Egypt before. Also, novel reassortant H9N2 viruses were detected in chicken holdings for the first time in Egypt. Most importantly, however, a novel reassortant HPAIV H5N2 was found on three chicken holdings in different areas of Egypt.

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Page publiée le 13 janvier 2021