Molecular characterization for non structural proteins of Avian Influenza Virus

Master's Thesis from the year 2015 in the subject Biology - Micro- and Molecular Biology, grade: -, , course: Influenza, language: English, abstract: Highly pathogenic avian influenza virus (HPAIV) H5N1 has been endemic in Egypt since 2006 and raised concern recently for its potential to evolve and be of highly transmissible among humans. Infection of HPAIV H5N1 has been described in experimentally challenged birds. However, pathogenicity of HPAIV H5N1, isolated in Egypt, has not been reported in naturally infected chickens and ducks, which could be unique due to distinct transmission routes and dosage of infection. Here we report a recent outbreak of HPAIV H5N1 in 2013, in commercial poultry farms in Sharkia Province, Egypt. The main symptoms were ecchymoses on the shanks and feet, cyanosis of the comb and wattles and subcutaneous edema of head and neck for chickens, and nervous signs (torticollis) for ducks. Within 48-72 hrs of the onset of illness, the average mortality rates were 22.8-30% and 28.5-40% in vaccinated chickens and non-vaccinated ducks, respectively. Tissue samples of chickens and ducks were collected for cross-section immunohistochemistry and realtime RT-PCR for specific viral RNA transcripts. Higher viral RNA transcripts were detected in tissues of chicken broilers and layers, including trachea, lung, spleen, intestine, brain, and serum, than those of ducks which have only viral RNA transcripts in trachea, lung, and liver tissues. In chickens, the highest viral RNA levels appeared to be in brain, trachea, and serum with significant differences detected between chicken broilers and layers in theses tissues in particular. Significant differences of the viral RNA were observed in trachea, lung, and liver tissues of ducks than those of chickens, indicating that HPAI H5N1 replicates with distinct tissue tropism between chickens and ducks. However, these samples from different birds cannot be compared because they came from natural outbreaks with uncertain timing of the course of infection. While the viral RNA was nearly detected in all tissues and serum collected indicating viral pan-tropism, the viral antigen was detected almost ubiquitously accordingly in all tissues including testicular tissues. Interestingly, viral antigen was also observed in endothelial cells of the most organs, and seen clearly in trachea and brain in particular as well as in mononuclear cells of various tissues particularly lungs. We performed phylogenetic analyses and compared the genomic sequences of the surface hemagglutinin (H) and non structural protein 1(NS1) among the isolated viruses, the HPAI H5N1 viruses.