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

This study's main objective was to update avian influenza (AI) epidemiological situation, including molecular characterization reassortment analysis and genotyping of circulating AI virus (AIV) subtypes in Egyptian poultry farms between 2017 2019. As a necessity for such work, improved diagnostic tools were developed AIV detection. Subtype H9N2 infections detected 27 out 39 examined frequently mixed with high pathogenic (HPAI)AIV H5N8 22/39 farms. Next-generation Sanger sequencing helped define novel reassortant HPAIV H5N2 low (LPAIV) Egypt. Systematic confirmed at least seven genotypes HPAI H5NX viruses clade 2.3.4.4b three LPAIV Several internal genes AIVs previously wild birds Egypt represented the genome reassortants both HP H5Nx suggesting local processes.