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