Genomic surveillance and evolution of co-circulating avian influenza H5N1 and H5N8 viruses in Egypt, 2022-2024

For over two decades, avian influenza virus (AIV) has significantly impacted the Egyptian poultry population, with multiple subtypes and genotypes contributing to significant economic and agricultural losses. As part of an ongoing national surveillance effort, this study aimed to monitor and genetically characterize AIV circulation across various poultry sectors in Egypt. Between 2022 and 2024, a total of 446,790 swab samples were collected, representing commercial farms (n = 25,057), backyard flocks (n = 403), and live bird markets "LBM" (n = 1250) to assess the prevalence and genetic diversity of circulating AIV strains. A total of 173 sampling units were found positive for high pathogenicity (HP) AIV H5, including farms (n = 17), backyards (n = 11), and LBMs (n = 145). The HPAIV of H5N8 subtype was dominant (n = 75) over the H5N1 (n = 27) subtypes among all sectors and bird species (chickens, ducks, turkeys). Whole genome sequence analysis of positive H5 samples revealed high similarity with HPAIVs of clade 2.3.4.4b, which has been confirmed phylogenetically. Two distinct subtypes H5N1 (EA-2021-AB genotype) and H5N8 (EA-2020-A genotype) were identified, with two variants detected within the H5N8 viruses. Evolutionary analyses indicate that Egyptian H5N8 viruses are under strong selection pressure and exhibit a higher nucleotide substitution rate compared to the Egyptian H5N1 viruses of clade 2.3.4.4b. With the evolving HPAI H5 virus's situation in different locations around the globe, including Egypt, this study underlines the importance of active surveillance in the timely detection of emerging AIV genotypes, monitoring virus evolution, and refining risk assessments.