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