Journal Article

Genetic Characterization and Pathogenesis of Highly Pathogenic Avian Influenza Virus A (H5N1) Isolated in Egypt During 2021–2023

Aboulhoda, Basma Emad, El-Shesheny, Rabeh, Webby, Richard J., Kamel, Mina Nabil, Ali, Mohamed Ahmed, Moatasim, Yassmin, Gabre, Refaat M., El Sayes, Mohamed, McKenzie, Pamela P., AbdAllah, Hend, Kandeil, Ahmed, Gomaa, Mokhtar, El Taweel, Ahmed, Kutkat, Omnia, AlKhazindar, Maha M., GabAllah, Mohamed, Kayali, Ghazi

2025

Overview

Highly pathogenic avian influenza (HPAI) viruses have recently had a substantial impact on global poultry production and public health. In Egypt, clade 2.3.4.4b HPAI H5N1 viruses were first isolated from wild birds in 2021 and then became dominant in domestic poultry. In this study, we aimed to genetically characterize the H5N1 viruses isolated in Egypt during 2021–2023 and examine the pathogenicity and transmissibility of two H5N1 strains isolated from wild and domestic poultry in chickens. We collected 7588 specimens from live bird markets including poultry, wild birds, and environmental samples. Influenza A viruses were detected in 20.94% (484/2311) of tested samples, and 17 isolates were identified as H5N1 through complete genome sequencing. Phylogenetic analysis revealed that all H5N1 viruses were closely related to Eurasian viruses and classified into three distinct genetic groups, suggesting multiple introductions likely linked to migratory birds. Experimental infections of chickens with two H5N1 isolates, A/Pintail/Egypt/RA19853OP/2021 and A/duck/Egypt/BA20361C/2022, showed efficient replication, systemic infection, and transmission by direct contact. These findings underscore the need for continued surveillance of H5N1 at the poultry-wild bird interface to identify circulating strains, evaluate their biological characteristics, and assess their zoonotic potential.

• Publisher: MDPI AG
• Subject: Analysis / Animals / Animals, Wild - virology / Antibiotics / Avian flu / Avian influenza / Avian influenza viruses / Birds / Birds - virology / Chickens - virology / Disease transmission / Disseminated infection / DNA sequencing / Ducks - virology / Egypt / Egypt - epidemiology / Genome, Viral / Genomes / Genomic analysis / Genomics / H5N1 viruses / Health aspects / highly pathogenic avian influenza / Infections / Influenza A / Influenza A Virus, H5N1 Subtype - classification / Influenza A Virus, H5N1 Subtype - genetics / Influenza A Virus, H5N1 Subtype - isolation & purification / Influenza A Virus, H5N1 Subtype - pathogenicity / Influenza in Birds - epidemiology / Influenza in Birds - transmission / Influenza in Birds - virology / Migratory birds / Nucleotide sequencing / Pathogenicity / Pathogens / Phylogeny / Poultry / Poultry - virology / Poultry Diseases - transmission / Poultry Diseases - virology / Poultry industry / Public health / Strains (organisms) / Surveillance / transmission / Virulence / virus surveillance / Viruses / wild birds