Concurrent circulation of avian influenza viruses H5N1 and H9N2 enhances the genetic evolution of reassortant viruses in Egyptian poultry populations

by Nahed Yehia, Mahmoud Ibrahim, Rawan Muhammad Shady, Ahmed Abd Elhalem Mohamed, Dalia Said, Mohamed E. Taha, Abdelsatar Arafa, Samah Eid, Mohamed A.

Shalaby, Uwe Truyen, Rea Maja Kobialka, Ahmed Abd El Wahed, Arianna Ceruti The co-circulation of the recently emerged H5N1 clade 2.3.4.4b and the endemic H9N2 avian influenza viruses (AIV) in poultry farms has led to significant economic losses and increased the likelihood of viral reassortment. Continuous and extensive surveillance with full genome sequencing is highly recommended.

The objective of this study was to monitor AIV circulating in Egyptian poultry populations throughout 2024 using molecular surveillance and to detect genetic reassortment events. A total of 50 chicken flocks that exhibited respiratory symptoms from seven governorates in Egypt were tested for avian influenza H5, H9, Infectious Bronchitis virus (IBV), and Newcastle Disease Virus (NDV) using real-time RT-PCR.

Four flocks that tested positive for H5 (AN1, AN6, AN7, and AN8) and three flocks that tested positive for H9N2 (AN2, AN3, and AN4) were selected for isolation and full-genome sequencing.