Phylogenetic and epidemiological characteristics of H9N2 Avian Influenza Viruses from 2020 to 2022 in Egypt

. ABSTRACT T he H9 low-pathogenic avian influenza (LPAI) viruses cause enormous economic harm despite their low pathogenicity. It became common in Egypt in 2011 and has undergone ongoing genetic evolution since then. To limit the virus's transmission, regular monitoring of its evolution is essential. The current study concentrated on the frequency and molecular characteristics of LPAI H9N2 viruses spreading throughout different Egyptian areas between 2020 and 2022. Using real-time PCR, 503 positive LPAI H9 cases were detected out of 29,319 cases, for a total prevalence rate of 1.7%. However, live bird market (LBM) had the highest LPAI H9N2 prevalence rate (10.6%), followed by household sector and farm (2 % and 1.3% respectively). The 33 samples were isolated in 11-day-old embryonated chicken eggs (ECEs) before being sequenced for partial hemagglutinin (HA). The H9 isolates were phylogenetically related to the Egy-2 G1-B branch (pigeon-like), which has been the prevalent circulating H9N2 genotype in Egypt since 2016. The findings of the sequence analysis revealed a clear genetic evolution compared to the original