Genomic analysis of Avian Influenza and Newcastle disease viruses in diseased pigeons from Egypt

• Background: Respiratory viral infections in pigeons induce a wide array of clinical disorders and lead to significant economic impacts due to elevated morbidity and mortality, as well as trade limitations. Avian influenza (AI) and Newcastle disease (ND) in pigeons pose a significant threat to avian health and poultry production systems. This study intended to screen and characterize respiratory viruses present in pigeons in Egypt, specifically avian influenza virus (AIV) and Newcastle disease virus (NDV). • Methods: A total of 50 samples were obtained from clinically suspected pigeons in the cities of Mansoura, Aga, and Meet Ghamr, located in Dakahlia Governorate, Egypt. The samples were exposed to rapid screening by real-time reverse transcriptase polymerase chain reaction (rRT-PCR) to amplify AIV as well as NDV. • Results: The rRT-PCR showed that all tested samples were free from AIV, while NDV was detected in 10 samples (20%). These NDV-positive samples were isolated in the allantoic cavity of embryonated chicken eggs, showing typical signs in inoculated embryos with embryo mortality. All 10 rRT-PCR-positive samples tested by RT-PCR were positive. Three positive samples were chosen for partial gene sequencing and phylogenetic analysis. Phylogenetic trees of three sequenced samples verified that the circulating NDV in Egyptian pigeons is classified as Genotype VII.1.1 velogenic. BioEdit analysis of the inferred amino acid sequences revealed that the circulating strains are virulent, having the specific virulent NDV cleavage site (112RRQKRF117). In contrast, the GII vaccination strains exhibit the lentogenic cleavage site (112GRQGKL117). • Conclusions: This study concluded that all of the isolated strains were very virulent NDV, and there was a significant gap between field isolates and current GII vaccine strains.