Abstract

Poultry production has been affected by multiple respiratory diseases triggering serious economic losses in Egypt. The current study aimed to investigate the situation and genetic evolution of respiratory diseases in Egypt during 2020. A total of 53 samples were collected from infected flocks suffering from respiratory signs and variable mortality rates from nine governorates in Egypt during 2020. The collected samples were examined for the detection of respiratory disease viruses (Avian influenza virus (AIV (H5N8, H9N2), Infectious bronchitis virus (IBV), and Newcastle disease virus (NDV)) by rRT-PCR. The single infection was confirmed in 90.6% (37.7% I.B, 30.2% AIV (H5N8), 9.4% I.B and 5.7% NDV) and co-infection of HPAIV (H5N8) + I.BV and LPAIV (H9N2) +IBV were detected in 3.8% of nine governorates. The HA gene of HPAIV (H5N8) was cluster to clad 2.3.4.4.1b in a new branch with characteristic specific mutations especially in T140A in antigenic site A and R72S in the receptor-binding site, compared to A/duck/Egypt/F446/2017 with low A.A identity percent with vaccinal strains of H5N1 and H5N2 reaching to 91.9-94% and 84.6%, respectively. The HA gene of AIV (H9N2) belonged to A/quail/Hong Kong/G1/97-like virus clustered with group B with a specific mutation (212I) that may affect the human transmission of the virus. The HVRs of S1 gene of IBV cluster to GI23 (Egy Var I) clad with multiple mutations in HVR1 and HVR2, compared to IBV/CU/4/2014 and low identity percent (68.3-78.8%) with vaccine strains (H120, M41, 4/91). In conclusion, respiratory disease continues to circulate and rapidly evolve in Egypt during 2020.