Molecular Characterization of Chicken Anaemia Virus Circulating in Commercial Poultry Flocks in Egypt during 2020

Chicken Anemia Virus (CAV) is an extremely contagious immunosuppressive disease causing high economic losses in poultry production. In the present study, tissue samples (bone marrow, thymus, and spleen) were collected from 86 different broiler chicken farms located in fourteen governorates in Egypt during 2020. They suffered from retard growth, weakness, and a drop in egg production with an observed mortality rate ranged 5-15%. A total of 26 samples were positive for CAV using PCR in six governorates in Lower Egypt with a 30% incidence rate, especially in Sharkia (78%), Ismailia (62.5%), and Alexandria (60%). The viral protein1 (VP1) gene of CAV was genetically characterized by sequencing of 10 selected viruses in six governorates. revealing that all Egyptian strains were clustered into two groups (A, B) that was distinct from vaccine strains (Del-Ros, Cux-1, and 26PA) which were clustered in group C. The seven Egyptian viruses in this study (A-Egypt-AN1-2020 to A-Egypt-AN7-2020) were clustered with the viruses from Japan, Argentina, and Malaysia in group A, and the other three viruses (A-Egypt-AN8-2020, A-Egypt-AN9-2020, A-Egypt-AN10-2020) were clustered with the viruses from Nigeria, and India in group B. The Egyptian viruses in the current study acquired new specific mutations clustering them into new subgroups (2A, 2B). By mutation analysis comparing with Del-Rose reference strains, V75I, M97L, and K139Q, E144Q were recorded in all viruses in the group A and B. All Egyptian viruses in the current study had specific new mutations at Y13N, H22N. Moreover, mutation at G74E in Egyptian viruses recorded in the current study was related to sub group 2A, I83V in three strains (A/Egypt/AN1/2020, A/Egypt/AN2/2020, A/Egypt/AN4/2020), and S140A in the hypervariable region was found in four strains (A/Egypt/AN1/2020, A/Egypt/AN2/2020, A/Egypt/AN4/2020 and A/Egypt/AN5/2020) in subgroup 2A. Furthermore, Q139 and Q144 amino acid substitutions, which are important in viral replication, were observed in all viruses. The field viruses in the study were distinct from the vaccinal strains by phylogenetic analysis and A.A. identity. In conclusion, the CAV was continuously circulating in Egypt from different genotypes. It acquired new specific mutations clustering them in a new subgroup, and it was distinct from vaccinal strains. Therefore, it is important to conduct continuous monitoring on the genetic evolution of CAV and further studies on the pathogenicity of the virus and the vaccine efficacy.