Current Genomic Characterization of Circulating Chicken Infectious Anemia Virus in Backyard and Commercial Chicken Flocks in Ismailia and Sharkia Provinces, Egypt

This study aimed to evaluate the occurrence, molecular characterization, partial sequencing, and phylogenetic analysis of the chicken infectious anemia virus (CIAV) circulating in chicken flocks in Ismailia and Sharkia Provinces, Egypt. Tissue pool samples (liver, thymus, spleen, and bone marrow) were collected from commercial and backyard flocks with anemia, uneven growth, and vaccinal failure history. The occurrence of CIAV was 51% (51/100) using specific primers through the polymerase chain reaction test, which was higher in the backyard (26/50) 52% than that in commercial flocks (25/50) 50%. The highest rate of CIAV detection was 77% (13/17) and 75% (9/12) in Saso and Arbor Acer breeds respectively, followed by the Baladi 52% (26/50) and Cobb 27 % (4/15). The histopathological study reflected severe lymphocytic depletions in lymphoid organs with the presence of apoptotic cells and eosinophilic intranuclear inclusion bodies. Partial sequence analysis of six selected field circulating CIAVs showed changes in VP1 at position H 22 Q, VP2 at position A 153 V, T 180 S and VP3 at position R 118 C indicating low affinity of the obtained viruses to grow in the cell line. Some obtained viruses showed mutations in the epitopic site which may develop escape mutation virus from the currently used vaccines. Phylogenetically, the six selected fields CIAVs were classified into two distinct groups. The continuous surveillance activities and epidemiological mapping for CIAV among Egyptian governorates using updating primers are essential to facilitate control program strategies.