Detection and Phylogenetic Analysis of Infectious Bursal Disease Virus Based on both Genome Segments A and B Isolated from Backyard Poultry Punjab, Pakistan

ABSTRACT In recent years, the re-emergence of virulent strains of infectious bursal disease virus (IBDV) has resulted in substantial economic losses in Pakistan despite mass and intense vaccination regimens. Infectious bursal disease (IBD) is one of the most important immunosuppressive diseases of the poultry and has been a constraint on sustainable food security around the globe, including Pakistan. This disease damages the bursa of Fabricius (BF), which causes immunosuppression in birds. A total of 50 tissue samples from backyard chicken flocks presenting suspected symptoms were collected during February 2020 and March 2021 for genetic characterization, followed by phylogentic analysis. A total of 4 isolates were sequenced based on partial VP1 and hyper-variable region of the VP2 genes simultaneously. According to phylogenetic analysis, the study isolates genotype A3B3 were identified as predominant strains in country backyard poultry. Concerning the identity matrix analysis of VP1 representative part, study isolates shared (87-88% nt; 95-96% aa) identity with the vvIBDV and (97-98% nt; 98-99% aa) with non-vvIBDV. While VP2 revealed (99-100% nt; 99-100% aa) identity with previously reported Pakistan vvIBDV strains and (91-95% nt; 91-95% aa) with non vvIBDV. Amino acid alignment analysis of VP1 revealed that current IBDVs have three characteristic aa residues of vvIBDV (287-A, 508-K, and 511-S) and four characteristic aa residues of non-vvIBDV (146-E, 147-G, 242-D and 390-L). While VP2 gene sequence alignment revealed eight characteristic aa residues of vvIBDV (222-A, 242-I, 253-Q, 256-I, 279-D, 284-A, 299-S, and 330-S and a distinct aa 384-I). Based on phylogeny, this is the first identification of IBDV segment reassortants having segment A of A3 (very virulent) and segment B of B3 (early Australian-like) genogroups reported in Pakistan backyard poultry. Further study is required to determine the pathogenicity of the IBDV reassortant and development of new policies for IBDV intervention in the country.