Deciphering the Natural Reassortment Dynamics of Infectious Bursal Disease Virus, Isolated from Field Outbreaks in Southern India, Through Complete Genome Sequencing

The present study was carried out to analyze the complete genome sequences of infectious bursal disease virus (IBDV) isolates obtained from field outbreaks in the southern regions of India. Bursal tissue samples were collected and screened by RT-PCR, targeting the VP2 gene. Positive samples were subjected to serological identification via AGID. Following this, eight samples (BGE14, BGE15, MDI14, THI14, EDE14, RPM14, VCN14, and NKL14) were subjected to virus isolation in 9 to 11-day-old embryonated chicken eggs, and their complete genomes were sequenced. Analysis of the VP2 hypervariable region (HVR) revealed that all eight isolates had five unique and highly conserved amino acids (A222, I242, Q249, I256, and S299). However, all the isolates reveal a substitution of Isoleucine by Valine at residue 294 (I294V). Furthermore, analysis of segment B from all Indian IBDV sequences revealed that the triplet amino acid pattern was NEG (residues 145-147) and the amino acid at position 242 was consistently D across all isolates. These findings suggest that segment B of the isolates in this study resembled that of vaccine strains and non-vvIBDV strains. Additionally, the presence of the signature D242 in all Indian isolates, characteristic of non-vvIBDV strains, implies a potential attenuation. Moreover, in the phylogenetic analysis of VP2-HVR, all isolates clustered with very virulent reference strains, while segment B clustered with classical attenuated strains. Notably, the phylogenetic analysis of VP2-HVR and VP1 of these viruses demonstrated genetic variances, suggesting evolutionary changes in segment B across all eight Indian isolates, likely indicative of natural genome reassortment resulting in these specific outbreaks in the flocks.