Whole genome sequencing of infectious bursal disease viruses isolated from a Californian outbreak unravels the underlying virulence markers and highlights positive selection incidence

Authors: NOUR, ISLAM - Orise Fellow; Blakey, Julia; Alvarez-Narvaez, Sonsiray; Mohanty, Sujit

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2023
Publication Date: 10/3/2023
Citation: Nour, I., Blakey, J.R., Alvarez Narvaez, S., Mohanty, S.K. 2023. Whole genome sequencing of infectious bursal disease viruses isolated from a Californian outbreak unravels the underlying virulence markers and highlights positive selection incidence. Viruses. 15(10):2044. https://doi.org/10.3390/v15102044.
DOI: https://doi.org/10.3390/v15102044

Interpretive Summary: Infectious bursal disease (IBD), a highly contagious viral infection of young chickens is caused by Infectious bursal disease virus (IBDV). The infection causes huge economic loss due to death. Extensive usage of live vaccines has resulted in the evolution of new viruses. So, there is a need to immediately identify these viruses once they are isolated. In this study we conducted whole genome sequencing analysis of two viruses and showed characteristic changes in each gene. This type of whole gene sequencing analysis will provide insights into the evolution and early detection of IBDVs circulating in a region thereby guiding the farmers to take necessary control measures which would lead to improved animal welfare and maintaining economical poultry products to the consumer.

Technical Abstract: Outbreaks of the immunosuppressive infectious bursal disease (IBD) are frequently reported worldwide, despite the vaccination regimes. A 2009 Californian IBD outbreak caused by rA and rB isolates was described as very virulent (vv) IBD virus (IBDV); however, molecular factors beyond this virulence were not fully uncovered. Therefore, segments of both isolates were amplified, successfully cloned, whole genome sequenced by Next Generation Sequencing, genotyped, and the leading virulence factors were entirely investigated in terms of phylogenetic and amino acid analysis and protein modeling for positive selection orientation and interaction analysis. rA and rB isolates displayed the highest amino acid identity (97.84–100%) with Genotype 3 strains. Interestingly, rA and rB contained all virulence hallmarks of hypervariable (HVR), including 222A, 242I, 249Q, 256I, 284A, 286T, 294I, 299S, and 318G, as well as the serine-rich heptapeptide sequence. Moreover, we pinpointed the A3B2 genotype of rA and rB, predominant in non-reassortants, and we highlighted the absence of recombination events. Furthermore, gene-wise phylogenetic analysis showed the entire genes of rA and rB clustered with the vvIBDVs and emphasized their share in IBDV virulence. VP5 showed a virulence marker, MLSL (amino acid sequence). VP2 encountered three significant novel mutations apart from the HVR, including G163E in rA and Y173C and V178A in rB, all residing within interacting motifs. VP4 contained 168Y, 173N, 203S, and 239D characteristic for the vv phenotype. A235V mutation was detected at the dsRNA binding domain of VP3. In VP1, the TDN triplet and the mutation (V4I) were detected, characteristic of hypervirulence occurring at the N-terminus responsible for protein priming. Although selection analysis revealed seven sites, codon 222 was the only statistically significant selection site. The VP2 modeling of rA and rB highlighted great structure fitness, with 96.14% Ramachandran favored positioning including the 222A, i.e., not influencing the structure stability. The 222A was found to be non-interface surface residue, associated with no interaction with the attachment-mediated ligand motif. Our findings provide pivotal insights into the evolution and underlying virulence factors and will assist in the development of control strategies via sequence-based continuous monitoring for the early detection of novel vv strains.