Immunoinformatics-driven design of a conserved RNA-dependent RNA polymerase-based multi-epitope vaccine against avian infectious bronchitis virus

Abstract

Background and Aim: Avian infectious bronchitis virus (IBV) is a highly contagious coronavirus that causes severe respiratory, renal, and reproductive disease in chickens, resulting in significant economic losses in the poultry industry worldwide. The high mutation and recombination rates of IBV, especially in structural proteins like the spike glycoprotein, limit the effectiveness of current live attenuated and inactivated vaccines. This study aimed to design and computationally evaluate a novel multi-epitope vaccine (MEV) targeting the highly conserved RNA-dependent RNA polymerase (RdRp) of IBV in order to provide broad and lasting immune protection. Materials and Methods: The RdRp protein (NCBI: NP_740629.1) was chosen as the vaccine target due to its high sequence conservation and crucial role in viral replication. B-cell, cytotoxic T-lymphocyte (CTL), and helper T-lymphocyte (HTL) epitopes were predicted using various immunoinformatics tools, followed by strict screening for antigenicity, non-allergenicity, non-toxicity, interferon-γ induction potential, and lack of homology with Gallus gallus proteins. The selected epitopes were assembled into a single construct with suitable linkers, incorporating avian β-defensin 8 as an N-terminal adjuvant. The vaccine candidate was analyzed in silico for physicochemical properties, structural stability, solubility, molecular docking with chicken Toll-like receptor 7 (TLR-7), molecular dynamics, and immune response simulation. Results: The final multi-epitope construct showed favorable physicochemical properties, including high stability (instability index: 25.74), hydrophilicity, and predicted solubility (Protein-Sol score: 0.504). Structural modeling and validation confirmed a reliable tertiary structure. Molecular docking demonstrated strong, stable binding to TLR-7, supported by multiple hydrogen bonds and salt bridges, while molecular dynamics analysis indicated sufficient flexibility for immune recognition. Immune simulations forecasted robust humoral and cellular immune responses, characterized by increased IgG levels, expansion of memory B and T cells, and a Th1-biased cytokine profile with significant interferon-γ production. Conclusion: This immunoinformatics-designed RdRp-based MEV is a promising candidate for broad-spectrum protection against IBV. By targeting a conserved non-structural protein, it may address limitations linked to strain-specific vaccines. In vitro and in vivo testing is needed to confirm its safety, immunogenicity, and protective efficacy in poultry. Keywords: avian infectious bronchitis virus, avian immunoinformatics, multi-epitope vaccine, poultry coronavirus, RNA-dependent RNA polymerase, toll-like receptor-7, vaccine design.