A Multi-Epitope Pan-Betacoronavirus Vaccine Construct Predicted to Elicit Broad-Spectrum and Durable Immune Protection: An Immunoinformatics Approach

Abstract

Abstract Recurrent zoonotic spillovers and continuous antigenic evolution among coronaviruses, including SARS-CoV, MERS-CoV, and SARS-CoV-2, highlight the urgent need for a broad-spectrum pan-betacoronavirus vaccine capable of eliciting cross-protective immunity. Conventional vaccines, while effective against specific strains, can be limited by antigenic mismatch and waning immunity. In this study, a comprehensive immunoinformatics and reverse vaccinology framework was employed to design a multi-epitope peptide vaccine targeting conserved regions within the receptor-binding domain (RBD) of these pathogenic coronaviruses. Cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and linear B-cell epitopes were predicted and screened for antigenicity, allergenicity, toxicity, and non-homology. Selected epitopes were assembled into a 285–amino acid multi-epitope construct using optimized linkers (AAY, GPGPG, EAAAK, and GGGGS) and human β-defensin 3 as an adjuvant to enhance immunogenicity. Structural modeling and refinement yielded a stable 3D model (C-score −3.60). Molecular docking of the post-refinement construct with the B-cell receptor (BCR) Fab model using ClusPro identified a highly ranked complex from a highly well-populated cluster (Cluster 1; 49 members), with a Lowest Energy score of −865.9, indicating favorable interface complementarity under the docking scoring function. Subsequent molecular dynamics simulation supported the structural integrity and dynamic stability of the complex throughout the 100-ns trajectory, indicating minimal backbone deviation and sustained intermolecular interactions in the simulated environment. Immune simulations using a prime–boost regimen predicted, within the computational framework, coordinated humoral and cellular responses, including enhanced antibody kinetics, elevated IL-2 and IFN-γ, and sustained memory Band T-cell populations. The selected epitope set showed an estimated global HLA population coverage of 93.28%, indicating broad predicted HLA representation across diverse populations. These results identify a promising in silico multi-epitope RBD-based pan-betacoronavirus vaccine candidate and provide a foundation for subsequent experimental validation of immunogenicity, safety, and breadth of protection in relevant in vitro and in vivo models.