Evolution-Informed Viroinformatics Identifies Conserved Immune Targets with Predicted Lower Mutational Vulnerability Across Betacoronaviruses

The extensive evolutionary diversity and continuous mutational adaptation of betacoronaviruses represent a major challenge to the development of broadly protective countermeasures. This study applied an evolution-informed Viroinformatics framework to systematically identify conserved and immune targets with predicted lower mutational vulnerability across betacoronaviruses. The workflow integrated comparative sequence conservation and phylogenetic analysis with immunoinformatics-based epitope screening, HLA population coverage, mutational escape profiling, structural modeling, molecular docking, and molecular dynamics simulations. Conserved cytotoxic T-lymphocyte and helper T-lymphocyte epitopes were prioritized based on immunogenicity, antigenicity, safety, HLA binding potential, evolutionary conservation, and predicted resistance to mutational escape. Combined MHC class I and II analysis predicted a theoretical global population coverage of 99.92%, which requires experimental validation. The resulting 409-amino-acid multiepitope construct was predicted to be antigenic, non-allergenic, and physiochemically stable. Structural validation showed that 99.7% of the residues were located within favored or additionally allowed regions. Molecular docking demonstrated favorable interaction of the vaccine construct with TLR7, while a 100 ns molecular dynamics simulation supported persistence of the predicted vaccine-receptor association. Overall, these findings provide a computational framework for prioritizing evolutionarily conserved immune targets and developing pre-emptive candidate epitopes showing predicted cross-betacoronavirus conservation within the analyzed dataset. Experimental studies evaluating HLA binding, cellular and humoral immunogenicity, recombinant expression, cross-reactivity, and in vivo protection are required to validate the predicted immunological potential and determine whether the proposed construct can provide broad protection against diverse betacoronaviruses.