Computationally Optimized H1 and H3 Hemagglutinin Messenger RNA Vaccines Confer Broad Protective Immunity Against Modern Influenza Viruses

Abstract

The hemagglutinin (HA) glycoprotein of seasonal influenza viruses undergoes continual antigenic drift, contributing to vaccine mismatch and reduced effectiveness of strain-specific seasonal vaccines. Although vaccination remains the most effective strategy for preventing influenza disease, conventional egg-based vaccine production requires several months and may not keep pace with viral evolution. Messenger RNA (mRNA) vaccines offer a promising alternative because they can be rapidly updated to encode emerging antigens and are manufactured through a scalable, cell-free process that avoids propagation associated adaptations. To address the challenges of antigenic drift and vaccine mismatch, we combined mRNA vaccine technology with Computationally Optimized Broadly Reactive Antigens (COBRA) to develop broadly protective influenza HA vaccines. These COBRA H1 and H3 mRNA HA vaccines elicited robust antigen-specific IgG, hemagglutination inhibition (HAI), and neutralizing antibody responses against diverse historical and contemporary influenza strains in cohorts of influenza naïve and pre-immune mice. Vaccination also induced strong cellular immunity, characterized by the expansion of antigen-specific antibody and cytokine secreting cells. These responses were further enhanced in animals with pre-existing influenza immunity, as demonstrated by an increased frequency of IFN-γ producing cells recognizing conserved HA stalk-based peptides. Together, these findings demonstrate that COBRA HA encoding mRNA vaccines can effectively leverage immunological memory while expanding responses to conserved HA epitopes, supporting improved protection against antigenically drifted strains. Thus, the combination of broadly reactive COBRA HA antigens with a rapidly adaptable and manufacturable mRNA platform represents a promising strategy for next-generation influenza vaccination. Importance Recent influenza seasons have demonstrated that vaccine mismatch can have significant public health consequences, leading to increased disease burden, hospitalizations, and transmission. Modern mRNA vaccines offer a promising alternative to traditional egg-based vaccines because they can be rapidly manufactured and updated to better match emerging viral variants while eliciting strong antiviral immune responses. Importantly, the flexibility of the mRNA platform enables the expression of custom-designed antigens optimized for broad protection. Advances in computational antigen design now make it possible to incorporate immunologically relevant epitopes from multiple circulating viruses into a single vaccine antigen. By expanding immune responses beyond strain-matched protection, these broadly reactive antigens can elicit antibodies that recognize both dominant and emerging viral variants. As a result, they have the potential to establish immune memory against antigenically diverse strains before they become prevalent in the population, improving vaccine effectiveness during periods of antigenic drift.