VaxSeer: Selecting influenza vaccines through evolutionary and antigenicity models

Current vaccines provide limited protection against rapidly evolving viruses. For example, the flu vaccine’s effectiveness has averaged below 40% for the past five years. Today, clinical outcomes of vaccine effectiveness can only be assessed retrospectively. Since vaccine strains are selected at least six months ahead of flu season, prospective estimation of their effectiveness is crucial but remains under-explored. In this paper, we propose an in-silico method named VaxSeer that selects vaccine strains based on their coverage scores, which quantifies expected vaccine effectiveness in future seasons. This score considers both the future dominance of circulating viruses and antigenic profiles of vaccine candidates. Based on historical WHO data, our approach consistently selects superior strains than the annual recommendations. Finally, the prospective coverage score exhibits a strong correlation with retrospective vaccine effectiveness and reduced disease burden, highlighting the promise of this framework in driving the vaccine selection process.