VaxSeer: Selecting influenza vaccines through evolutionary and antigenicity models

Abstract

Even though vaccines have the potential to significantly alleviate the disease burden of epidemics such as the seasonal flu, current influenza vaccines offer limited protection. According to the Centers for Disease Control and Prevention (CDC), vaccine effectiveness has hovered below 50% for the past decade. Identifying the optimal strains to use in a vaccine is central to increasing its efficacy. However, this task is challenging due to the antigenic drift that occurs during the flu season. In this paper, we propose to select vaccines based on their escapability score, a metric that quantifies the antigenic similarity of vaccine strains with future dominant strains and demonstrates a strong correlation with clinical vaccine effectiveness. We introduce a deep learning-based approach that predicts both the antigenic properties of vaccine strains and the dominance of future circulating viruses, enabling efficient virtual screening of a large number of vaccine compositions. We utilized historical antigenic analysis data from the World Health Organization (WHO) to demonstrate that our model selects vaccine strains that reliably improve over the recommended ones.