From sequences to strategies: Early detection of new SARS-CoV-2 variants via genetic distance to reduce hospitalizations

The COVID-19 pandemic highlighted the critical need for robust methods to monitor viral evolution and detect emerging variants of concern (VOCs). This study expanded an unsupervised clustering algorithm, based on Levenshtein distance, to track and predict variant predominance across six European countries from 2020 to January 2024. We also investigated the influence of genetic distances and containment strategies on hospitalization rates. Spike protein sequences were transformed into temporal chains. A deep neural network (DNN) was trained to classify emerging chains as likely dominant, while a CatBoost model assessed important variables, and simulations explored modifying vaccine genetic distance, containment measures, and vaccination coverage. Approximately 5,000 sequences per week enabled early chain detection within four weeks. The DNN achieved high classification performance for identifying future predominant chains within 3-4 weeks of detection. Genetic distance metrics between consecutive chains and between circulating and vaccine strains were among the most informative variables associated with hospitalization patterns. Model-based simulations suggested that scenarios involving improved vaccine matching or stronger containment measures were associated with lower predicted hospitalization burdens. Doubling vaccination coverage alone had minimal effect but showed additional reductions when combined with strict containment. Our findings from this integrated framework highlight the potential relevance of genetic distance metrics and public health interventions when assessing hospitalization risk associated with emerging variants.