VaccineScout: A Computational Framework for Guiding the Composition and Valency of SARS-CoV-2 Vaccine Updates

The continual evolution of SARS-CoV-2 necessitates periodic vaccine updates to maintain immunity against newly emerging variants. However, vaccine design remains largely guided by experimental serological studies, and there is no publicly available computational framework to help systematically prioritize vaccine variants and guide valency selection. Here, we analyze over 14 million SARS-CoV-2 genomes collected globally between 2021 and 2025 and find that over half of spike amino acid sequences (primary vaccine target) observed during the first six months after vaccine selection were already c

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