Generative prediction of real-world prevalent SARS-CoV-2 mutation with in silico virus evolution

Predicting the mutation prevalence trends of emerging viruses in the real world is an efficient means to update vaccines or drugs in advance. It is crucial to develop a computational method for the prediction of real-world prevalent SARS-CoV-2 mutations considering the impact of multiple selective pressures within and between hosts. Here, a deep-learning generative framework for real-world prevalent SARS-CoV-2 mutation prediction, named ViralForesight, is developed on top of protein language models and in silico virus evolution. Through the paradigm of host-to-herd in silico virus evolution, ViralForesight reproduced previous real-world prevalent SARS-CoV-2 mutations for multiple lineages with superior performance. More importantly, ViralForesight correctly predicted the future prevalent mutations that dominated the COVID-19 pandemic in the real world more than half a year in advance with in vitro experimental validation. Overall, ViralForesight demonstrates a proactive approach to the prevention of emerging viral infections, accelerating the process of discovering future prevalent mutations with the power of generative deep learning.