The complexity and speed of evolution in viruses with RNA genomes makes predictive identification of variants with epidemic or pandemic potential challenging. In recent years, machine learning has become an increasingly capable technology for addressing this challenge, as advances in methods and computational power have dramatically improved the performance of models and led to their widespread adoption across industries and disciplines. Nascent applications of machine learning technology to virus research have now expanded, providing new tools for handling large-scale datasets and leading to a reshaping of existing workflows for phenotype prediction, phylogenetic analysis, drug discovery and more. This review explores how machine learning has been applied to and has impacted the study of viruses, before addressing the strengths and limitations of its techniques and finally highlighting the next steps that are needed for the technology to reach its full potential in this challenging and ever-relevant research area.
Keywords: RNA viruses; SARS-CoV-2; deep learning; machine learning; virus evolution; virus phenotype prediction.