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bioRxiv · 10.1101/2023.04.19.537460

Machine learning detection of SARS-CoV-2 high-risk variants

Li, L.·Li, C.·Li, N.·Zou, D.·Zhao, W.·Xue, Y.·Zhang, Z.·Bao, Y.·Song, S.
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Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved many high-risk variants, resulting in repeated COVID-19 waves of pandemic during the past years. Therefore, accurate early-warning of high-risk variants is vital for epidemic prevention and control. Here we construct a machine learning model to predict high-risk variants of SARS-CoV-2 by LightGBM algorithm based on several important haplotype network features. As demonstrated on a series of different retrospective testing datasets, our model achieves accurate prediction of all variants of concern (VOC) and most variants of interest (AUC=0.96). Prediction based on the latest sequences shows that the newly emerging lineage BA.5 has the highest risk score and spreads rapidly to become a major epidemic lineage in multiple countries, suggesting that BA.5 bears great potential to be a VOC. In sum, our machine learning model is capable to early predict high-risk variants soon after their emergence, thus greatly improving public health preparedness against the evolving virus.

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Li, L., Li, C., Li, N., Zou, D., Zhao, W., Xue, Y., Zhang, Z., Bao, Y., Song, S.. 2023-04-20. Machine learning detection of SARS-CoV-2 high-risk variants. https://doi.org/10.1101/2023.04.19.537460

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