Co-mutation modules capture the evolution and transmission patterns of SARS-CoV-2

Abstract The rapid spread and huge impact of the COVID-19 pandemic caused by emerging SARS-CoV-2 have driven large efforts for sequencing analyzing viral genomes. Mutation analyses revealed that virus keeps mutating shows a certain degree genetic diversity, which could result in alteration its infectivity pathogenicity. Therefore, appropriate delineation variants enables us to understand evolution transmission patterns. By focusing on nucleotides co-substituted, we first identified 42 co-mutation modules consist at least two co-substituted during evolution. Then based these modules, classified population into 43 groups further phylogenetic relationships among number inconsistent were validated with trees. Intuitively, tracked tempo-spatial patterns groups, 11 geographic-specific. Different epidemic periods showed specific co-circulating where dominant existed had multiple sub-groups parallel Our work capture SARS-CoV-2, can contribute guiding prevention control pandemic. An interactive website grouping genomes visualizing spatio-temporal distribution is available https://www.jianglab.tech/cmm-grouping/.