Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-19 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, with limited progress. Here we applied phylogenetic supertree analysis to study the origin and evolution of SARS-CoV-2. Phylogenetic supertree analysis firmly disputes the accuracy of bat coronavirus RaTG13 be the last common ancestor of SARS- CoV-2s reported in other phylogenetic tree analysis based on viral genome sequences, although RaTG13 shows 96.5% similarity with SARS-CoV-2 in the genome. Therefore, viewing RaTG13 as the last common ancestor of SARS-CoV-2 would seriously mislead phylogenetic inference of SARS-CoV-2. Importantly, the discovery of evolution and mutation in SARS-CoV-2s was achieved by phylogenetic supertree analysis. Taken together, the phylogenetic supertree showed extraordinary priority on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.