Assessing Uncertainty n the Rooting of the SARS-CoV-2 Phylogeny

The rooting of the SARS-CoV-2 phylogeny is important for understanding the origin and early spread of the virus. Previously published phylogenies have used different rootings that do not always provide consistent results. We investigate several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. We show that methods based on the molecular clock tend to place the root in the B clade, whereas methods based on outgroup rooting tend to place the root in the A clade. The results from the two approaches are statistically incompatible, possibly as a consequence of deviations from a molecular clock or excess back-mutations. We also show that none of the methods provide strong statistical support for the placement of the root in any particular edge of the tree. These results suggest that phylogenetic evidence alone is unlikely to identify the origin of the SARS-CoV-2 virus and we caution against strong inferences regarding the early spread of the virus based solely on such evidence.

Automated summary

Research on the rooting of the SARS-CoV-2 phylogeny shows that methods based on molecular clock tend to place the root in the B clade, while outgroup rooting methods tend to place it in the A clade. However, these results are statistically incompatible, and none of the methods provide strong statistical support for the placement of the root in any specific edge of the tree. This suggests that phylogenetic evidence alone is unlikely to identify the origin of the SARS-CoV-2 virus, cautioning against strong inferences about the early spread of the virus based solely on this evidence.