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

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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.

Early SARS-CoV-2 genomic data are insufficient to confidently root the phylogenetic tree by phylogenetic methods aloneSupported

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The molecular clock rooting places the root in the B clade with high confidence, whereas outgroup rooting places the root in the A clade with similarly high confidence. The reason for this discrepancy is unclear... Although molecular clock rooting and the outgroup rooting strategies internally give qualitatively similar results, they are largely incompatible with each other.

Outgroup-based and date-based rooting methods give conflicting results for the early SARS-CoV-2 phylogenetic treeVerified

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

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Link: https://academic.oup.com/mbe/article/38/4/1537/6028993
Archived copy: https://web.archive.org/web/20250424134348/https://academic.oup.com/mbe/article/38/4/1537/6028993
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Versions: One known
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Facts checked: Nov 9, 2026

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Nov 9, 2026FactsFacts fetcher · Facts looked up
Nov 8, 2026Entered the graphEntered the graph; no copy stored