ArticleMolecular biology and evolution2021
Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Review
- Review
- Heterogeneous Evolution Among SARS-CoV-2 Genes and Variants of Concern.Journal of medical virology · 2025Article
- The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree.Molecular biology and evolution · 2025Article
- Protein structures unravel the signatures and patterns of deep time evolution.QRB discovery · 2024Review
- Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak.Virus evolution · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Article
- Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model.Zoological research · 2023Article
- Review
- Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market.Virus evolution · 2023Article
- Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations.Virus evolution · 2023Article
- The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2.Science (New York, N.Y.) · 2022Article
- Genomic epidemiological models describe pathogen evolution across fitness valleys.Science advances · 2022Article
- A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary.Virus evolution · 2022Article
- A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity.Environmental research · 2022Article
- TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.Bioinformatics (Oxford, England) · 2022Article
- On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy.Viruses · 2022Article
- Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution.Environmental research · 2022Article
- Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types.Microbes and infection · 2022Article
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4 authors.
Funding
Abstract
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.
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