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Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny.
Pipes, Lenore; Wang, Hongru; Huelsenbeck, John P; Nielsen, Rasmus.
Afiliação
  • Pipes L; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.
  • Wang H; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.
  • Huelsenbeck JP; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.
  • Nielsen R; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.
Mol Biol Evol ; 38(4): 1537-1543, 2021 04 13.
Article em En | MEDLINE | ID: mdl-33295605
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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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Filogenia / Genoma Viral / SARS-CoV-2 / COVID-19 / Mutação Tipo de estudo: Health_economic_evaluation / Prognostic_studies / Risk_factors_studies Limite: Animals / Humans Idioma: En Revista: Mol Biol Evol Assunto da revista: BIOLOGIA MOLECULAR Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Filogenia / Genoma Viral / SARS-CoV-2 / COVID-19 / Mutação Tipo de estudo: Health_economic_evaluation / Prognostic_studies / Risk_factors_studies Limite: Animals / Humans Idioma: En Revista: Mol Biol Evol Assunto da revista: BIOLOGIA MOLECULAR Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos