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The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

Jonathan E. Pekar, Andrew Magee, Edyth Parker, Niema Moshiri, Katherine Izhikevich, Jennifer L. Havens, Karthik Gangavarapu, Lorena Mariana Malpica Serrano, Alexander Crits-Christoph, Nathaniel L. Matteson, Mark Zeller, Joshua I. Levy, Jade C. Wang, Scott Hughes, Jungmin Lee, Heedo Park, Man-Seong Park, Katherine Ching Zi Yan, Raymond Tzer Pin Lin, Mohd Noor Mat Isa, Yusuf Muhammad Noor, Tetyana I. Vasylyeva, Robert F. Garry, Edward C. Holmes, Andrew Rambaut, Marc A. Suchard, Kristian G. Andersen, Michael Worobey, Joel O. WertheimSciencePublished Aug 26, 2022doi 10.1126/science.abp8337 Original︎ ↗Archived copy

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We identified numerous instances of C/C and T/T genomes sharing rare mutations with lineage A or lineage B viruses, often sequenced in the same laboratory, indicating that these intermediate genomes are likely artifacts of contamination or bioinformatics.

Intermediate A-B SARS-CoV-2 genomes existed among early human casesInconclusivedenies

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Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. ... Lineage B exhibits more divergence from the root of the tree than would be expected if lineage A were the ancestral virus in humans.

The correct rooting of the early SARS-CoV-2 phylogenetic tree is uncertainSupporteddenies

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The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

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Kind: journal article
Authors: Jonathan E. Pekar, Andrew Magee, Edyth Parker, Niema Moshiri, Katherine Izhikevich, Jennifer L. Havens, Karthik Gangavarapu, Lorena Mariana Malpica Serrano, Alexander Crits-Christoph, Nathaniel L. Matteson, Mark Zeller, Joshua I. Levy, Jade C. Wang, Scott Hughes, Jungmin Lee, Heedo Park, Man-Seong Park, Katherine Ching Zi Yan, Raymond Tzer Pin Lin, Mohd Noor Mat Isa, Yusuf Muhammad Noor, Tetyana I. Vasylyeva, Robert F. Garry, Edward C. Holmes, Andrew Rambaut, Marc A. Suchard, Kristian G. Andersen, Michael Worobey, Joel O. Wertheim
Publisher: Science
Published: Aug 26, 2022
DOI: 10.1126/science.abp8337
Link: https://www.science.org/doi/10.1126/science.abp8337
Archived copy: https://web.archive.org/web/20251106053700/https://www.science.org/doi/10.1126/science.abp8337
Stored text: None; quoted passages only
Claims extracted: Not recorded
Versions: One known
Copies: None recorded
Corrections: None recorded
Facts checked: Nov 9, 2026

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