Preprint Open Access

SARS-CoV-2 emergence very likely resulted from at least two zoonotic events

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


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  <identifier identifierType="DOI">10.5281/zenodo.6342616</identifier>
  <creators>
    <creator>
      <creatorName>Pekar, Jonathan E.</creatorName>
      <givenName>Jonathan E.</givenName>
      <familyName>Pekar</familyName>
      <affiliation>Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Magee, Andrew</creatorName>
      <givenName>Andrew</givenName>
      <familyName>Magee</familyName>
      <affiliation>Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Parker, Edyth</creatorName>
      <givenName>Edyth</givenName>
      <familyName>Parker</familyName>
      <affiliation>Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Moshiri, Niema</creatorName>
      <givenName>Niema</givenName>
      <familyName>Moshiri</familyName>
      <affiliation>Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Izhikevich, Katherine</creatorName>
      <givenName>Katherine</givenName>
      <familyName>Izhikevich</familyName>
      <affiliation>Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Havens, Jennifer L.</creatorName>
      <givenName>Jennifer L.</givenName>
      <familyName>Havens</familyName>
      <affiliation>Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Gangavarapu, Karthik</creatorName>
      <givenName>Karthik</givenName>
      <familyName>Gangavarapu</familyName>
      <affiliation>Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Malpica Serrano, Lorena M.</creatorName>
      <givenName>Lorena M.</givenName>
      <familyName>Malpica Serrano</familyName>
      <affiliation>Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Crits-Christoph, Alexander</creatorName>
      <givenName>Alexander</givenName>
      <familyName>Crits-Christoph</familyName>
      <affiliation>W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Matteson, Nathaniel L.</creatorName>
      <givenName>Nathaniel L.</givenName>
      <familyName>Matteson</familyName>
      <affiliation>Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Zeller, Mark</creatorName>
      <givenName>Mark</givenName>
      <familyName>Zeller</familyName>
      <affiliation>Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Levy, Joshua I.</creatorName>
      <givenName>Joshua I.</givenName>
      <familyName>Levy</familyName>
      <affiliation>Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Wang, Jade C.</creatorName>
      <givenName>Jade C.</givenName>
      <familyName>Wang</familyName>
      <affiliation>New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY 11101, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Hughes, Scott</creatorName>
      <givenName>Scott</givenName>
      <familyName>Hughes</familyName>
      <affiliation>New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY 11101, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Lee, Jungmin</creatorName>
      <givenName>Jungmin</givenName>
      <familyName>Lee</familyName>
      <affiliation>Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.</affiliation>
    </creator>
    <creator>
      <creatorName>Park, Heedo</creatorName>
      <givenName>Heedo</givenName>
      <familyName>Park</familyName>
      <affiliation>Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.</affiliation>
    </creator>
    <creator>
      <creatorName>Park, Man-Seong</creatorName>
      <givenName>Man-Seong</givenName>
      <familyName>Park</familyName>
      <affiliation>Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.</affiliation>
    </creator>
    <creator>
      <creatorName>Ching Zi Yan, Katherine</creatorName>
      <givenName>Katherine</givenName>
      <familyName>Ching Zi Yan</familyName>
      <affiliation>National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.</affiliation>
    </creator>
    <creator>
      <creatorName>Tzer Pin Lin, Raymond</creatorName>
      <givenName>Raymond</givenName>
      <familyName>Tzer Pin Lin</familyName>
      <affiliation>National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.</affiliation>
    </creator>
    <creator>
      <creatorName>Mat Isa, Mohd Noor</creatorName>
      <givenName>Mohd Noor</givenName>
      <familyName>Mat Isa</familyName>
      <affiliation>Malaysia Genome and Vaccine Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia.</affiliation>
    </creator>
    <creator>
      <creatorName>Muhammad Noor, Yusuf</creatorName>
      <givenName>Yusuf</givenName>
      <familyName>Muhammad Noor</familyName>
      <affiliation>Malaysia Genome and Vaccine Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia.</affiliation>
    </creator>
    <creator>
      <creatorName>Vasylyeva, Tetyana I.</creatorName>
      <givenName>Tetyana I.</givenName>
      <familyName>Vasylyeva</familyName>
      <affiliation>Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Garry, Robert F.</creatorName>
      <givenName>Robert F.</givenName>
      <familyName>Garry</familyName>
      <affiliation>Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Holmes, Edward C.</creatorName>
      <givenName>Edward C.</givenName>
      <familyName>Holmes</familyName>
      <affiliation>Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.</affiliation>
    </creator>
    <creator>
      <creatorName>Rambaut, Andrew</creatorName>
      <givenName>Andrew</givenName>
      <familyName>Rambaut</familyName>
      <affiliation>Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FL, UK.</affiliation>
    </creator>
    <creator>
      <creatorName>Suchard, Marc A.</creatorName>
      <givenName>Marc A.</givenName>
      <familyName>Suchard</familyName>
      <affiliation>Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Andersen, Kristian G.</creatorName>
      <givenName>Kristian G.</givenName>
      <familyName>Andersen</familyName>
      <affiliation>Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Worobey, Michael</creatorName>
      <givenName>Michael</givenName>
      <familyName>Worobey</familyName>
      <affiliation>Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Wertheim, Joel O.</creatorName>
      <givenName>Joel O.</givenName>
      <familyName>Wertheim</familyName>
      <affiliation>Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.</affiliation>
    </creator>
  </creators>
  <titles>
    <title>SARS-CoV-2 emergence very likely resulted from at least two zoonotic events</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2022</publicationYear>
  <subjects>
    <subject>SARS-CoV-2; zoonosis; phylodynamics; molecular clock</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2022-02-26</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Preprint"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/6342616</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.6291627</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Understanding the circumstances that lead to pandemics is critical to their prevention. Here, we analyze the pattern and origin of genomic diversity of SARS-CoV-2 early in the COVID-19 pandemic. We show that the SARS-CoV-2 genomic diversity prior to February 2020 comprised only two distinct viral lineages&amp;mdash;denoted A and B&amp;mdash;with no transitional haplotypes. Novel phylodynamic rooting methods, coupled with epidemic simulations, indicate that these two lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses and occurred in late-November/early-December 2019 and no earlier than the beginning of November 2019, while the introduction of lineage A likely occurred within weeks of the first event. These findings define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. Hence, as with SARS-CoV-1 in 2002 and 2003, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.&lt;/p&gt;</description>
  </descriptions>
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