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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  <dc:creator>Pekar, Jonathan E.</dc:creator>
  <dc:creator>Magee, Andrew</dc:creator>
  <dc:creator>Parker, Edyth</dc:creator>
  <dc:creator>Moshiri, Niema</dc:creator>
  <dc:creator>Izhikevich, Katherine</dc:creator>
  <dc:creator>Havens, Jennifer L.</dc:creator>
  <dc:creator>Gangavarapu, Karthik</dc:creator>
  <dc:creator>Malpica Serrano, Lorena M.</dc:creator>
  <dc:creator>Crits-Christoph, Alexander</dc:creator>
  <dc:creator>Matteson, Nathaniel L.</dc:creator>
  <dc:creator>Zeller, Mark</dc:creator>
  <dc:creator>Levy, Joshua I.</dc:creator>
  <dc:creator>Wang, Jade C.</dc:creator>
  <dc:creator>Hughes, Scott</dc:creator>
  <dc:creator>Lee, Jungmin</dc:creator>
  <dc:creator>Park, Heedo</dc:creator>
  <dc:creator>Park, Man-Seong</dc:creator>
  <dc:creator>Ching Zi Yan, Katherine</dc:creator>
  <dc:creator>Tzer Pin Lin, Raymond</dc:creator>
  <dc:creator>Mat Isa, Mohd Noor</dc:creator>
  <dc:creator>Muhammad Noor, Yusuf</dc:creator>
  <dc:creator>Vasylyeva, Tetyana I.</dc:creator>
  <dc:creator>Garry, Robert F.</dc:creator>
  <dc:creator>Holmes, Edward C.</dc:creator>
  <dc:creator>Rambaut, Andrew</dc:creator>
  <dc:creator>Suchard, Marc A.</dc:creator>
  <dc:creator>Andersen, Kristian G.</dc:creator>
  <dc:creator>Worobey, Michael</dc:creator>
  <dc:creator>Wertheim, Joel O.</dc:creator>
  <dc:date>2022-02-26</dc:date>
  <dc:description>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—denoted A and B—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.</dc:description>
  <dc:identifier>https://zenodo.org/record/6342616</dc:identifier>
  <dc:identifier>10.5281/zenodo.6342616</dc:identifier>
  <dc:identifier>oai:zenodo.org:6342616</dc:identifier>
  <dc:language>eng</dc:language>
  <dc:relation>doi:10.5281/zenodo.6291627</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:subject>SARS-CoV-2; zoonosis; phylodynamics; molecular clock</dc:subject>
  <dc:title>SARS-CoV-2 emergence very likely resulted from at least two zoonotic events</dc:title>
  <dc:type>info:eu-repo/semantics/preprint</dc:type>
  <dc:type>publication-preprint</dc:type>
</oai_dc:dc>
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