February 26, 2022 Preprint Open Access

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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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.6342616", 
  "language": "eng", 
  "title": "SARS-CoV-2 emergence very likely resulted from at least two zoonotic events", 
  "issued": {
    "date-parts": [
      [
        2022, 
        2, 
        26
      ]
    ]
  }, 
  "abstract": "<p>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&mdash;denoted A and B&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.</p>", 
  "author": [
    {
      "family": "Pekar, Jonathan E."
    }, 
    {
      "family": "Magee, Andrew"
    }, 
    {
      "family": "Parker, Edyth"
    }, 
    {
      "family": "Moshiri, Niema"
    }, 
    {
      "family": "Izhikevich, Katherine"
    }, 
    {
      "family": "Havens, Jennifer L."
    }, 
    {
      "family": "Gangavarapu, Karthik"
    }, 
    {
      "family": "Malpica Serrano, Lorena M."
    }, 
    {
      "family": "Crits-Christoph, Alexander"
    }, 
    {
      "family": "Matteson, Nathaniel L."
    }, 
    {
      "family": "Zeller, Mark"
    }, 
    {
      "family": "Levy, Joshua I."
    }, 
    {
      "family": "Wang, Jade C."
    }, 
    {
      "family": "Hughes, Scott"
    }, 
    {
      "family": "Lee, Jungmin"
    }, 
    {
      "family": "Park, Heedo"
    }, 
    {
      "family": "Park, Man-Seong"
    }, 
    {
      "family": "Ching Zi Yan, Katherine"
    }, 
    {
      "family": "Tzer Pin Lin, Raymond"
    }, 
    {
      "family": "Mat Isa, Mohd Noor"
    }, 
    {
      "family": "Muhammad Noor, Yusuf"
    }, 
    {
      "family": "Vasylyeva, Tetyana I."
    }, 
    {
      "family": "Garry, Robert F."
    }, 
    {
      "family": "Holmes, Edward C."
    }, 
    {
      "family": "Rambaut, Andrew"
    }, 
    {
      "family": "Suchard, Marc A."
    }, 
    {
      "family": "Andersen, Kristian G."
    }, 
    {
      "family": "Worobey, Michael"
    }, 
    {
      "family": "Wertheim, Joel O."
    }
  ], 
  "type": "article", 
  "id": "6342616"
}