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 IsaYusuf Muhammad Noor, Tetyana I. Vasylyeva, Robert F. Garry, Edward C. Holmes, Andrew Rambaut, Marc A. Suchard, Kristian G. Andersen, Michael Worobey, Joel O. Wertheim

Research output: Contribution to journalArticlepeer-review

73 Citations (Scopus)


Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted “A” and “B.” 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. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.

Original languageEnglish
Pages (from-to)960-966
Number of pages7
Issue number6609
Publication statusPublished - 2022 Aug 26

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© 2022 American Association for the Advancement of Science. All rights reserved.

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