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. Wertheim

doi:10.1126/science.abp8337

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 journal › Article › peer-review

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Abstract

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 language	English (US)
Pages (from-to)	960-966
Number of pages	7
Journal	Science
Volume	377
Issue number	6609
DOIs	https://doi.org/10.1126/science.abp8337
State	Published - Aug 26 2022
Externally published	Yes

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Pekar, J. E., Magee, A., Parker, E., Moshiri, N., Izhikevich, K., Havens, J. L., Gangavarapu, K., Serrano, L. M. M., Crits-Christoph, A., Matteson, N. L., Zeller, M., Levy, J. I., Wang, J. C., Hughes, S., Lee, J., Park, H., Park, M. S., Yan, K. C. Z., Lin, R. T. P., ... Wertheim, J. O. (2022). The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science, 377(6609), 960-966. https://doi.org/10.1126/science.abp8337

Pekar, JE, Magee, A, Parker, E, Moshiri, N, Izhikevich, K, Havens, JL, Gangavarapu, K, Serrano, LMM, Crits-Christoph, A, Matteson, NL, Zeller, M, Levy, JI, Wang, JC, Hughes, S, Lee, J, Park, H, Park, MS, Yan, KCZ, Lin, RTP, Isa, MNM, Noor, YM, Vasylyeva, TI, Garry, RF, Holmes, EC, Rambaut, A, Suchard, MA, Andersen, KG, Worobey, M & Wertheim, JO 2022, 'The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2', Science, vol. 377, no. 6609, pp. 960-966. https://doi.org/10.1126/science.abp8337

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abstract = "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.",

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

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AU - Havens, Jennifer L.

AU - Gangavarapu, Karthik

AU - Serrano, Lorena Mariana Malpica

AU - Crits-Christoph, Alexander

AU - Matteson, Nathaniel L.

AU - Zeller, Mark

AU - Levy, Joshua I.

AU - Wang, Jade C.

AU - Hughes, Scott

AU - Lee, Jungmin

AU - Park, Heedo

AU - Park, Man Seong

AU - Yan, Katherine Ching Zi

AU - Lin, Raymond Tzer Pin

AU - Isa, Mohd Noor Mat

AU - Noor, Yusuf Muhammad

AU - Vasylyeva, Tetyana I.

AU - Garry, Robert F.

AU - Holmes, Edward C.

AU - Rambaut, Andrew

AU - Suchard, Marc A.

AU - Andersen, Kristian G.

AU - Worobey, Michael

AU - Wertheim, Joel O.

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

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