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.


This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.

Cite as

Pekar, J., Magee, A., Parker, E., Moshiri, N., Izhikevich, K., Havens, J., Gangavarapu, K., Malpica Serrano, L., Crits-Christoph, A., Matteson, N., Zeller, M., Levy, J., Wang, J., Hughes, S., Lee, J., Park, H., Park, M., Ching Zi Yan, K., Lin, R., Mat Isa, M., Noor, Y., Vasylyeva, T., Garry, R., Holmes, E., Rambaut, A., Suchard, M., Andersen, K., Worobey, M. & Wertheim, J. 2022, 'The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2', Science, 377(6609), pp. 960-966. https://doi.org/10.1126/science.abp8337

Downloadable citations

Download HTML citationHTML Download BIB citationBIB Download RIS citationRIS
Last updated: 13 October 2022
Was this page helpful?