SARS-CoV-2 emergence very likely resulted from at least two zoonotic events
- Pekar, Jonathan E.1
- Magee, Andrew2
- Parker, Edyth3
- Moshiri, Niema4
- Izhikevich, Katherine4
- Havens, Jennifer L.1
- Gangavarapu, Karthik2
- Malpica Serrano, Lorena M.5
- Crits-Christoph, Alexander6
- Matteson, Nathaniel L.3
- Zeller, Mark3
- Levy, Joshua I.3
- Wang, Jade C.7
- Hughes, Scott7
- Lee, Jungmin8
- Park, Heedo8
- Park, Man-Seong8
- Ching Zi Yan, Katherine9
- Tzer Pin Lin, Raymond9
- Mat Isa, Mohd Noor10
- Muhammad Noor, Yusuf10
- Vasylyeva, Tetyana I.11
- Garry, Robert F.12
- Holmes, Edward C.13
- Rambaut, Andrew14
- Suchard, Marc A.15
- Andersen, Kristian G.3
- Worobey, Michael5
- Wertheim, Joel O.11
- 1. Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.
- 2. Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
- 3. Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- 4. Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.
- 5. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
- 6. W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
- 7. New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY 11101, USA.
- 8. Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.
- 9. National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.
- 10. Malaysia Genome and Vaccine Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia.
- 11. Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
- 12. Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA.
- 13. Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
- 14. Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FL, UK.
- 15. Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
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.