The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2-Reference-Cited by-同舟云学术

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

Published:2022-08-26 Issue:6609 Volume:377 Page:960-966
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Pekar Jonathan E.¹²^ORCID,Magee Andrew³^ORCID,Parker Edyth⁴^ORCID,Moshiri Niema⁵^ORCID,Izhikevich Katherine⁵⁶,Havens Jennifer L.¹^ORCID,Gangavarapu Karthik³^ORCID,Malpica Serrano Lorena Mariana⁷^ORCID,Crits-Christoph Alexander⁸,Matteson Nathaniel L.⁴,Zeller Mark⁴,Levy Joshua I.⁴^ORCID,Wang Jade C.⁹^ORCID,Hughes Scott⁹,Lee Jungmin¹⁰^ORCID,Park Heedo¹⁰¹¹^ORCID,Park Man-Seong¹⁰¹¹^ORCID,Ching Zi Yan Katherine¹²^ORCID,Lin Raymond Tzer Pin¹²^ORCID,Mat Isa Mohd Noor¹³^ORCID,Noor Yusuf Muhammad¹³^ORCID,Vasylyeva Tetyana I.¹⁴^ORCID,Garry Robert F.¹⁵¹⁶¹⁷^ORCID,Holmes Edward C.¹⁸^ORCID,Rambaut Andrew¹⁹^ORCID,Suchard Marc A.³²⁰²¹^ORCID,Andersen Kristian G.⁴²²^ORCID,Worobey Michael⁷^ORCID,Wertheim Joel O.¹⁴^ORCID

Affiliation:

1. Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.

2. Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093, USA.

3. Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

4. Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.

5. Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA.

6. Department of Mathematics, University of California, San Diego, La Jolla, CA 92093, USA.

7. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.

8. W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.

9. New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY 11101, USA.

10. Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.

11. BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea.

12. National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.

13. Malaysia Genome and Vaccine Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia.

14. Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.

15. Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.

16. Zalgen Labs, Frederick, MD 21703, USA.

17. Global Virus Network (GVN), Baltimore, MD 21201, USA.

18. Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.

19. Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh EH9 3FL, UK.

20. Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

21. Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA.

22. Scripps Research Translational Institute, La Jolla, CA 92037, USA.

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.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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