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

Pekar JE 1 , Magee A 2 , Parker E 3 , Moshiri N 4 , Izhikevich K 4 , Havens JL 1 Show all authors , Gangavarapu K 2 , Malpica Serrano LM 5 , Crits-Christoph A 6 , Matteson NL 3 , Zeller M 3 , Levy JI 3 , Wang JC 7 , Hughes S 7 , Lee J 8 , Park H 8 , Park MS 8 , Ching Zi Yan K 9 , Lin RTP 9 , Mat Isa MN 10 , Noor YM 10 , Vasylyeva TI 11 , Garry RF 12 , Holmes EC 13 , Rambaut A 14 , Suchard MA 2 , Andersen KG 3 , Worobey M 5 , Wertheim JO 11

Affiliations 

  • 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, MD 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 Department of Microbiology and Immunology, School of Medicine, Tulane University, 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
Science, 2022 Aug 26;377(6609):960-966.
PMID: 35881005 DOI: 10.1126/science.abp8337

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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