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The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2.
Pekar, Jonathan E; Magee, Andrew; Parker, Edyth; Moshiri, Niema; Izhikevich, Katherine; Havens, Jennifer L; Gangavarapu, Karthik; Malpica Serrano, Lorena Mariana; Crits-Christoph, Alexander; Matteson, Nathaniel L; Zeller, Mark; Levy, Joshua I; Wang, Jade C; Hughes, Scott; Lee, Jungmin; Park, Heedo; Park, Man-Seong; Ching Zi Yan, Katherine; Lin, Raymond Tzer Pin; Mat Isa, Mohd Noor; Noor, Yusuf Muhammad; Vasylyeva, Tetyana I; Garry, Robert F; Holmes, Edward C; Rambaut, Andrew; Suchard, Marc A; Andersen, Kristian G; Worobey, Michael; Wertheim, Joel O.
  • Pekar JE; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
  • Magee A; Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093, USA.
  • Parker E; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
  • Moshiri N; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
  • Izhikevich K; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
  • Havens JL; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
  • Gangavarapu K; Department of Mathematics, University of California, San Diego, La Jolla, CA 92093, USA.
  • Malpica Serrano LM; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
  • Crits-Christoph A; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
  • Matteson NL; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
  • Zeller M; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
  • Levy JI; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
  • Wang JC; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
  • Hughes S; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
  • Lee J; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY 11101, USA.
  • Park H; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY 11101, USA.
  • Park MS; Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.
  • Ching Zi Yan K; Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.
  • Lin RTP; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea.
  • Mat Isa MN; Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea.
  • Noor YM; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea.
  • Vasylyeva TI; National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.
  • Garry RF; National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.
  • Holmes EC; Malaysia Genome and Vaccine Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia.
  • Rambaut A; Malaysia Genome and Vaccine Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia.
  • Suchard MA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
  • Andersen KG; Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
  • Worobey M; Zalgen Labs, Frederick, MD 21703, USA.
  • Wertheim JO; Global Virus Network (GVN), Baltimore, MD 21201, USA.
Science ; 377(6609): 960-966, 2022 08 26.
Article in English | MEDLINE | ID: covidwho-1962060
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pandemics / Viral Zoonoses / SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Limits: Animals / Humans Language: English Journal: Science Year: 2022 Document Type: Article Affiliation country: Science.abp8337

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pandemics / Viral Zoonoses / SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Limits: Animals / Humans Language: English Journal: Science Year: 2022 Document Type: Article Affiliation country: Science.abp8337