Emergence of an early SARS-CoV-2 epidemic in the United States.

Autor:	Zeller M; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: zellerm@scripps.edu., Gangavarapu K; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: gkarthik@scripps.edu., Anderson C; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA., Smither AR; Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA., Vanchiere JA; Department of Pediatrics, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA 71130, USA., Rose R; BioInfoExperts LLC, Thibodaux, Louisiana, USA., Snyder DJ; Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA., Dudas G; Gothenburg Global Biodiversity Centre (GGBC), Gothenburg, Sweden., Watts A; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada., Matteson NL; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA., Robles-Sikisaka R; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA., Marshall M; Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA., Feehan AK; Ochsner Clinic Foundation, New Orleans, Louisiana, USA., Sabino-Santos G Jr; Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Centre for Virology Research, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP 14049900, Brazil., Bell-Kareem AR; Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA., Hughes LD; Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA., Alkuzweny M; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA., Snarski P; Heart and Vascular Institute, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA., Garcia-Diaz J; Ochsner Clinic Foundation, New Orleans, Louisiana, USA., Scott RS; Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA., Melnik LI; Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA., Klitting R; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA., McGraw M; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA., Belda-Ferre P; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA., DeHoff P; Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA., Sathe S; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA., Marotz C; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA., Grubaugh ND; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA., Nolan DJ; BioInfoExperts LLC, Thibodaux, Louisiana, USA., Drouin AC; Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA., Genemaras KJ; Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA., Chao K; Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA., Topol S; Scripps Research Translational Institute, La Jolla, CA 92037, USA., Spencer E; Scripps Research Translational Institute, La Jolla, CA 92037, USA., Nicholson L; Scripps Research Translational Institute, La Jolla, CA 92037, USA., Aigner S; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA., Yeo GW; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA., Farnaes L; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA., Hobbs CA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA., Laurent LC; Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA., Knight R; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA., Hodcroft EB; Biozentrum, University of Basel, Basel, Switzerland., Khan K; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada; Department of Medicine, University of Toronto, Toronto, Canada., Fusco DN; Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70114, USA., Cooper VS; Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA., Lemey P; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium; Global Virology Network., Gardner L; Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA., Lamers SL; BioInfoExperts LLC, Thibodaux, Louisiana, USA., Kamil JP; Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA., Garry RF; Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Zalgen Labs LLC, Germantown, MD, USA., Suchard MA; Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA., Andersen KG; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Research Translational Institute, La Jolla, CA 92037, USA. Electronic address: andersen@scripps.edu.
Jazyk:	angličtina
Zdroj:	Cell [Cell] 2021 Sep 16; Vol. 184 (19), pp. 4939-4952.e15. Date of Electronic Publication: 2021 Jul 27.
DOI:	10.1016/j.cell.2021.07.030
Abstrakt:	The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics. Competing Interests: Declaration of interests M.A.S. reports grants from the National Institutes of Health, European Research Council, and Wellcome Trust during the conduct of this research and grants and contracts from the Bill & Melinda Gates Foundation, Janssen Research and Development, Private Health Management, IQVIA, and the U.S. Department of Veterans Affairs outside the submitted work. S.L.L., R.R., and D.J.N. are employed by BioInfoexperts LLC. R.F.G. reports grants from the National Institutes of Health, the Coalition for Epidemic Preparedness Innovations, the Burroughs Wellcome Fund, the Wellcome Trust, the Center for Disease Prevention and Control, and the European & Developing Countries Clinical Trials Partnership. He is the co-founder and Chief Scientific Advisor of Zalgen Labs, a biotechnology company developing countermeasures to emerging viruses, including SARS-CoV-2. K.G.A. has received consulting fees and compensated expert testimony on SARS-CoV-2 and the COVID-19 pandemic. (Copyright © 2021 Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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