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

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Emergence of an early SARS-CoV-2 epidemic in the United States
Cell ( IF 64.5 ) Pub Date : 2021-07-27 , DOI: 10.1016/j.cell.2021.07.030
Mark Zeller ₁ , Karthik Gangavarapu ₁ , Catelyn Anderson ₁ , Allison R Smither ₂ , John A Vanchiere ₃ , Rebecca Rose ₄ , Daniel J Snyder ₅ , Gytis Dudas ₆ , Alexander Watts ₇ , Nathaniel L Matteson ₁ , Refugio Robles-Sikisaka ₁ , Maximilian Marshall ₈ , Amy K Feehan ₉ , Gilberto Sabino-Santos ₁₀ , Antoinette R Bell-Kareem ₂ , Laura D Hughes ₁₁ , Manar Alkuzweny ₁ , Patricia Snarski ₁₂ , Julia Garcia-Diaz ₉ , Rona S Scott ₁₃ , Lilia I Melnik ₂ , Raphaëlle Klitting ₁ , Michelle McGraw ₁ , Pedro Belda-Ferre ₁₄ , Peter DeHoff ₁₅ , Shashank Sathe ₁₆ , Clarisse Marotz ₁₇ , Nathan D Grubaugh ₁₈ , David J Nolan ₄ , Arnaud C Drouin ₁₉ , Kaylynn J Genemaras ₂₀ , Karissa Chao ₂₀ , Sarah Topol ₂₁ , Emily Spencer ₂₁ , Laura Nicholson ₂₁ , Stefan Aigner ₂₂ , Gene W Yeo ₂₂ , Lauge Farnaes ₂₃ , Charlotte A Hobbs ₂₃ , Louise C Laurent ₁₅ , Rob Knight ₂₄ , Emma B Hodcroft ₂₅ , Kamran Khan ₂₆ , Dahlene N Fusco ₂₇ , Vaughn S Cooper ₅ , Phillipe Lemey ₂₈ , Lauren Gardner ₈ , Susanna L Lamers ₄ , Jeremy P Kamil ₁₃ , Robert F Garry ₂₉ , Marc A Suchard ₃₀ , Kristian G Andersen ₃₁

Affiliation

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
Department of Pediatrics, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA 71130, USA.
BioInfoExperts LLC, Thibodaux, Louisiana, USA.
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.
Gothenburg Global Biodiversity Centre (GGBC), Gothenburg, Sweden.
Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada.
Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA.
Ochsner Clinic Foundation, New Orleans, Louisiana, USA.
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.
Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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.
Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA.
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 Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA.
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.
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.
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
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.
Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA.
Scripps Research Translational Institute, La Jolla, CA 92037, USA.
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.
Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA.
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.
Biozentrum, University of Basel, Basel, Switzerland.
Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada; Department of Medicine, University of Toronto, Toronto, Canada.
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.
Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium; Global Virology Network.
Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Zalgen Labs LLC, Germantown, MD, USA.
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.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Research Translational Institute, La Jolla, CA 92037, USA.

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.

中文翻译：

美国出现早期 SARS-CoV-2 流行病

由于检测不足，美国 (US) 出现的 COVID-19 疫情在很大程度上未被发现。新奥尔良经历了最早和最快的疫情爆发之一，恰逢狂欢节。为了深入了解 SARS-CoV-2 在美国的出现以及大规模事件如何加速传播，我们对路易斯安那州第一波 COVID-19 疫情期间的 SARS-CoV-2 基因组进行了测序。我们发现，与美国其他州相比，路易斯安那州的 SARS-CoV-2 多样性有限，并且 SARS-CoV-2 的一次引入导致了路易斯安那州几乎所有的早期传播。通过分析流动性和基因组数据，我们发现 SARS-CoV-2 在狂欢节之前就已经出现在新奥尔良，而狂欢节极大地加速了传播。我们的研究让人们了解了大规模事件期间的超级传播如何在美国早期疫情爆发期间发挥了关键作用，并且可以极大地加速流行病的传播。

更新日期：2021-09-17

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