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Emergence of an early SARS-CoV-2 epidemic in the United States
Mark Zeller; Karthik Gangavarapu; Catelyn Anderson; Allison R. Smither; John A. Vanchiere; Rebecca Rose; Gytis Dudas; Daniel J. Snyder; Alexander Watts; Nathaniel L. Matteson; Refugio Robles-Sikisaka; Maximilian Marshall; Amy K. Feehan; Gilberto Sabino-Santos Jr; Antoinette Bell-Kareem; Laura D. Hughes; Manar Alkuzweny; Patricia Snarski; Julia Garcia-Diaz; Rona S. Scott; Lilia I. Melnik; Raphaelle Klitting; Michelle McGraw; Pedro Belda-Ferre; Peter DeHoff; Shashank Sathe; Clarisse Marotz; Nathan Grubaugh; David J. Nolan; Arnaud C. Drouin; Kaylynn J. Genemaras; Karissa Chao; Sarah Topol; Emily Spencer; Laura Nicholson; Stefan Aigner; Gene W. Yeo; Lauge Farnaes; Charlotte A. Hobbs; Louise C. Laurent; Rob Knight; Emma B. Hodcroft; Kamran Khan; Dahlene N. Fusco; Vaughn S. Cooper; Phillipe Lemey; Lauren Gardner; Susanna L. Lamers; Jeremy P. Kamil; Robert F. Garry; Marc A. Suchard; Kristian G. Andersen.
Affiliation
  • Mark Zeller; Scripps Research
  • Karthik Gangavarapu; Scripps Research
  • Catelyn Anderson; Scripps Research
  • Allison R. Smither; Tulane University
  • John A. Vanchiere; Louisiana State University
  • Rebecca Rose; Bioinfoexperts
  • Gytis Dudas; University of Gothenburg
  • Daniel J. Snyder; University of Pittsburgh
  • Alexander Watts; Bluedot
  • Nathaniel L. Matteson; Scripps Research
  • Refugio Robles-Sikisaka; Scripps Research
  • Maximilian Marshall; Johns Hopkins University
  • Amy K. Feehan; Ochsner Clinic Foundation
  • Gilberto Sabino-Santos Jr; Tulane University
  • Antoinette Bell-Kareem; Tulane University
  • Laura D. Hughes; Scripps Research
  • Manar Alkuzweny; Scripps Research
  • Patricia Snarski; Tulane University
  • Julia Garcia-Diaz; Ochsner Clinic Foundation
  • Rona S. Scott; Louisiana State University
  • Lilia I. Melnik; Tulane University
  • Raphaelle Klitting; Scripps Research
  • Michelle McGraw; Scripps Research
  • Pedro Belda-Ferre; University of California San Diego
  • Peter DeHoff; University of California San Diego
  • Shashank Sathe; University of California San Diego
  • Clarisse Marotz; University of California San Diego
  • Nathan Grubaugh; Yale University
  • David J. Nolan; Bioinfoexperts
  • Arnaud C. Drouin; Tulane University
  • Kaylynn J. Genemaras; Tulane University
  • Karissa Chao; Tulane University
  • Sarah Topol; Scripps Research
  • Emily Spencer; Scripps Research
  • Laura Nicholson; Scripps Research
  • Stefan Aigner; University of California San Diego
  • Gene W. Yeo; University of California San Diego
  • Lauge Farnaes; Rady Children's Institute for Genomic Medicine, San Diego
  • Charlotte A. Hobbs; Rady Children's Institute for Genomic Medicine, San Diego
  • Louise C. Laurent; University of California San Diego
  • Rob Knight; University of California San Diego
  • Emma B. Hodcroft; University of Basel
  • Kamran Khan; Bluedot
  • Dahlene N. Fusco; Tulane University
  • Vaughn S. Cooper; University of Pittsburgh
  • Phillipe Lemey; KU Leuven
  • Lauren Gardner; Johns Hopkins University
  • Susanna L. Lamers; Bioinfoexperts
  • Jeremy P. Kamil; Louisiana State University
  • Robert F. Garry; Tulane University
  • Marc A. Suchard; University of California Los Angeles
  • Kristian G. Andersen; Scripps Research
Preprint in English | medRxiv | ID: ppmedrxiv-21251235
Journal article
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ABSTRACT
The emergence of the early COVID-19 epidemic in the United States (U.S.) went largely undetected, due to a lack of adequate testing and mitigation efforts. The city of New Orleans, Louisiana experienced one of the earliest and fastest accelerating outbreaks, coinciding with the annual Mardi Gras festival, which went ahead without precautions. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large, crowded events may have accelerated early 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 initially had limited sequence diversity compared to other U.S. states, and that one successful introduction of SARS-CoV-2 led to almost all of the early SARS-CoV-2 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 that the festival dramatically accelerated transmission, eventually leading to secondary localized COVID-19 epidemics throughout the Southern U.S.. 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 COVID-19 epidemics on a local and regional scale.
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Full text: Available Collection: Preprints Database: medRxiv Language: English Year: 2021 Document type: Preprint
Full text: Available Collection: Preprints Database: medRxiv Language: English Year: 2021 Document type: Preprint
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