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, Daniel J. Snyder, Gytis Dudas, Alexander Watts, Nathaniel L. Matteson, Refugio Robles-Sikisaka, Maximilian Marshall, Amy K. Feehan, Gilberto Sabino-Santos, Antoinette R. Bell-Kareem, Laura D. Hughes, Manar Alkuzweny, Patricia Snarski, Julia Garcia-Diaz, Rona S. ScottLilia I. Melnik, Raphaëlle Klitting, Michelle McGraw, Pedro Belda-Ferre, Peter DeHoff, Shashank Sathe, Clarisse Marotz, Nathan D. 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

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)4939-4952.e15
Issue number19
StatePublished - Sep 16 2021


  • SARS-CoV-2
  • genomic epidemiology
  • mobility
  • phylogenetics
  • viral emergence
  • viral sequencing

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology


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