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

Cell. 2021 Sep 16;184(19):4939-4952.e15. doi: 10.1016/j.cell.2021.07.030. Epub 2021 Jul 27.

Abstract

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.

Keywords: SARS-CoV-2; genomic epidemiology; mobility; phylogenetics; viral emergence; viral sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / epidemiology*
  • COVID-19 / transmission
  • Databases as Topic
  • Disease Outbreaks
  • Epidemics*
  • Humans
  • Louisiana / epidemiology
  • Phylogeny
  • Risk Factors
  • SARS-CoV-2 / classification
  • SARS-CoV-2 / physiology*
  • Texas
  • Travel
  • United States / epidemiology