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. Scott; Lilia 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

doi:10.1016/j.cell.2021.07.030

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

Microbiology And Immunology

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

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.

Original language	English (US)
Pages (from-to)	4939-4952.e15
Journal	Cell
Volume	184
Issue number	19
DOIs	https://doi.org/10.1016/j.cell.2021.07.030
State	Published - Sep 16 2021

Keywords

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

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

Access to Document

10.1016/j.cell.2021.07.030

Cite this

Zeller, M., Gangavarapu, K., Anderson, C., Smither, A. R., Vanchiere, J. A., Rose, R., Snyder, D. J., Dudas, G., Watts, A., Matteson, N. L., Robles-Sikisaka, R., Marshall, M., Feehan, A. K., Sabino-Santos, G., Bell-Kareem, A. R., Hughes, L. D., Alkuzweny, M., Snarski, P., Garcia-Diaz, J., ... Andersen, K. G. (2021). Emergence of an early SARS-CoV-2 epidemic in the United States. Cell, 184(19), 4939-4952.e15. https://doi.org/10.1016/j.cell.2021.07.030

Zeller, M, Gangavarapu, K, Anderson, C, Smither, AR, Vanchiere, JA, Rose, R, Snyder, DJ, Dudas, G, Watts, A, Matteson, NL, Robles-Sikisaka, R, Marshall, M, Feehan, AK, Sabino-Santos, G, Bell-Kareem, AR, Hughes, LD, Alkuzweny, M, Snarski, P, Garcia-Diaz, J, Scott, RS, Melnik, LI, Klitting, R, McGraw, M, Belda-Ferre, P, DeHoff, P, Sathe, S, Marotz, C, Grubaugh, ND, Nolan, DJ, Drouin, AC, Genemaras, KJ, Chao, K, Topol, S, Spencer, E, Nicholson, L, Aigner, S, Yeo, GW, Farnaes, L, Hobbs, CA, Laurent, LC, Knight, R, Hodcroft, EB, Khan, K, Fusco, DN, Cooper, VS, Lemey, P, Gardner, L, Lamers, SL, Kamil, JP, Garry, RF, Suchard, MA & Andersen, KG 2021, 'Emergence of an early SARS-CoV-2 epidemic in the United States', Cell, vol. 184, no. 19, pp. 4939-4952.e15. https://doi.org/10.1016/j.cell.2021.07.030

@article{48eeacaf72e045e78c33f8556729dec5,

title = "Emergence of an early SARS-CoV-2 epidemic in the United States",

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",

author = "Mark Zeller and Karthik Gangavarapu and Catelyn Anderson and Smither, {Allison R.} and Vanchiere, {John A.} and Rebecca Rose and Snyder, {Daniel J.} and Gytis Dudas and Alexander Watts and Matteson, {Nathaniel L.} and Refugio Robles-Sikisaka and Maximilian Marshall and Feehan, {Amy K.} and Gilberto Sabino-Santos and Bell-Kareem, {Antoinette R.} and Hughes, {Laura D.} and Manar Alkuzweny and Patricia Snarski and Julia Garcia-Diaz and Scott, {Rona S.} and Melnik, {Lilia I.} and Rapha{\"e}lle Klitting and Michelle McGraw and Pedro Belda-Ferre and Peter DeHoff and Shashank Sathe and Clarisse Marotz and Grubaugh, {Nathan D.} and Nolan, {David J.} and Drouin, {Arnaud C.} and Genemaras, {Kaylynn J.} and Karissa Chao and Sarah Topol and Emily Spencer and Laura Nicholson and Stefan Aigner and Yeo, {Gene W.} and Lauge Farnaes and Hobbs, {Charlotte A.} and Laurent, {Louise C.} and Rob Knight and Hodcroft, {Emma B.} and Kamran Khan and Fusco, {Dahlene N.} and Cooper, {Vaughn S.} and Phillipe Lemey and Lauren Gardner and Lamers, {Susanna L.} and Kamil, {Jeremy P.} and Garry, {Robert F.} and Suchard, {Marc A.} and Andersen, {Kristian G.}",

note = "Publisher Copyright: {\textcopyright} 2021 Elsevier Inc.",

year = "2021",

month = sep,

day = "16",

doi = "10.1016/j.cell.2021.07.030",

language = "English (US)",

volume = "184",

pages = "4939--4952.e15",

journal = "Cell",

issn = "0092-8674",

publisher = "Elsevier B.V.",

number = "19",

}

TY - JOUR

T1 - Emergence of an early SARS-CoV-2 epidemic in the United States

AU - Zeller, Mark

AU - Gangavarapu, Karthik

AU - Anderson, Catelyn

AU - Smither, Allison R.

AU - Vanchiere, John A.

AU - Rose, Rebecca

AU - Snyder, Daniel J.

AU - Dudas, Gytis

AU - Watts, Alexander

AU - Matteson, Nathaniel L.

AU - Robles-Sikisaka, Refugio

AU - Marshall, Maximilian

AU - Feehan, Amy K.

AU - Sabino-Santos, Gilberto

AU - Bell-Kareem, Antoinette R.

AU - Hughes, Laura D.

AU - Alkuzweny, Manar

AU - Snarski, Patricia

AU - Garcia-Diaz, Julia

AU - Scott, Rona S.

AU - Melnik, Lilia I.

AU - Klitting, Raphaëlle

AU - McGraw, Michelle

AU - Belda-Ferre, Pedro

AU - DeHoff, Peter

AU - Sathe, Shashank

AU - Marotz, Clarisse

AU - Grubaugh, Nathan D.

AU - Nolan, David J.

AU - Drouin, Arnaud C.

AU - Genemaras, Kaylynn J.

AU - Chao, Karissa

AU - Topol, Sarah

AU - Spencer, Emily

AU - Nicholson, Laura

AU - Aigner, Stefan

AU - Yeo, Gene W.

AU - Farnaes, Lauge

AU - Hobbs, Charlotte A.

AU - Laurent, Louise C.

AU - Knight, Rob

AU - Hodcroft, Emma B.

AU - Khan, Kamran

AU - Fusco, Dahlene N.

AU - Cooper, Vaughn S.

AU - Lemey, Phillipe

AU - Gardner, Lauren

AU - Lamers, Susanna L.

AU - Kamil, Jeremy P.

AU - Garry, Robert F.

AU - Suchard, Marc A.

AU - Andersen, Kristian G.

PY - 2021/9/16

Y1 - 2021/9/16

N2 - 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.

AB - 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.

KW - SARS-CoV-2

KW - genomic epidemiology

KW - mobility

KW - phylogenetics

KW - viral emergence

KW - viral sequencing

UR - http://www.scopus.com/inward/record.url?scp=85114753027&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85114753027&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2021.07.030

DO - 10.1016/j.cell.2021.07.030

M3 - Article

C2 - 34508652

AN - SCOPUS:85114753027

SN - 0092-8674

VL - 184

SP - 4939-4952.e15

JO - Cell

JF - Cell

IS - 19

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this