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 | |
| State | Published - Sep 16 2021 |
| Externally published | Yes |
Keywords
- SARS-CoV-2
- genomic epidemiology
- mobility
- phylogenetics
- viral emergence
- viral sequencing
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
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Emergence of an early SARS-CoV-2 epidemic in the United States. / Zeller, Mark; Gangavarapu, Karthik; Anderson, Catelyn et al.
In: Cell, Vol. 184, No. 19, 16.09.2021, p. 4939-4952.e15.Research output: Contribution to journal › Article › peer-review
}
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.
N1 - Funding Information: M.A.S. reports grants from the National Institutes of Health, European Research Council, and Wellcome Trust during the conduct of this research and grants and contracts from the Bill & Melinda Gates Foundation, Janssen Research and Development, Private Health Management, IQVIA, and the U.S. Department of Veterans Affairs outside the submitted work. S.L.L., R.R., and D.J.N. are employed by BioInfoexperts LLC. R.F.G. reports grants from the National Institutes of Health, the Coalition for Epidemic Preparedness Innovations, the Burroughs Wellcome Fund, the Wellcome Trust, the Center for Disease Prevention and Control, and the European & Developing Countries Clinical Trials Partnership. He is the co-founder and Chief Scientific Advisor of Zalgen Labs, a biotechnology company developing countermeasures to emerging viruses, including SARS-CoV-2. K.G.A. has received consulting fees and compensated expert testimony on SARS-CoV-2 and the COVID-19 pandemic. Funding Information: We thank the administrators of the GISAID database for supporting rapid and transparent sharing of genomic data during the COVID-19 pandemic and all our colleagues sharing data on GISAID. A full list acknowledging the authors submitting genome sequence data used in this study can be found in Table S2. The research leading to these results has received funding from the National Institutes of Health (grants U19AI135995, 3U19AI135995-03S2, UL1TR002550, U01AI151812, U01AI124302, R01AI153044, and R01HG006139), the CDC BAA contract 75D30120C09795, the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement no. 725422-ReservoirDOCS), and from the European Union's Horizon 2020 project MOOD (grant agreement no. 874850). The Artic Network receives funding from the Wellcome Trust through project 206298/Z/17/Z. P.L. acknowledges support by the Research Foundation?Flanders (?Fonds voor Wetenschappelijk Onderzoek?Vlaanderen?; G066215N, G0D5117N, and G0B9317N). S.L.L. acknowledges support by the National Science Foundation Small Business Innovation Research grants 2027424 and 1830867. We also gratefully acknowledge support from NVIDIA Corporation and Advanced Micro Devices, Inc., with the donation of parallel computing resources used for this research. Conceptualization, M.Z. K.G. C.A. P.L. J.P.K. S.L.L. L.G. R.F.G. M.A.S. and K.G.A.; Methodology, M.Z. K.G. M.A.S. and K.G.A.; Software Programming, K.G. P.L. and M.A.S.; Formal Analysis, M.Z. K.G. D.J.S. M.A. M. Marshall, R.R. V.S.C. P.L. and M.A.S.; Investigation, M.Z. C.A. A.R.S. D.J.N. G.S.-S. A.R.B.-K. P.S. L.I.M. K.J.G. K.C. D.J.S. R.R.-S. and R.K.; Resources, A.R.S. J.A.V. R.S.S. J.G.-D. A.K.F. A.C.D. D.N.F. and J.P.K.; Data Curation, M.Z. K.G. C.A. D.J.S. M.A. M. Marshall, R.R. V.S.C. and M.A.S.; Writing ? Original Draft, M.Z. K.G. M.A.S. and K.G.A.; Writing ? Review & Editing, M.Z. K.G. C.A. P.L. J.P.K. S.L.L. L.G. R.F.G. M.A.S. and K.G.A; Visualization Preparation, M.Z. K.G. and P.L.; Supervision, P.L. J.P.K. S.L.L. L.G. R.F.G. M.A.S. and K.G.A.; Project Administration, M.Z. C.A. M. McGraw, S.T. E.S. and L.N.; Funding Acquisition, J.P.K. S.L.L. L.G. R.F.G. M.A.S. and K.G.A.; All authors contributed to interpreting and reviewing the manuscript. M.A.S. reports grants from the National Institutes of Health, European Research Council, and Wellcome Trust during the conduct of this research and grants and contracts from the Bill & Melinda Gates Foundation, Janssen Research and Development, Private Health Management, IQVIA, and the U.S. Department of Veterans Affairs outside the submitted work. S.L.L. R.R. and D.J.N. are employed by BioInfoexperts LLC. R.F.G. reports grants from the National Institutes of Health, the Coalition for Epidemic Preparedness Innovations, the Burroughs Wellcome Fund, the Wellcome Trust, the Center for Disease Prevention and Control, and the European & Developing Countries Clinical Trials Partnership. He is the co-founder and Chief Scientific Advisor of Zalgen Labs, a biotechnology company developing countermeasures to emerging viruses, including SARS-CoV-2. K.G.A. has received consulting fees and compensated expert testimony on SARS-CoV-2 and the COVID-19 pandemic. Funding Information: We thank the administrators of the GISAID database for supporting rapid and transparent sharing of genomic data during the COVID-19 pandemic and all our colleagues sharing data on GISAID. A full list acknowledging the authors submitting genome sequence data used in this study can be found in Table S2 . The research leading to these results has received funding from the National Institutes of Health (grants U19AI135995 , 3U19AI135995-03S2 , UL1TR002550 , U01AI151812 , U01AI124302 , R01AI153044 , and R01HG006139 ), the CDC BAA contract 75D30120C09795 , the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 725422-ReservoirDOCS ), and from the European Union ’s Horizon 2020 project MOOD (grant agreement no. 874850 ). The Artic Network receives funding from the Wellcome Trust through project 206298/Z/17/Z . P.L. acknowledges support by the Research Foundation—Flanders (“Fonds voor Wetenschappelijk Onderzoek—Vlaanderen”; G066215N , G0D5117N , and G0B9317N ). S.L.L. acknowledges support by the National Science Foundation Small Business Innovation Research grants 2027424 and 1830867 . We also gratefully acknowledge support from NVIDIA Corporation and Advanced Micro Devices, Inc. , with the donation of parallel computing resources used for this research. Publisher Copyright: © 2021 Elsevier Inc.
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 -