Evidence map›Paper›PMID 33564781›Full record

ArticlemedRxiv : the preprint server for health sciences2021

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 and 42 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

52 authors.

Mark ZellerDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Karthik GangavarapuDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Catelyn AndersonDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Allison R SmitherDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
John A VanchiereDepartment of Pediatrics, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA 71130, USA.
Rebecca RoseBioInfoExperts LLC, Thibodaux, Louisiana, USA.
Daniel J SnyderDepartment of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA, 15219, USA.
Gytis DudasGothenburg Global Biodiversity Centre (GGBC), Gothenburg, Sweden.
Alexander WattsLi Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.
Nathaniel L MattesonDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Refugio Robles-SikisakaDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Maximilian MarshallDepartment of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA.
Amy K FeehanOchsner Clinic Foundation, New Orleans, Louisiana, USA.
Gilberto Sabino-SantosDepartment of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA.
Antoinette R Bell-KareemDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
Laura D HughesDepartment of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Manar AlkuzwenyDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Patricia SnarskiHeart and Vascular Institute, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
Julia Garcia-DiazOchsner Clinic Foundation, New Orleans, Louisiana, USA.
Rona S ScottDepartment of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA.
Lilia I MelnikDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
Raphaälle KlittingDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Michelle McGrawDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Pedro Belda-FerreDepartment of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Peter DeHoffDepartment of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA.
Shashank SatheDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.
Clarisse MarotzDepartment of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Nathan GrubaughDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
David J NolanBioInfoExperts LLC, Thibodaux, Louisiana, USA.
Arnaud C DrouinDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
Kaylynn J GenemarasDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
Karissa ChaoDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
Sarah TopolScripps Research Translational Institute, La Jolla, CA 92037, USA.
Emily SpencerScripps Research Translational Institute, La Jolla, CA 92037, USA.
Laura NicholsonScripps Research Translational Institute, La Jolla, CA 92037, USA.
Stefan AignerDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.
Gene W YeoDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.
Lauge FarnaesRady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA.
Charlotte A HobbsRady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA.
Louise C LaurentDepartment of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA.
Rob KnightDepartment of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Emma B HodcroftBiozentrum, University of Basel, Basel, Switzerland.
Kamran KhanLi Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.
Dahlene N FuscoDepartment of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA.
Vaughn S CooperDepartment of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA, 15219, USA.
Phillipe LemeyDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium.
Lauren GardnerDepartment of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA.
Susanna L LamersBioInfoExperts LLC, Thibodaux, Louisiana, USA.
Jeremy P KamilDepartment of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA.
Robert F GarryDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
Marc A SuchardDepartment of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Kristian G AndersenDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Funding

Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9M
Technology CoreU19AI135995 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Kristian Graugaard Andersen · 2018 to 2026
$32.0M
Scripps Translational Science InstituteUL1TR002550 · NCATS · SCRIPPS RESEARCH INSTITUTE, THE · PI TOPOL, ERIC JEFFREY · 2018 to 2022
$28.9M
West African Emerging Infectious Disease Research Center (WA-EIDRC)U01AI151812 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI ANDERSEN, KRISTIAN GRAUGAARD, GARRY, ROBERT F · 2020 to 2024
$13.2M
Predicting the emergence of antibiotic resistance through multi-omics approaches and Immune System-surveillanU01AI124302 · NIAID · BOSTON COLLEGE · PI BENTO, JOSE, COOPER, VAUGHN · 2016 to 2020
$10.2M
Genomics, GPUs, and Next Generation Computational StatisticsR01HG006139 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SOBEL, ERIC · 2011 to 2023
$5.1M
Statistical Innovation to Integrate Sequences and Phenotypes for Scalable Phylodynamic InferenceR01AI153044 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Marc A. Suchard · 2021 to 2026
$2.4M
NCATS NIH HHS UL1 TR001863NCATS NIH HHS UL1 TR002550NHGRI NIH HHS R01 HG006139NIAID NIH HHS R01 AI153044NIAID NIH HHS U01 AI124302NIAID NIH HHS U01 AI151812NIAID NIH HHS U19 AI135995Wellcome Trust
6 · The paper itself

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.

Identifiers

PMID33564781
PMCPMC7872376

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.