ArticleCell2021
Emergence of an early SARS-CoV-2 epidemic in the United States.
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Article in Cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35citing papers in PubMed
–field-weighted citation impact
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Who cites it
35 citing papers in PubMed.
- Lassa virus live tracking and lineage assignment: how nextstrain can enhance surveillance and public health in Africa and beyond.Emerging microbes & infections · 2026Article
- Containment of a Multi-index B.1.1.7 Outbreak on a University Campus Through a Genomically Informed Public Health Response.Open forum infectious diseases · 2026Article
- Reconstructing the early spatial spread of pandemic respiratory viruses in the United States.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Reconstructing the early spatial spread of pandemic respiratory viruses in the United States.medRxiv : the preprint server for health sciences · 2025Article
- Phylodynamics of SARS-CoV-2 Lineages B.1.1.7, B.1.1.529 and B.1.617.2 in Nigeria Suggests Divergent Evolutionary Trajectories.Pathogens (Basel, Switzerland) · 2025Article
- Genomic diversity and surveillance of SARS-CoV-2 in Nigeria.BMC genomics · 2025Article
- Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States.Emerging infectious diseases · 2025Article
- Spatiotemporal evolution and transmission dynamics of Alpha and Delta SARS-CoV-2 variants contributing to sequential outbreaks in Cambodia during 2021.Communications medicine · 2024Article
- Diverse BCR usage and T cell activation induced by different COVID-19 sequential vaccinations.mBio · 2024Article
- Understanding the link between COVID-19, blood pressure and obesity: Perspectives from the New Orleans experience.American heart journal plus : cardiology research and practice · 2024Article
- Estimating population infection rates from non-random testing data: Evidence from the COVID-19 pandemic.PloS one · 2024Article
- Article
- Characteristics of Mpox Infections in Louisiana in the 2022 Outbreak.AIDS research and human retroviruses · 2023Review
- Optimizing ancestral trait reconstruction of large HIV Subtype C datasets through multiple-trait subsampling.Virus evolution · 2023Article
- Impact of opinion dynamics on the public health damage inflicted by COVID-19 in the presence of societal heterogeneities.Frontiers in digital health · 2023Article
- Reversal of the unique Q493R mutation increases the affinity of Omicron S1-RBD for ACE2.Computational and structural biotechnology journal · 2023Article
- Estimating the undetected emergence of COVID-19 in the US.PloS one · 2023Article
- SARS-CoV-2 Genomic Diversity in Households Highlights the Challenges of Sequence-Based Transmission Inference.mSphere · 2022Article
- Article
- SARS-CoV-2 Spatiotemporal Genomic and Molecular Analysis of the First Wave of the COVID-19 Pandemic in Macaé, the Brazilian Capital of Oil.International journal of molecular sciences · 2022Article
Corrections and comments
- Update of
Authors and funding
52 authors.
Mark ZellerDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: zellerm@scripps.edu.
Karthik GangavarapuDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: gkarthik@scripps.edu.
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; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
Gytis DudasGothenburg Global Biodiversity Centre (GGBC), Gothenburg, Sweden.
Alexander WattsLi Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, 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; Centre for Virology Research, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP 14049900, Brazil.
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; Department of Physiology, Tulane University School of Medicine, 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.
Lilia I MelnikDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
Raphaëlle 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 Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, 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; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA.
Clarisse MarotzDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA.
Nathan D 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; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA.
Kaylynn J GenemarasDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA.
Karissa ChaoDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, 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; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA.
Gene W YeoDepartment of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, 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 Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, 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; Bluedot, Toronto, Canada; Department of Medicine, University of Toronto, Toronto, Canada.
Dahlene N FuscoDepartment of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70114, USA.
Vaughn S CooperDepartment of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
Phillipe LemeyDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium; Global Virology Network.
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.
Robert F GarryDepartment of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Zalgen Labs LLC, Germantown, MD, USA.
Marc A SuchardDepartment of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, 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; Scripps Research Translational Institute, La Jolla, CA 92037, USA. Electronic address: andersen@scripps.edu.
Funding
Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9MTracking & Evaluation CoreU54GM104940 · NIGMS · LSU PENNINGTON BIOMEDICAL RESEARCH CTR · PI Peter Todd Katzmarzyk · 2012 to 2026
$69.1MTechnology CoreU19AI135995 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Kristian Graugaard Andersen · 2018 to 2026
$32.0MScripps Translational Science InstituteUL1TR002550 · NCATS · SCRIPPS RESEARCH INSTITUTE, THE · PI TOPOL, ERIC JEFFREY · 2018 to 2022
$28.9MWest African Emerging Infectious Disease Research Center (WA-EIDRC)U01AI151812 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI ANDERSEN, KRISTIAN GRAUGAARD, GARRY, ROBERT F · 2020 to 2024
$13.2MPredicting the emergence of antibiotic resistance through multi-omics approaches and Immune System-surveillanU01AI124302 · NIAID · BOSTON COLLEGE · PI BENTO, JOSE, COOPER, VAUGHN · 2016 to 2020
$10.2MGenomics, GPUs, and Next Generation Computational StatisticsR01HG006139 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SOBEL, ERIC · 2011 to 2023
$5.1MStatistical Innovation to Integrate Sequences and Phenotypes for Scalable Phylodynamic InferenceR01AI153044 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Marc A. Suchard · 2021 to 2026
$2.4MNCATS 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 AI135995NIGMS NIH HHS U54 GM104940Wellcome Trust
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.
Indexed as
EpidemicsCOVID-19Databases as TopicDisease OutbreaksHumansLouisianaPhylogenyRisk FactorsSARS-CoV-2TexasTravelUnited Statesgenomic epidemiologymobilityphylogeneticsSARS-CoV-2viral emergenceviral sequencing
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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.