Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area

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  • Thielen, P.M
    • Other Affiliation: Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
  • Wohl, S
    • Other Affiliation: Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
  • Mehoke, T
    • Other Affiliation: Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
  • Ramakrishnan, S
    • Other Affiliation: Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
  • Kirsche, M
    • Other Affiliation: Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
  • Falade-Nwulia, O
    • Other Affiliation: Department of Medicine, Division of Infectious Disease, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
  • Trovão, N.S
    • Other Affiliation: NIH, Fogarty International Center, Bethesda, MD, United States
  • Ernlund, A
    • Other Affiliation: Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
  • Howser, C
    • Other Affiliation: Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
  • Sadowski, N
    • Other Affiliation: Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD, United States
  • Morris, C.P
    • Other Affiliation: Department of Pathology, Division of Medical Microbiology, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
  • Hopkins, M
    • Other Affiliation: Department of Pathology, Division of Medical Microbiology, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
  • Schwartz, M
    • Other Affiliation: Department of Pathology, Division of Medical Microbiology, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
  • Fan, Y
    • Other Affiliation: Departments of Biomedical Engineering and Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, United States
  • Gniazdowski, V
    • Other Affiliation: Department of Pathology, Division of Medical Microbiology, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
  • Lessler, J
    • Affiliation: Gillings School of Global Public Health, Department of Epidemiology
    • Other Affiliation: Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
  • Sauer, L
    • Other Affiliation: Department of Medicine, Division of Infectious Disease, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
  • Schatz, M.C
    • Other Affiliation: Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
  • Evans, J.D
    • Other Affiliation: Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
  • Ray, S.C
    • Other Affiliation: Department of Medicine, Division of Infectious Disease, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
  • Timp, W
    • Other Affiliation: Department of Medicine, Division of Infectious Disease, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
  • Mostafa, H.H
    • Other Affiliation: Department of Pathology, Division of Medical Microbiology, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
Abstract
  • The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within 3 weeks of the first COVID-19 detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2 - the virus that causes COVID-19 - in the region. We analyzed 620 samples collected from the Johns Hopkins Health System during March 11-31, 2020, comprising 28.6% of the total cases in Maryland and Washington, DC. From these samples, we generated 114 complete viral genomes. Analysis of these genomes alongside a subsampling of over 1000 previously published sequences showed that the diversity in this region rivaled global SARS-CoV-2 genetic diversity at that time and that the sequences belong to all of the major globally circulating lineages, suggesting multiple introductions into the region. We also analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and found that clinically severe cases had viral genomes belonging to all major viral lineages. We conclude that efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and the interconnectedness of the region as a whole.
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  • Article
Rights statement
  • In Copyright
License
  • Attribution 4.0 International
Journal title
  • JCI Insight
Journal volume
  • 6
Journal issue
  • 6
Language
  • English
Version
  • Publisher
Funder
  • Johns Hopkins University, JHU
  • Alfred P. Sloan Foundation
  • National Institutes of Health, NIH: HHSN272201400007C
  • Johns Hopkins Hospital, JHH
  • National Institute of Allergy and Infectious Diseases, NIAID: R01AI134384
  • National Human Genome Research Institute, NHGRI: R01HG010538, U41HG006620
  • National Science Foundation, NSF: DBI-1627442
  • Gordon and Betty Moore Foundation, GBMF
ISSN
  • 2379-3708
Publisher
  • American Society for Clinical Investigation

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