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

Thielen, Peter M, Wohl, Shirlee, Mehoke, Thomas, Ramakrishnan, Srividya, Kirsche, Melanie, Falade-Nwulia, Oluwaseun, Trovão, Nídia S, Ernlund, Amanda, Howser, Craig, Sadowski, Norah, Morris, C Paul, Hopkins, Mark, Schwartz, Matthew, Fan, Yunfan, Gniazdowski, Victoria, Lessler, Justin, Sauer, Lauren, Schatz, Michael C, Evans, Jared D, Ray, Stuart C, Timp, Winston, Mostafa, Heba H (March 2021) Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area. JCI Insight, 6 (6). ISSN 2379-3708

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DOI: 10.1172/jci.insight.144350


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.

Item Type: Paper
Subjects: diseases & disorders
bioinformatics > genomics and proteomics
diseases & disorders > viral diseases
diseases & disorders > viral diseases > coronavirus
diseases & disorders > viral diseases > coronavirus > covid 19
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Schatz lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 22 March 2021
Date Deposited: 07 May 2021 17:38
Last Modified: 25 Jan 2024 19:37
PMCID: PMC8026189

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