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Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore–Washington metropolitan area
Peter M. Thielen, … , Winston Timp, Heba H. Mostafa
Peter M. Thielen, … , Winston Timp, Heba H. Mostafa
Published March 22, 2021
Citation Information: JCI Insight. 2021;6(6):e144350. https://doi.org/10.1172/jci.insight.144350.
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Research Article COVID-19

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

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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.

Authors

Peter M. Thielen, Shirlee Wohl, Thomas Mehoke, Srividya Ramakrishnan, Melanie Kirsche, Oluwaseun Falade-Nwulia, Nídia S. Trovão, Amanda Ernlund, Craig Howser, Norah Sadowski, C. Paul Morris, Mark Hopkins, Matthew Schwartz, Yunfan Fan, Victoria Gniazdowski, Justin Lessler, Lauren Sauer, Michael C. Schatz, Jared D. Evans, Stuart C. Ray, Winston Timp, Heba H. Mostafa

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Figure 1

COVID-19 diagnostic response during initial SARS-CoV-2 surveillance in the JHHS.

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COVID-19 diagnostic response during initial SARS-CoV-2 surveillance in t...
(A) Cumulative number of positive tests in Washington, DC, and the state of Maryland (white bars) and within the JHHS (black bars). (B) SARS-CoV-2 RT-PCR CT value (S-gene) versus days from patient symptom onset. Data fit with LOESS curve (white regression line). Two outliers (days from onset = 5 weeks, CT value = 30 and days from onset = 28 days, CT value = 31) are not shown. (C) Age distribution of SARS-CoV-2 patients within the JHHS. JHHS, Johns Hopkins Health System; CT, threshold cycle.

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