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

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 3

JHHS sequences and patient outcome.

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JHHS sequences and patient outcome. (A) Maximum likelihood tree of subsa...
(A) Maximum likelihood tree of subsampled SARS-CoV-2 global data set and all 114 sequences generated in this study. Ambulatory (blue) includes all patients with no known admission to the hospital. Hospital admission (light red) includes admitted patients with no known admission to the ICU, including patients administered oxygen. (B) Clinical metadata and virus lineage. Each column represents 1 of the 114 patients with virus sequenced in this study, and columns are grouped by disposition within each lineage. Unless otherwise specified: black, yes; white, no; gray, unknown. Disposition: black, still in hospital or deceased as of May 15, 2020; dark gray, discharged; and white, never admitted. Race: black, Black; white, White; gray, other. “Other” includes < 10 each of American Indian/Alaska Native, Hispanic ethnicity (not otherwise specified as Black or White), other race not specified, or unknown. Sex: black, female; white, male. Enrollment criteria (top down): Fever, cough, and shortness of breath. Symptoms (top down): body ache, GI. Comorbidities (top down): cardiac disease, lung disease, diabetes, obese, alcohol, history of smoking (current and former smokers), and immunocompromised. Outcome (top down): hospital admission, supplementary oxygen, ICU admission, and ventilator administration. JHHS, Johns Hopkins Health System.