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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 4

Geographical context of sequences from the Baltimore–Washington metropolitan area.

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Geographical context of sequences from the Baltimore–Washington metropol...
(A) Maximum likelihood tree. Filled tips belong to sequences generated in this study. Major phylogenetic lineages (defined as lineages from the Pango nomenclature system (14) found in greater than 5% of samples in our subsampled global data set) are indicated by color blocks and labeled. (B) Evolutionary divergence in geographic groups. Violin plots represent the distribution of pairwise genetic distances between all sequences for samples collected in each listed geographic group. Colors are as in A, with filled violins containing sequences from this study. Black vertical lines depict the mean pairwise genetic distance between all samples in each regional group. (C) Map of the Baltimore–Washington metropolitan area. The number of sequences in this study with home locations in each area as defined by the first 3 digits of the patient zip code (ZIP3 area; Washington, DC outlined in black, all others gray) is indicated by shading of that region (darker, more sequences) and pie chart area. Pie charts show the proportion of sequences from each ZIP3 area belonging to each major lineage. Sequence counts between 1 and 5 are shown as 5 sequences. MD, Maryland; VA, Virginia; DC, District of Columbia; WA, Washington; CA, California; ID, Idaho; LA, Louisiana; NY, New York.

Copyright © 2021 American Society for Clinical Investigation
ISSN 2379-3708

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