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.
Highlights
SARS-CoV-2, the virus that causes COVID-19, established itself worldwide within 2 months of its emergence in Wuhan, China [1]
In the United States, diagnostic capacity for SARS-CoV-2 was limited until early March 2020 due to regulatory challenges associated with limited Emergency Use Authorization (EUA) for laboratory-developed testing
The first detection of SARS-CoV-2 in the region was reported on March 5, 2020, by the Maryland Department of Health, and a State of Emergency was immediately declared in Maryland [21]
Summary
SARS-CoV-2, the virus that causes COVID-19, established itself worldwide within 2 months of its emergence in Wuhan, China [1]. Generation and analysis of pathogen genomic data have been key components of this research [3,4,5,6,7,8] and provide critical insights into the emergence and spread of SARS-CoV-2 and the dynamics of emerging infections in general. In the United States, diagnostic capacity for SARS-CoV-2 was limited until early March 2020 due to regulatory challenges associated with limited Emergency Use Authorization (EUA) for laboratory-developed testing. Ongoing work has continued to deepen our understanding of SARS-CoV-2, including use of pathogen sequence data to help reconstruct the transmission of the virus into and around the United States [12]
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