Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference
- J. Maximilian Fels1,14,
- Saad Khan2,14,
- Ryan Forster2,14,
- Karin A. Skalina3,13,
- Surksha Sirichand4,
- Amy S. Fox3,5,
- Aviv Bergman2,3,6,7,
- William B. Mitchell5,8,
- Lucia R. Wolgast3,
- Wendy Szymczak3,
- Robert H. Bortz III1,
- M. Eugenia Dieterle1,
- Catalina Florez1,9,
- Denise Haslwanter1,
- Rohit K. Jangra1,
- Ethan Laudermilch1,
- Ariel S. Wirchnianski1,10,
- Jason Barnhill9,
- David L. Goldman1,5,11,
- Hnin Khine5,12,
- D. Yitzchak Goldstein3,
- Johanna P. Daily1,4,
- Kartik Chandran1 and
- Libusha Kelly1,2
- 1Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
- 2Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
- 3Department of Pathology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York 10461, USA;
- 4Department of Medicine (Infectious Diseases), Albert Einstein College of Medicine, Bronx, New York 10461, USA;
- 5Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
- 6Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
- 7The Santa Fe Institute, Santa Fe, New Mexico 87501, USA;
- 8Division of Pediatric Hematology/Oncology, Children's Hospital at Montefiore, Bronx, New York 10461, USA;
- 9Department of Chemistry and Life Science, United States Military Academy at West Point, West Point, New York 10996, USA;
- 10Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
- 11Division of Pediatric Infectious Diseases, Children's Hospital at Montefiore, Bronx, New York 10467, USA;
- 12Division of Pediatric Emergency Medicine, Children's Hospital at Montefiore, Bronx, New York 10467, USA
- Corresponding authors: libusha.kelly{at}einsteinmed.org; kartik.chandran{at}einsteinmed.org; jdaily{at}montefiore.org; dogoldst{at}montefiore.org; hkhine{at}montefiore.org; dagoldma{at}montefiore.org
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↵14 These authors contributed equally to this work.
Abstract
The Bronx was an early epicenter of the COVID-19 pandemic in the United States. We conducted temporal genomic surveillance of 104 SARS-CoV-2 genomes across the Bronx from March to October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS-CoV-2 genomic diversity. Mapping the trajectories of mutations, we found that although some became “endemic” to the Bronx, other, novel mutations rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between cases of reinfection and persistent infection in two pediatric patients. We propose that limited, targeted, temporal genomic surveillance has clinical and epidemiological utility in managing the ongoing COVID pandemic.
Footnotes
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[Supplemental material is available for this article.]
- Received March 18, 2022.
- Accepted June 24, 2022.
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