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Genomic surveillance of SARS-CoV-2 in the Bronx enables clinical and epidemiological inference


The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of SARS-CoV-2 genomes across the Bronx from March-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 variants, we found that while some have become ‘endemic’ to the Bronx, other, novel variants rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between a case of reinfection and a case of persistent infection. We propose that limited, targeted, temporal genomic surveillance has clinical and epidemiological utility in managing the ongoing COVID pandemic.

Authors: J. Maximilian Fels, Saad Khan, Ryan Forster, Karin A. Skalina, Surksha Sirichand, Amy S. Fox, Aviv Bergman, William B. Mitchell, Lucia R. Wolgast, Wendy Szymczak, Robert H. Bortz III, M. Eugenia Dieterle, Catalina Florez, Denise Haslwanter, Rohit K. Jangra, Ethan Laudermilch, Ariel S. Wirchnianski, Jason Barnhill, David L. Goldman, Hnin Khine, D. Yitzchak Goldstein, Johanna P. Daily, Kartik Chandran, Libusha Kelly

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