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

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

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.