Fels, J. Maximilian; 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 Haslwanterl Rohit K. Jangra; Ethan Laudermilch; Ariel S. Wirchnianski; Jason Barnhill; David L. Goldman; Hnin Khine; D. Yitzchak Goldstein; Johanna P. Daily; Kartik Chandran and Libusha Kelly

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.