@article{2cf2d30efe664596912c4e20d7b3fefd,
title = "Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference",
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.",
author = "Fels, {J. Maximilian} and Saad Khan and Ryan Forster and Skalina, {Karin A.} and Surksha Sirichand and Fox, {Amy S.} and Aviv Bergman and Mitchell, {William B.} and Wolgast, {Lucia R.} and Wendy Szymczak and Bortz, {Robert H.} and Dieterle, {M. Eugenia} and Catalina Florez and Denise Haslwanter and Jangra, {Rohit K.} and Ethan Laudermilch and Wirchnianski, {Ariel S.} and Jason Barnhill and Goldman, {David L.} and Hnin Khine and Goldstein, {D. Yitzchak} and Daily, {Johanna P.} and Kartik Chandran and Libusha Kelly",
note = "Funding Information: L.K. is supported in part by a Peer Reviewed Cancer Research Program Career Development Award from the United States Department of Defense (CA171019) and a grant from the Ullmann Family Foundation. Computational resources were supported by an award from the Google Cloud Research Credits program (GCP19980904) to L.K. S.K. is supported by the Einstein Medical Scientist Training Program (2T32GM007288-45) and by a National Institutes of Health (NIH) T32 Fellowship in Geographic Medicine and Emerging Infectious Diseases (2T32AI070117-13). K.A.S. is supported by an NIH F30 Fellowship (F30CA200411) and T32 Fellowship (T32GM007288). Publisher Copyright: {\textcopyright} 2022 Fels et al.",
year = "2022",
month = aug,
doi = "10.1101/mcs.a006211",
language = "English (US)",
volume = "8",
journal = "Cold Spring Harbor molecular case studies",
issn = "2373-2873",
publisher = "Cold Spring Harbor Laboratory Press",
number = "5",
}