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

ABSTRACT: 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.

SUBMITTER: Fels JM

PROVIDER: S-EPMC7885943 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference.

Fels J Maximilian JM Khan Saad S Forster Ryan R Skalina Karin A KA Sirichand Surksha S Fox Amy S AS Bergman Aviv A Mitchell William B WB Wolgast Lucia R LR Szymczak Wendy W Bortz Robert H RH Dieterle M Eugenia ME Florez Catalina C Haslwanter Denise D Jangra Rohit K RK Laudermilch Ethan E Wirchnianski Ariel S AS Barnhill Jason J Goldman David L DL Khine Hnin H Goldstein D Yitzchak DY Daily Johanna P JP Chandran Kartik K Kelly Libusha L

medRxiv : the preprint server for health sciences 20220317

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 became 'endemic' to the Bronx, other, novel variants rose in pr ...[more]

PMID: 33594384

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Dataset Information

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

Publications

Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference.

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