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

IF 1.8 Q3 MEDICINE, RESEARCH & EXPERIMENTAL Cold Spring Harbor Molecular Case Studies Pub Date : 2022-07-13 DOI:10.1101/mcs.a006211

J Maximilian Fels, Saad Khan, Ryan Forster, Karin A Skalina, Surksha Sirichand, Amy S Fox, Aviv Bergman, William B Mitchell, Lucia R Wolgast, Wendy A Szymczak, Robert H Bortz, 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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Abstract

The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of 104 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 mutations, we found that while 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.

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在布朗克斯大流行的第一年，对 SARS-CoV-2 进行基因组监测，从而得出临床和流行病学推论。

布朗克斯是美国 COVID-19 大流行的早期中心。从 2020 年 3 月到 10 月，我们在布朗克斯对 104 个 SARS-CoV-2 基因组进行了时间基因组监测。虽然 SARS-CoV-2 世系的本地结构与纽约市和纽约州的结构一致，但时间取样显示了 SARS-CoV-2 基因组多样性的动态变化。在绘制突变轨迹图时，我们发现有些突变已成为布朗克斯的 "地方病"，而其他新型突变则在夏末秋初流行起来。地理分辨基因组使我们能够区分两名儿童患者的再感染和持续感染病例。我们建议，有限的、有针对性的、时间性的基因组监测对管理正在进行的 COVID 大流行具有临床和流行病学方面的作用。

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来源期刊

Cold Spring Harbor Molecular Case Studies MEDICINE, RESEARCH & EXPERIMENTAL-

CiteScore

3.20

自引率

0.00%

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期刊介绍： Cold Spring Harbor Molecular Case Studies is an open-access, peer-reviewed, international journal in the field of precision medicine. Articles in the journal present genomic and molecular analyses of individuals or cohorts alongside their clinical presentations and phenotypic information. The journal''s purpose is to rapidly share insights into disease development and treatment gained by application of genomics, proteomics, metabolomics, biomarker analysis, and other approaches. The journal covers the fields of cancer, complex diseases, monogenic disorders, neurological conditions, orphan diseases, infectious disease, gene therapy, and pharmacogenomics. It has a rapid peer-review process that is based on technical evaluation of the analyses performed, not the novelty of findings, and offers a swift, clear path to publication. The journal publishes: Research Reports presenting detailed case studies of individuals and small cohorts, Research Articles describing more extensive work using larger cohorts and/or functional analyses, Rapid Communications presenting the discovery of a novel variant and/or novel phenotype associated with a known disease gene, Rapid Cancer Communications presenting the discovery of a novel variant or combination of variants in a cancer type, Variant Discrepancy Resolution describing efforts to resolve differences or update variant interpretations in ClinVar through case-level data sharing, Follow-up Reports linked to previous observations, Plus Review Articles, Editorials, and Position Statements on best practices for research in precision medicine.