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Emergence of a Novel SARS-CoV-2 Variant in Southern California

Educational Objective
To identify the key insights or developments described in this article
1 Credit CME

A spike in COVID-19 has occurred in Southern California since October 2020. Analysis of SARS-CoV-2 in Southern California prior to October indicated most isolates originated from clade 20C that likely emerged from New York via Europe early in the pandemic.1 Since then, novel variants of SARS-CoV-2 including those seen in the UK (20I/501Y.V1/B.1.1.7), South Africa (20H/501Y.V2/B.1.351), and Brazil (P.1/20J/501Y.V3/B.1.1.248) have emerged, with the concern of increased infectivity and virulence.2,3 Thus, we analyzed variants of SARS-CoV-2 in Southern California to establish whether one of these known strains or a novel variant had emerged.

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Article Information

Accepted for Publication: February 1, 2021.

Published Online: February 11, 2021. doi:10.1001/jama.2021.1612

Corresponding Author: Jasmine T. Plummer, PhD, Cedars Sinai Medical Center, 8700 Beverly Blvd, SSB365, Los Angeles, CA 90048 (jasmine.plummer@cshs.org).

Author Contributions: Drs Plummer and Vail had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis. Drs Plummer and Vail codirected the study.

Concept and design: Zhang, Plummer, Vail.

Acquisition, analysis, or interpretation of data: All authors.

Drafting of the manuscript: Plummer, Vail.

Critical revision of the manuscript for important intellectual content: All authors.

Statistical analysis: Zhang, Vail.

Obtained funding: Plummer, Vail.

Administrative, technical, or material support: Davis, Chen, Sincuir Martinez, Plummer, Vail.

Supervision: Plummer, Vail.

Conflict of Interest Disclosures: Dr Vail reported receiving personal fees from Illumina outside the submitted work. No other disclosures were reported.

Funding/Support: This project was funded by an internal grant to Dr Plummer provided by the Department of Biomedical Sciences, Cedars-Sinai Medical Center.

Role of the Funder/Sponsor: The funder had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

Additional Contributions: We thank Yizhou Wang, PhD, Applied Genomics, Computational and Translational Core, for demultiplexing files and Jeffrey Golden, MD, Burns and Allen Research Institute, for assistance with editing. Neither received compensation.

Additional Information: Data used in this study have been deposited to GISAID with accession ESP_ISL_824555-824741.

References
1.
Zhang  W , Govindavari  JP , Davis  BD ,  et al.  Analysis of genomic characteristics and transmission routes of patients with confirmed SARS-CoV-2 in Southern California during the early stage of the US COVID-19 pandemic.   JAMA Netw Open. 2020;3(10):e2024191. doi:10.1001/jamanetworkopen.2020.24191PubMedGoogle Scholar
2.
Lauring  AS , Hodcroft  EB .  Genetic variants of SARS-CoV-2—what do they mean?   JAMA. Published online January 6, 2021. doi:10.1001/jama.2020.27124PubMedGoogle Scholar
3.
Tang  JW , Tambyah  PA , Hui  DS .  Emergence of a new SARS-CoV-2 variant in the UK.   J Infect. Published online December 28, 2020. doi:10.1016/j.jinf.2020.12.024PubMedGoogle Scholar
4.
Hadfield  J , Megill  C , Bell  SM ,  et al.  Nextstrain: real-time tracking of pathogen evolution.   Bioinformatics. 2018;34(23):4121-4123. doi:10.1093/bioinformatics/bty407PubMedGoogle ScholarCrossref
5.
Shu  Y , McCauley  J .  GISAID: Global Initiative on Sharing All Influenza Data—from vision to reality.   Euro Surveill. 2017;22(13):30494. doi:10.2807/1560-7917.ES.2017.22.13.30494PubMedGoogle ScholarCrossref
6.
Li  Q , Wu  J , Nie  J ,  et al.  The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity.   Cell. 2020;182(5):1284-1294. doi:10.1016/j.cell.2020.07.012PubMedGoogle ScholarCrossref
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