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Public Health

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

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To identify the key insights or developments described in this article

1 Credit CME

JAMA

Published Online: February 11, 2021

Research Letter

Article Information and Disclosures

Wenjuan Zhang, PhD¹;

Brian D. Davis, BSc²;

Stephanie S. Chen, BSc²;

Jorge M. Sincuir Martinez, BS¹;

Jasmine T. Plummer, PhD²;

Eric Vail, MD¹

Author Affiliations

¹Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
²Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California

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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

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.2020.24191 PubMed Google Scholar

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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/bty407 PubMed Google Scholar Crossref

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.2017.22.13.30494 PubMed Google Scholar Crossref

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.2020.07.012 PubMed Google Scholar Crossref

AMA CME Accreditation Information

Credit Designation Statement: The American Medical Association designates this Journal-based CME activity activity for a maximum of 1.00  AMA PRA Category 1 Credit(s)™. Physicians should claim only the credit commensurate with the extent of their participation in the activity.

Successful completion of this CME activity, which includes participation in the evaluation component, enables the participant to earn up to:

1.00 Medical Knowledge MOC points in the American Board of Internal Medicine's (ABIM) Maintenance of Certification (MOC) program;;
1.00 Self-Assessment points in the American Board of Otolaryngology – Head and Neck Surgery’s (ABOHNS) Continuing Certification program;
1.00 MOC points in the American Board of Pediatrics’ (ABP) Maintenance of Certification (MOC) program;
1.00 Lifelong Learning points in the American Board of Pathology’s (ABPath) Continuing Certification program; and
1.00 CME points in the American Board of Surgery’s (ABS) Continuing Certification program

It is the CME activity provider's responsibility to submit participant completion information to ACCME for the purpose of granting MOC credit.