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. 2021 Apr 6;325(13):1324-1326.
doi: 10.1001/jama.2021.1612.

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

Wenjuan Zhang  1 , Brian D Davis  2 , Stephanie S Chen  2 , Jorge M Sincuir Martinez  1 , Jasmine T Plummer  2 , Eric Vail  1
Affiliations

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

Wenjuan Zhang et al. JAMA. .

Abstract

This research describes findings of sequencing and phylogenetic analyses of SARS-CoV-2 isolates from symptomatic patients cared for at Cedar-Sinai Medical Center in November-December 2020 during a regional surge in cases and hospitalizations.

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Conflict of interest statement

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

Figures

Figure 1.
Figure 1.. Phylogenetic Relationship of CSMC Samples to Global SARS-CoV-2 Genomes
Phylogenetic tree of 185 Cedars-Sinai Medical Center (CSMC) SARS-CoV-2 isolates and a global subsampling of 1480 isolates collected from December 2019 to January 2021 reveals a novel subcluster within 20C that share 5 mutations (ORF1a: I4205V, ORF1b: D1183Y, S: S13I; W152C; L452R), designated as CAL.20C (20C/S.452R). The phylogenetic tree shows the relationship of CAL.20C to other circulating lineages. The branch length (x-axis) reflects numbers of mutations accumulated before being discovered, and clades are designated based on Nextstrain nomenclature. The UK variant (501Y.V1), South African variant (501Y.V2), and Brazil variant (501Y.V3) are shown.
Figure 2.
Figure 2.. Timeline for the Emergence of a Novel Southern California Variant, CAL.20C, Among All SARS-CoV-2 Circulating Variants Observed
Diagrammatic representation of circulating SARS-CoV-2 variant frequencies. A, Includes 10 431 samples from the state of California. B, Includes 4829 samples from Southern California.
See this image and copyright information in PMC

Comment in

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.2020.24191 - DOI - PMC - PubMed
    1. Lauring AS, Hodcroft EB. Genetic variants of SARS-CoV-2—what do they mean? JAMA. Published online January 6, 2021. doi:10.1001/jama.2020.27124 - DOI - PubMed
    1. 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.2020.12.024 - DOI - PMC - PubMed
    1. 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 - DOI - PMC - PubMed
    1. 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 - DOI - PMC - PubMed

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