Aspike in COVID-19 has occurred in Southern California since October2020.Analysis of SARS-CoV-2 in Southern California prior to October indicated most isolates originated from clade20C that likely emerged from New York via Europe early in the pandemic。1个Since then，novel variants of SARS-Cov-2including 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单击功能区上，3Thus，we analyzed variants of SARS-CoV-2in Southern California to establish whether one of these known strains or anovel variant had emerged。
Regulatory review with waiver of consent was completed by Cedars-Sinai Medical Center（CSMC）。从同步存储器和ambulatory存储器，primary care，and employee health）that tested positive for SARS-CoV-2 collected from November 222020，to December 282020，at CSMC with cycle threshold values less less less than 30，a random sample from selected runs and dates within the collection period was sequenced and analyzed（eMethods in the支持，支持）。In addition，phylogenetic analysis was conducted with CSMC samples and globally representative genomes on January112021，by utilizing Nextstrain，a collection of open-source tools for visualizing the genetics behind the spread of viral outbreaks。4个全球Initiative on Sharing All Influenza Data，viral genomic data，5collected between December212019，and January112021（eMethods in the支持，支持）。
从以下CSMC中选择，collected between March4200and January222021.Southern California was defined as including the following counties:Imperial，Kern，Los Angeles，Orange，Riverside，San Bernardino，San Diego，San Luis Obispo，Santa Barbara，and Ventura。
Of2311 samples at CSMC，192 were selected and 185（67 inpatient；118outpatient）underwent phylogenetic analysis，along with1480representative genomes using Nextstrain.A diverse set of lineages with2main clusters was identified（火焰1）。The smaller of the 2 clusters was from the 20G lineage and accounted for22%（40of185）of the samples。The larger cluster（36%；67 of 185）consisted of a novel variant descended from cluster20C，defined by5 mutations（ORF1a:I4205V，ORF1b:D1183Y，S:S13I；W152C；L452R）and designated CAL.20C（20C/S:452R；/B.1.429）。
Analysis of 10 431 samples from California，including4829 from Southern California，revealed that CAL.20Cwas first observed in July2020in1 of 1247 samples from Los Angeles County and not detected in Southern California again until Octover.Since then，this variant’s prevalence has increased in the state of California and in Southern California California，35%（86 of 247）和44%（37 of 85）of all samples collected in January，respectively（火焰2）。
Sequence analysis of 405 871global samples on GISAID on January222021，revealed that CAL.20Cwas only found in Southern California in Octover2020（4cases）。In November2020,30cases were also identified in Northern California and individual cases in5additional states.As of January222021，CAL.20C has been detected in26states and other countries（支持，支持）。
Anovel variant of SARS-Cov-2，CAL.20C，was identified，which emerged in Southern California contemporaneously with the local surge in cases.Unlike clade20G，currently the largest reported clade in North America，this strain is defined by3mutations in the S protein characterizing it as subclade of 20C.The S protein L452R mutation is within a known receptor binding domain that has been found to be resistant to certain spike（S）protein monoclonal antibodies。6个Because this study was limited to databases of publicly available genomes and a comparatively small set of local samples，the possibility of collection bias cannot be ruled out.Additionally，as clinical outcomes have yet to be established， the functional effect of this strain regarding infectivity and disease severity remains uncertain.Nevertheless，the identification of this novel strain is important to frontline and global surveillance of this evolving virus。
已接受的发布：February12021。
已发布的联机：February112021.doi:10.1001/jama.2021.1612
核心审计：Jasmine T.Plummer，PhD，Cedars Sinai Medical Center，8700 Beverly Blvd，SSB365，Los Angeles，CA90048（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。
严重警告：All authors。
统计分析：Zhang，Vail。
Obtained funding：Plummer，Vail。
管理员，技术支持：Davis，Chen，Sincuir Martinez，Plummer，Vail。
超级vision：Plummer，Vail。
接口磁盘：Dr Vail reported receiving personal fees from Illumina outside the submitted work.Noother disclosures were reported。
功能/支持：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。
其他内容：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。
其他信息：Data used in this study have been deposited to GISAID with accession ESP_ISL_824555-824741。
1。张扬，张扬W，GovindavariJP，DavisBD、，et al.Analysis of genomic characteristics and transmission routes of patients with confirmed SARS-Cov-2in Southern California during the early stage of the US COVID-19pandemic。
JAMA Netw Open.2020；3（10）：e2024191。doi:10.1001/jamanetworkopen.2020.24191PubMedGoogle Scholar