A spike in coronavirus disease 2019 (COVID-19) has occurred in Southern California since October 2020. Analysis of the severe acute respiratory syndrome coronavirus (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. Methods | Regulatory review with waiver of consent was completed by Cedars-Sinai Medical Center (CSMC). From all samples from symptomatic inpatients and ambulatory care (urgent care, primary care, and employee health) that tested positive for SARS-CoV-2 collected from November 22, 2020, to December 28, 2020, at CSMC with cycle threshold values less than 30, a random sample from selected runs and dates within the collection period was sequenced and analyzed (Supplement). In addition, phylogenetic analysis was conducted with CSMC samples and globally representative genomes on January 11, 2021, by utilizing Nextstrain, a collection of open-source tools for visualizing the genetics behind the spread of viral outbreaks. 4 The representative global samples were randomly chosen using a computer algorithm from more than 400 000 available genomes on GISAID (Global Initiative on Sharing All Influenza Data), an open-access global collection of viral genomic data, 5 collected between December 21, 2019, and January 11, 2021 (Supplement). The proportional prevalence of each clade over time in samples from California as a whole and Southern California specifically and presence of any novel lineages discovered worldwide was calculated using publicly available sequences from GISAID (including samples from CSMC), collected between
Since October 2020, novel strains of SARS-CoV-2 including B.1.1.7, have been identified to be of global significance from an infection and surveillance perspective. While this strain (B.1.1.7) may play an important role in increased COVID rates in the UK, there are still no reported strains to account for the spike of cases in Los Angeles (LA) and California as a whole, which currently has some of the highest absolute and per-capita COVID transmission rates in the country. From the early days of the pandemic when LA only had a single viral genome uploaded onto GISAID we have been at the forefront of generating and analyzing the SARS-CoV-2 sequencing data from the LA region. We report a novel strain emerging in Southern California. Most current cases in the catchment population in LA fall into two distinct subclades: 1) 20G (24% of total) is the predominant subclade currently in the United States 2) a relatively novel strain in clade 20C, CAL.20C strain (∼36% of total) is defined by five concurrent mutations. After an analysis of all of the publicly available data and a comparison to our recent sequences, we see a dramatic growth in the relative percentage of the CAL.20C strain beginning in November of 2020. The predominance of this strain coincides with the increased positivity rate seen in this region. Unlike 20G, this novel strain CAL.20C is defined by multiple mutations in the S protein, a characteristic it shares with both the UK and South African strains, both of which are of significant clinical and scientific interest
IMPORTANCE In late December 2019, an outbreak of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. Data on the routes of transmission to Los Angeles, California, the US West Coast epicenter for coronavirus disease 2019 (COVID-19), and subsequent community spread are limited. OBJECTIVE To determine the transmission routes of SARS-CoV-2 to Southern California and elucidate local community spread within the Los Angeles metropolitan area. DESIGN, SETTING, AND PARTICIPANTS This case series included 192 consecutive patients with reverse transcription-polymerase chain reaction (RT-PCR) test results positive for SARS-CoV-2 who were evaluated at Cedars-Sinai Medical Center in Los Angeles, California, from March 22 to April 15, 2020. Data analysis was performed from April to May 2020. MAIN OUTCOMES AND MEASURES SARS-CoV-2 viral genomes were sequenced. Los Angeles isolates were compared with genomes from global subsampling and from New York, New York; Washington state; and China to determine potential sources of viral dissemination. Demographic data and outcomes were collected. RESULTS The cohort included 192 patients (median [interquartile range] age, 59.5 [43-75] years; 110 [57.3%] men). The genetic characterization of SARS-CoV-2 isolates in the Los Angeles population pinpointed community transmission of 13 patients within a 3.81 km 2 radius. Variation landscapes of this case series also revealed a cluster of 10 patients that contained 5 residents at a skilled nursing facility, 1 resident of a nearby skilled nursing facility, 3 health care workers, and a family member of a resident of one of the skilled nursing facilities. Person-to-person transmission was detected in a cluster of 5 patients who shared the same single-nucleotide variation in their SARS-CoV-2 genomes. High viral genomic diversity was identified: 20 Los Angeles isolates (15.0%) resembled SARS-CoV-2 genomes from Asia, while 109 Los Angeles isolates (82.0%) were similar to isolates originating from Europe. Analysis of other common respiratory viral pathogens did not reveal coinfection in the cohort. CONCLUSIONS AND RELEVANCE These findings highlight the precision of detecting person-toperson transmission and accurate contact tracing directly through SARS-CoV-2 genome isolation and sequencing. Development and application of phylogenetic analyses from the Los Angeles population established connections between COVID-19 clusters locally and throughout the US.
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