Increase In CAL.20C in California Since November
#15,735
Four days ago, in California DPH Statement On L452R Variant Linked To Several Large COVID Outbreaks, we looked at a Sunday night press conference and CPHD statement on a rapidly spreading new variant in California.
While initially referred to as the L452R variant, it has since been designated CAL.20C.
On Wednesday (Jan 20th) a preprint article appeared on MedRxiv from researchers at Cedars Sinai Medical Center describing this new variant which carries, among other mutations - L452R - an amino acid change that has been linked to increased resistance to some neutralizing antibodies (see CELL Report).
First a link, and the abstract from the Preprint , followed by a excerpts from a press released from Cedars Sinai M.C.
Emergence of a novel SARS-CoV-2 strain in Southern California, USA
Wenjuan Zhang, Brian Davis, Stephanie S Chen, Jorge Sincuir Martinez, Jasmine T Plummer, Eric Vail
doi: https://doi.org/10.1101/2021.01.18.21249786
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Abstract
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.
(SNIP)
Discussion:
These findings add to our current understanding of COVID-19 transmission within the US, specifically that the recent surge in COVID-19 positive cases in Southern California coincides with the emergence of a unique strain, CAL.20C. Given the independent emergence of geographically isolated, clinically relevant strains such as B.1.1.7 (UK) and B.1.351 (South Africa), the CAL.20C strain may be partially responsible for the magnitude of the surge in COVID-19 on the West Coast of the US. The S protein L452R mutation is within a known receptor binding domain that has been found to be markedly resistant to certain monoclonal antibodies to the spike protein(4).
Mutations in this domain may be resistant to polyclonal sera as seen in convalescent patients or those post vaccination(5). The functional effect of this mutation in concert with other detected mutations in CAL.20C, both in terms of infectivity and antibody resistance is unknown at this time. The identification of this novel strain is important to frontline and global surveillance of this constantly evolving virus and has a direct impact on public health, especially vaccination efforts.
While the full impact of this emerging variant remains unknown, its appearance coincides with the recent rise in COVID cases in Southern California, raising concerns over its transmissibility. Whether, and how much, of an effect the L452R mutation might have on antibody treatments, reinfection rates, or vaccine effectiveness has yet to be determined.
For more background on this variant you may wish to peruse the Cedars Sinai press release below.
Local COVID-19 Strain Found in Over One-Third of Los Angeles Patients
Cedars-Sinai Investigators Say That New Local Strain, Designated as CAL.20C, May Be Contributing to Pandemic Surge
A new strain of the coronavirus has been found in more than one-third of COVID-19 cases in Los Angeles and may be contributing to the acceleration of the recent surge of cases across Southern California, according to new research from Cedars-Sinai.
The strain, which the investigators designated as CAL.20C, is believed to be in part responsible for the dramatic increase in cases over the last two months. The Cedars-Sinai findings did not indicate whether the strain is more deadly than current forms of the coronavirus.
CAL.20C is distinct from the virus version identified in Britain—known as B.1.1.7—that is spreading in the U.S. and is believed to be highly transmissible. In Southern California, B.1.1.7 has been found in scattered coronavirus cases in Los Angeles, San Diego and San Bernardino counties. In contrast, the CAL.20C strain was identified in 36.4% of cases in the Cedars-Sinai study.
CAL.20C includes a virus variant that the California Department of Public Health reported Jan. 17 based on data submitted by Cedars-Sinai and other investigators. This variant, dubbed L452R, is one of five recurring mutations that constitute the CAL.20C strain, which is propagating across the country, starting in Los Angeles.
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