A new SARS-CoV-2 variant, CAL.20C, has been detected in southern California amid an increase in local infections and spread through and outside the United States, according to a research letter released yesterday in JAMA.
Researchers at the Cedars-Sinai Medical Center (CSMC) in Los Angeles analyzed COVID-19 strains before and after the increase in cases in southern California in October 2020. Before October, most coronavirus strains there originated from the 20C group (group of viruses originated from the same ancestor), which originated in Europe in the early stages of the pandemic in New York.
CAL.20C, or 20C / S: 452R; / B1429, was first seen in 1 of 1,247 COVID-19 samples in Los Angeles County, but was only observed in the region again in October, when four cases were detected. While CAL.20C was first found in southern California in October, 30 cases were identified in the northern part of the state in November, and five other states reported the variant.
By January 22, the variant had grown to 35% of all coronavirus strains in California and 44% of all samples in the southern part of the state and was detected in 26 states as well as other states. CAL.20C is one of several other widely distributed variants, such as those first identified in the United Kingdom (B117), South Africa (B1351) and Brazil (B11248).
Unknown infectivity, severity
The researchers randomly evaluated and evaluated 185 SARS-CoV-2 samples from the CSMC COVID-19 hospital and clinic patients from November 22 to December 28, 2020. Using Nextstrain, a group of open-source tools to visualize the genetics behind . the transmission of viral outbreaks, they also evaluate the evolutionary development and diversification of the samples and those of 1,480 worldwide representative genomes.
They identified two strains behind two major COVID-19 clusters, the smallest of which was from the 20G lineage (currently the largest group in North America), making up 22% of the samples. The larger group, found in 36% of the samples, consists of the new CAL.20C variant, which is derived from the 20C clay and contains five mutations: ORF1a: I4205V, ORF1b: D1183Y, S: S13I; W152C; and L452R. The latter three mutations affect the COVID-19 peak protein and may facilitate binding to cells.
The authors noted that the bias of the collection and a relatively small set of local samples could have skewed their results, adding that the behavior of CAL.20C is still unknown. “In addition, as clinical outcomes have not yet been determined, the functional effect of this strain with respect to infectivity and severity of the disease remains uncertain,” they wrote. “Nevertheless, the identification of this new strain is important for the frontline and global surveillance of this developing virus.”
Co-author Jasmine Plummer, PhD, said in an email that the medical center has begun testing the new variant. “At Cedars-Sinai, we began functional studies to evaluate each mutation in the vein protein, test for antibodies, and neutralize cell proliferation by using the CAL.20C strain to verify that it is no longer contagious or faster than others. tribes, “she said.
“We are also increasing our clinical sample population to look at the outcome, e.g., severity.”
Global virus monitoring required
In an editorial in the same journal, John Mascola, MD; Barney Graham, MD, PhD; and Anthony Fauci, MD, all of the National Institute of Allergy and Infectious Diseases, noted that the B117 variant, which has eight mutations in the coronavirus ear protein, is estimated to be 30% to 80% more transmissible and 30% more potent. be lethal than other strains. Although the B1351 variant is also transmissible than other strains, there is no evidence that it is more lethal.
However, Mascola and colleagues said emerging variants could become resistant to COVID-19 treatments such as monoclonal antibodies. “The common strains in the US appear to be sensitive to therapeutic monoclonal antibodies; however, recent evolutionary history raises concerns that the virus may be only a few mutations of more substantive resistance,” they write.
Although mutations may also decrease the efficacy of the vaccine, data to date indicate that currently authorized coronavirus vaccines would still be able to prevent infections with these variants, but according to the authors will need updates over time as variants develop.
“It is unclear whether changes in the vaccine composition will be necessary to effectively control the COVID-19 pandemic. However, it is prudent to be prepared,” they wrote. “Some companies have indicated plans to manufacture and test vaccines based on emerging variants, and such studies will provide important information about the possibility of broadening the immune response.”
Mascola and colleagues called for a systematic global approach to COVID-19 monitoring, detection and distribution of vaccines, including in vitro evaluation of sensitivity to monoclonal antibodies and vaccines, protection of vaccines against new strains in animals, and field data containing viral identify sequence of breakthrough infections. in vaccinated.
“SARS-CoV-2 will be with the world population for some time and has clearly shown that it is prone to rapid antigen variation, providing a ‘wake-up call’ that is a sustained effort to pan-SARS-CoV-2 vaccine is justified, ”the authors said.