A new variant of SARS-CoV-2, CAL.20C, has been detected in southern California amid an increase in local infections and is spreading across the United States and beyond, according to a research letter published yesterday in JAMA.
Researchers at Cedars-Sinai Medical Center (CSMC) in Los Angeles analyzed strains of COVID-19 before and after the increase in cases in Southern California in October 2020. Before October, most coronavirus strains originated from the clade 20C (group of viruses evolved from the same ancestor), which emerged in New York via Europe in the early stages of the pandemic.
CAL.20C, or 20C / S: 452R; / B1429, was first seen in 1 of the 1,247 COVID-19 samples in Los Angeles County in July, but was not seen again in the region until October, when four cases were detected. Although CAL.20C was found only in southern California in October, in November, 30 cases were identified in the northern part of the state, and five other states reported the variant.
On January 22, the variant grew to represent 35% of all strains of coronavirus in California and 44% of all samples in the southern part of the state and was detected in 26 states, as well as in other countries. CAL.20C is one of several other widely circulating variants, such as those first identified in the United Kingdom (B117), South Africa (B1351) and Brazil (B11248).
Unknown infectivity, severity
The researchers sequenced and randomly analyzed 185 SARS-CoV-2 samples from those collected from all patients at the CSMC COVID-19 hospital and clinic from November 22 to December 28, 2020. Using Nextstrain, a group of open source tools for visualizing the genetics behind the transmission of viral outbreaks, they also assessed the evolutionary development and diversification of the samples and 1,480 globally representative genomes.
They identified two strains behind two main COVID-19 clusters, the smallest of which was of the 20G strain (currently the largest clade in North America), making up 22% of the samples. The largest cluster, found in 36% of the samples, was composed of the new variant CAL.20C, which descended from clade 20C and has five mutations: ORF1a: I4205V, ORF1b: D1183Y, S: S13I; W152C; and L452R. The last three mutations affect the spike protein COVID-19 and may allow easier binding to cells.
The authors noted that the collection bias and a relatively small set of local samples may have distorted their results, adding that the behavior of CAL.20C is still unknown. “Furthermore, as the clinical results have not yet been established, the functional effect of this strain in relation to infectivity and disease severity remains uncertain,” they wrote. “However, the identification of this new strain is important for global and frontline surveillance of this evolving virus.”
Co-author Jasmine Plummer, PhD, said by email that the medical center has started testing the new variant. “At Cedars-Sinai, we have started functional studies to evaluate each mutation in the spike protein, neutralizing antibody assays and cell proliferation using the CAL.20C strain to verify that it is no longer infectious or growing faster than other strains,” he said. Is it over there.
“We are also increasing our population of clinical samples to observe the result, for example, the severity.”
Global virus surveillance required
In an editorial in the same magazine, John Mascola, MD; Barney Graham, MD, PhD; and Anthony Fauci, MD, all from the National Institute of Allergy and Infectious Diseases, noted that variant B117, which has eight mutations in the coronavirus peak protein, is estimated to be 30% to 80% more transmissible and may be 30% more deadly than other strains. Although the B1351 variant is also considered to be more transmissible than other strains, there is no evidence that it is more deadly.
However, Mascola and colleagues said that the emerging variants may become resistant to COVID-19 treatments, such as monoclonal antibodies. “Strains prevalent in the United States appear to remain sensitive to therapeutic monoclonal antibodies; however, recent evolutionary history raises concerns that the virus could be just a few mutations away from more substantive resistance,” they wrote.
While the mutations may also decrease the vaccine’s effectiveness, the data so far suggest that currently authorized coronavirus vaccines may still be able to prevent infection with these variants, but will require updates over time as the variants evolve, according to with the authors.
“It is not clear whether changes in vaccine composition will be needed 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 these studies will provide important information about the potential for enhancing the immune response.”
Mascola and colleagues called for a systematic global approach to the surveillance, tracking and distribution of COVID-19 vaccines, including in vitro assessment of monoclonal antibody and vaccine sensitivity, protection of the vaccine against new strains in animals and field data identifying viral sequences invasive infections in vaccinated people.
“SARS-CoV-2 will be with the global population for some time and has clearly shown its trend towards rapid antigenic variation, providing a ‘warning’ that a sustained effort to develop a pan-SARS-CoV-2 vaccine is warranted,” said the authors.