A new coronavirus strain discovered in Los Angeles may be behind the surge in cases there

The homegrown variant could have a similar structural change to one that emerged in South Africa

By Nicole Karlis

Senior Writer

Published January 25, 2021 6:13PM (EST)

Distressed doctor wearing protective suit to fight coronavirus pandemic (Getty Images)
Distressed doctor wearing protective suit to fight coronavirus pandemic (Getty Images)

Newly mutated strains of the novel coronavirus spotted around the world — such as the ones ravaging the United Kingdom and South Africa — are spurring fear they could become dominant here in the U.S., too. Now, Americans have a newly homegrown strain to worry about — and public health experts suspect that it could have been the cause of southern California's most recent surge.

Recently, U.S. scientists were searching for signs of the UK coronavirus variant, known as B 1.1.7, in California when they stumbled upon something different. Coronavirus strain B 1.1.7 has a transmission rate that is 50 to 70 percent greater and may be more deadly, which has prompted studies to see how much it has infected the US population. Yet while looking for B 1.1.7, scientists stumbled upon a novel strain that has peculiar mutations, which is now being dubbed CAL.20C. According to a paper published by researchers at Cedars-Sinai, that has yet to be peer-reviewed, the new SARS-CoV-2 strain appeared to account for at least 36 percent of COVID-19 cases in the Los Angeles area and 24 percent in southern California in December 2020. That correlates with a huge surge in coronavirus infections in southern California at the time. 

"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 researchers wrote in the paper. "The predominance of this strain coincides with the increased positivity rate seen in this region."

In mid-January, scientific modeling estimated that one in three L.A. County residents had been infected with the coronavirus. While the southern California surge seems to be dying down, scientists are concerned that a further mutation of the CAL.20C strain, called L452R, has a structural change similar to the variant found in South Africa.

As Salon previously reported, variant 20C/501Y.V2, also known as the B.1.351 lineage — which emerged in Durban, South Africa — is alarming because the mutation occurs on the virus' so-called outer "Spike," or the proteins on the outer layer of the virus that resemble spikes like those on a sea urchin. Mutations to Spike have a chance at disguising the virus's appearance to the immune system of someone who already has coronavirus antibodies, which can make it easier to bypass immune protection. L452R's could be similar to the South African strain in that regard.

"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," the Cedars-Sinai researchers wrote in the paper. They note that mutations to the spike protein could be "resistant" to antibodies from previous coronavirus infections with other strains.

But scientists say it's not time to panic yet, as we do not know for certain if this variant of the new strain is resistant to vaccination or not. Identifying the variant is the first step of many to understanding how and if this variant is more transmissible — or, worse, if it could change how one's immune system responds to a vaccine.

Dean Blumberg, chief of pediatric infectious diseases and associate professor in the Department of Pediatrics at the University of California, Davis, told Salon he would characterize this paper as a "preliminary report." The coronavirus, he said, naturally mutates every two weeks or so.

"So you're always going to get various mutations and different strains," Blumberg said. "Some of these strains make mutations that will be minor and will make very little difference in terms of how they infect people in terms of the rate, or severity of infection, and then others are more significant."

Blumberg echoed concerns about several of the mutations for the CAL.20C strain occuring primarily on the Spike protein.

"This could make them more efficient at binding and being transmitted and infecting cells," Blumberg said. "But that's not clear to me from reading this paper whether the mutations make this a more fit virus or not, and so that's why I'm not sure of the significance yet."

Blumberg added that it's "good news" that we are finding these variants. Before, the U.S. was behind in sequencing the coronavirus— hence, the discovery of the variant B 1.1.7 in the U.K., which was preceded by its discovery in the United States. Moreover, it is unclear whether this new variant is behind Southern California's surge.

"We don't know if this is just coincidental that this is just the current variant that is being transmitted or we don't know if it could be because of this variant being more efficiently transmitted, that that's why there is a surge in cases," Blumberg said. "We need to look into that."

Other scientists agree.

"It may have contributed to this surge, or simply gone along for the ride,"  Dr. Charles Chiu, a laboratory medicine specialist at University of California-San Francisco told the Los Angeles Times.

When it comes to prioritizing variants and which ones are the most concerning, Blumberg said "there are a lot of things to be concerned about," but like the variants found in the U.K. and South Africa, which we have more information on at this moment. Blumberg said more information is needed before the California variant reaches the same level of concern. 

"This variant, they don't know that much about yet, so it's not rising to that level of concern," he said. "Just because we don't have that information."

By Nicole Karlis

Nicole Karlis is a senior writer at Salon, specializing in health and science. Tweet her @nicolekarlis.

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