A coronavirus variant first identified in Denmark has ripped through Northern California – including outbreaks at nursing homes, jails and a hospital in the San Jose area – prompting state and local officials to investigate whether it may be more transmissible.
California officials disclosed the rise of the variant Sunday night after genetic monitoring linked it to a fast-growing share of new cases, as well as to the outbreaks in Santa Clara County, which includes San Jose.
This rising variant is distinct from the highly contagious mutation discovered by Britain, which has also been found in California, and which federal health officials say could become the dominant strain in the United States by March based on its higher transmissibility.
Experts stress that they need to look more closely at the circumstances of the Northern California outbreaks, as well as at the latest variant – this one, known as L452R – before declaring it more contagious or more dangerous than the virus already broadly circulating.
The L452R variant was first detected in northern Europe in March and has since been confirmed in more than a dozen states, including California in May. The discovery did not garner much attention at the time because all viruses change constantly as they replicate. But public health authorities deem some variants to be “of concern” if evidence suggests that they might be more contagious, potentially deadlier or resistant to vaccines.
California publicized the latest variant at a late Sunday news conference after researchers identified it in about 25% of samples collected between Dec. 14 and Jan. 3, a surge from 3.8% of samples collected in the preceding three-week period.
“That is suggestive, and it’s a little worrisome,” Charles Chiu, a virologist at the University of California at San Francisco said at the briefing. But Chiu said it was too early to conclude that the variant is more infectious; scientists do not know whether their sampling was representative or whether the variant’s increase might be due to random chance or superspreader events.
Officials urged people to follow public health guidelines to minimize the risk of contracting the variant as new daily cases in the hard-hit state plateau at more than 38,000, while deaths average more than 515 daily.
“It’s too soon to know if this variant will spread more rapidly than others,” said Erica Pan, the state epidemiologist, “but it certainly reinforces the need for all Californians to wear masks and reduce mixing with people outside their immediate households to help slow the spread of the virus.”
Genetic sequencing of viruses is still limited in the United States, preventing health officials from having a real-time picture of all the strains of coronavirus spreading across the country and their prevalence.
California’s preliminary data is based on fewer than 400 samples that overwhelmingly came from the state’s north. Southern California is the heaviest-hit part of the state, with deaths in Los Angeles County reaching one every seven minutes and ICU beds and supplemental oxygen running out, though hospitalizations may have begun to plateau. Environmental regulators on Sunday temporarily lifted limits on cremations because of a backlog in Los Angeles County.
The L452R strain in California raised alarms because it is associated with several large outbreaks in Santa Clara County, including one at a hospital that infected at least 90 people and killed one staff member. Officials at Kaiser Permanente San Jose Medical Center said a staff member wearing an inflatable Christmas tree costume to spread holiday cheer probably spread coronavirus-laden droplets.
Sara Cody, Santa Clara County’s top public health official, described that episode as a “very unusual outbreak with a lot of illnesses, and it seemed to spread quite fast.” The county is working with state health officials and the CDC to investigate what happened, she said.
Cody said the outbreak could have been driven by factors unrelated to the variant, such as changes in ventilation or personal protective equipment practices at the hospital.
“The takeaway is not that we need to start worrying about this,” Cody said Sunday. “The takeaway is, this is a variant that’s becoming more prevalent, and we need to lean in and understand more about it.”
County officials on Monday disclosed other places where the variant had been found as a result of aggressive genetic sequencing, “including cases associated with the Kaiser outbreak, skilled nursing facility outbreaks, cases in jails and shelters, and specimens from testing sites in the community,” according to a statement. “This suggests that the variant is now relatively common in our community.”
Chiu, the virologist who conducted the genetic sequencing, said a deeper investigation must be done to determine if the strain is more transmissible like the one found in the United Kingdom.
He also raised concerns that a mutation associated with the variant might make it more resistant to vaccines because it occurs in a critical part of the spike protein that is targeted by the vaccines, but he added that the virus must be grown in a lab and tested more fully before any conclusions can be drawn.
“Mutations happen all the time,” said William Hanage, an epidemiologist at the Harvard university T.H. Chan School of Public Health. “Some of them take off and the great majority of them don’t. The main reason why we are paying attention to this is because this mutation has previously been noted as being of particular concern in terms of diminishing the efficacy of the immune response.”
Carlos del Rio, a professor of medicine and global health at Emory University, said the rising prevalence of the variant shows the urgent need for more genetic sequencing in the United States and for greater compliance with public health measures such as wearing masks and avoiding crowds.
“We really need to hunker down because if you are really concerned about mutations, stop transmission,” del Rio said. “The more mutations you see, the more uncontrolled transmission you will see.”
After starting the new year with record-high case numbers, deaths and hospitalizations, the United States is starting to see signs of slowing spread despite fears of a post-holiday surge that would continue through January. The seven-day average of new infections has slowed since Tuesday, and hospitalizations have started to plateau, according to Washington Post tracking.
Still, Scott Gottlieb, a former Food and Drug Administration commissioner, warned that the advent of more transmissible variants could reverse that progress.
“As current epidemic surge peaks, we may see 3-4 weeks of declines in new cases but then new variant will take over,” Gottlieb tweeted Sunday, referring to the variant discovered in Britain. “It’ll double in prevalence about every week. It’ll change the game and could mean we have persistent high infection through spring until we vaccinate enough people.”