In late December, scientists in California began screening coronavirus samples for a rapidly spreading new variant that had just been identified in the UK.
They found it, albeit in relatively few samples. The scientists made another undesirable discovery: California had produced its own variant.
This mutant, which belongs to a line called CAL.20C, appeared to have appeared in July but was low by November. Then it began to spread quickly.
According to a new study that has not yet been published, CAL.20C accounted for more than half of the virus genome samples collected in Los Angeles laboratories on Jan. 13.
“We had our own problem that didn’t come from Europe,” said Jasmine Plummer, a scientist at Cedars-Sinai Medical Center in Los Angeles who worked on the new study. “It really originated here and it has had a chance to show up and waver on vacation.”
There is no evidence that CAL.20C is more lethal than other variants. And scientists need to do more research to determine if CAL.20C is actually more contagious than other forms of the virus.
However, Eric Vail, director of molecular pathology at Cedars-Sinai, said it is possible that CAL.20C is playing a big role in the increase in cases that have overwhelmed hospitals in southern California. “I am confident this is a contagious strain of the virus,” said Dr. Vail.
Dr. Charles Chiu, a virologist at the University of California at San Francisco, said he and his colleagues found the variant in about 20 to 30 percent of the samples sequenced across the state. “It just popped up under our noses and now it’s rising in several counties,” he said. “By and large, it’s safe to say that it will spread outside of California.”
Researchers are also looking for CAL.20C in other states, said Dr. Plummer, and have so far found it in Arizona, Connecticut, Maryland, New Mexico, Nevada, New York, Texas, Utah, Washington, and Wyoming, as well as the District of Columbia. It’s not yet clear how common it is outside of California.
Last week the Centers for Disease Control and Prevention issued a formal warning of the variant that is flooding the UK. Although this mutant, named B.1.1.7, is still relatively rare in the US, accounting for less than half a percent of infections, the agency said it could be responsible for the majority of the country’s cases by March.
A spokesman for the agency said the CDC is working with California to learn more about the new variant. “It is currently not known whether this variant differs from other SARS-CoV-2 viruses, whether these differences may have contributed to its development or whether this development was just a coincidental event,” he said.
“I’ll say this particular variant is one to look at,” said Kristian Andersen, a virologist at the Scripps Research Institute who discovered one of the first samples of B.1.1.7 in the US. However, he cautioned that it is still unclear whether CAL.20C is becoming more common because it has a biological benefit or just by accident.
If both B.1.1.7 and CAL.20C are more contagious than other variants, it is not clear how competition between the two will develop. “CAL.20C has a big head start,” said Dr. Vail. “Even if B.1.1.7 is more infectious overall, we may never see a big increase in it here in LA.”
Since scientists first identified the new coronavirus in China a year ago, they have been tracking the creation of new mutations that occur randomly and are passed on to new generations of viruses as they replicate in our bodies.
Jan. 19, 2021, 6:10 p.m. ET
Many mutations are harmful to the virus and make replication worse. Many others are neutral. But researchers have now discovered some that are worrying because they appear to help the virus infect people more efficiently.
In the first few months of the pandemic, a mutation occurred in a line that then dominated much of the world. The mutation known as D614G is believed to make the virus more easily transmitted from person to person compared to variants without D614G.
In December, researchers in the UK found B.1.1.7, which is about 50 percent more transmissible than previous versions of the virus. Variation is a driving factor behind the increase in cases and hospital stays.
B.1.1.7 was in the USA in early November. This is according to a study published online Tuesday by biologists Brendan Larsen and Michael Worobey of the University of Arizona. That would mean the variant was in circulation for two months before it was discovered.
In California, researchers looking for B.1.1.7 found an unusual mutation in their samples. The mutation called L452R changes the shape of a protein called Spike that adorns the surface of the coronavirus.
“We came across this really unexpected finding and followed it up from there,” said Dr. Vail.
The mutation has appeared in various virus lines over the past year. Scientists studied L452R because it could help coronaviruses attach to our cells and infect them.
In California, Dr. Vail, Dr. Plummer and her colleagues found that whenever they came across a variant with the L452 mutation, they had four other characteristic mutations. That combination, they said, suggested that it was a single line that had emerged at some point in California. The researchers named each virus that carries all five mutations CAL.20C.
The California Department of Health held a press conference Sunday evening to announce that the L452 mutation is becoming increasingly common in California. On Monday evening, Cedars-Sinai published a press release on its study, which will be published shortly on the preprint website MedRxiv.
The Cedars-Sinai team is part of a nationwide network of researchers who have tracked mutations in the coronavirus. They randomly selected nasal swabs from patients who tested positive for Covid-19 and then collected genetic material from the swabs.
The researchers pieced the fragments together to reconstruct the virus’s entire genome and then looked for characteristic mutations. They then compared their own results with other viral genomes that were sequenced in the state and country.
The researchers found the earliest sample of CAL.20C in July in Los Angeles. They couldn’t find another sample until October. The variant became more common in November, reaching 36 percent of the Cedars-Sinai samples in December and 50 percent last week.
Outside scientists are concerned about the new findings, but say it’s still unclear whether the mutations in the California variant give it an advantage – or whether they just happen to show up so frequently.
For example, the samples that scientists are examining may be biased. It’s also possible that CAL.20C got more common thanks to some big super-spreader events.
“I think we need to be careful before we conclude that a particular line is spreading due to a transference advantage, rather than randomly riding a wave caused by human behavior,” said Dr. Worobey.
If it turns out to be more contagious, Dr. Plummer, CAL.20C could be partially responsible for the recent debilitating surge in cases in Southern California’s hospitals.
As the total number of cases increased, Dr. Plummer and her colleague found that the percentage of CAL.20C had also increased. This would be consistent with the idea that this is a more contagious variant. “I mean, the numbers speak for themselves,” she said.
Dr. Chiu also noted that the variant has been implicated in a number of outbreaks that have infected large numbers of people. “There is worrying evidence that this variant could be highly transmissible,” he said.
Dr. Chiu and his colleagues are now expanding the variant into cells to see how quickly they multiply compared to other variants. The researchers will also observe how well antibodies against CAL.20C produced by vaccines work.
Other scientists are also investigating the frequency increase of the variant in California more closely. They are looking for evidence that could determine whether biology or chance is responsible for their rise.
“That’s the job that needs to be done,” said Dr. Vail. “We just don’t have that information.”