In late December, scientists in California began searching for coronavirus samples for a rapidly spreading new variant that had just been identified in Britain.
They found it, though in relatively few samples. But in the process, the scientists once again made an unwelcome discovery: California had produced its own variant.
The mutant, which is part of a genus known as CAL.20C, appears to have emerged in July but was low until November. Then it started spreading fast.
According to CAL.20C, more than half of the virus genome samples collected on January 13 were in Los Angeles laboratories, according to a new study that has not yet been published.
“We had our own problem that did not come from Europe,” said Jasmine Plummer, a researcher at Cedars-Sinai Medical Center in Los Angeles who was working on the new study. “It really originated here, and it had the chance to come forward and come forward.”
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.
But Eric Vail, the director of molecular pathology at Cedars-Sinai, said it is possible that CAL.20C is playing a major role in the rise of cases that have overwhelmed hospitals in Southern California. “I’m pretty confident that it’s a more contagious strain of the virus,” said Dr. Vail said.
Dr. Charles Chiu, a virologist at the University of California, San Francisco, said he and his colleagues across the state find the variant in about 20 to 30 percent of the samples followed. “It just popped up under our noses, and now it’s rising in several provinces,” he said. “In general, it is safe to say that it will spread outside of California.”
Researchers are also looking for CAL.20C in other states, said dr. Plummer said and has 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 is not yet clear how common it is outside of California.
Last week, the Centers for Disease Control and Prevention issued a formal warning about the variety of Britain. Although the mutant, named B.1.1.7, is still relatively rare in the United States, which accounts for less than half of the infections, the agency said it would be responsible for the majority of the country’s affairs by March .
A spokesman for the agency said the CDC is working with California to learn more about the new variant. “Currently, it is not known whether this variant is different from other SARS-CoV-2 viruses, whether the differences may have contributed to its emergence, and whether this emergence was merely a random event,” he said.
“I would say that this particular variant is one to look at,” says Kristian Andersen, a virologist at the Scripps Research Institute, who discovered one of the first samples of B.1.1.7 in the United States. But he warned that it is still unclear whether CAL.20C is becoming more common because it has a biological benefit, or just coincidence.
If both B.1.1.7 and CAL.20C are both more contagious than other variants, it is not clear how a competition between them will sort out. “CAL.20C has a big lead,” said dr. Vail said. “Even though B.1.1.7 is generally more infected, we can never see a big boom here in LA”
Since scientists first identified the new coronavirus in China a year ago, they have been following the emergence of new mutations, which are randomly generated and transmitted to new generations of viruses as they recur in our bodies.
Many mutations are harmful to the virus and aggravate it when repeated. Many others are neutral. But researchers have already discovered what is worrying because it appears to help the virus infect humans more effectively.
In the early months of the pandemic, a mutation arose in a generation that then ruled over the entire world. The mutation, also known as D614G, now makes it easier for the virus to be transmitted from person to person, compared to variants without it.
In December, researchers in Britain found B.1.1.7, which is about 50 percent more transmissible than previous versions of the virus. The variant is an important factor in the increase in cases and hospitalizations there.
B.1.1.7 was in the United States in early November, according to a study published Tuesday by biologists Brendan Larsen and Michael Worobey of the University of Arizona. This would mean that the variant was in circulation for two months before it was detected.
In California, researchers looking for B.1.1.7 began to notice an unusual mutation in their samples. The mutation, called L452R, changes the shape of a protein called spike, which adorns the surface of the coronavirus.
“We came across this really unexpected finding and went from there,” said dr. Vail said.
The mutation has surfaced in various virus lines over the past year. Scientists have studied L452R because it can help coronaviruses attach to and infect our cells.
In California, dr. Vail, dr. Plummer and their colleagues found that when they encountered a variant with the L452 mutation, it also had four other characteristic mutations. The combination, according to them, indicated that they were dealing with a single generation that originated in California at some point. The researchers named each virus with all five mutations CAL.20C.
The California Department of Health held a news conference Sunday night to announce that the L452 mutation is becoming more prevalent in California. On Monday night, Cedars-Sinai released a news release about its study, which will soon be posted on the preprint website MedRxiv.
The Cedars-Sinai team is part of a network of researchers across the country that have been monitoring mutations in the coronavirus. They selected random nasal swabs from patients who tested positive for Covid-19, and then collected genetic material from the swabs.
The researchers pooled the fragments to reconstruct the entire genome of the virus and then looked for characteristic mutations. They then compare their own findings with other viral genomes that are consecutive in the state and country.
The researchers found the earliest sample of CAL.20C in July in Los Angeles. They could only get another sample in October. The variant was more prevalent in November, with 36 percent of the samples from Cedars-Sinai in December and 50 percent last week.
External scientists are concerned about the new findings, but say it is still unclear whether the California variant’s mutations give it an advantage – or whether it just happens to show so much.
There may be a bias in the samples that scientists look at, for example. It is also possible that CAL.20C became more common due to some major super-distributor events.
“I think we need to be careful before we conclude that a particular gender is spreading as a result of a transmission advantage rather than because it happened to be a wave caused by human behavior,” said Dr. Worobey said.
If it does turn out to be more contagious, dr. Plummer said, CAL.20C could possibly be partly responsible for the recent crippling increase in cases in Southern California hospitals.
As the total number of cases increased, dr. Plummer and her colleague found, the CAL.20C percentage also rose. This would be consistent with the idea that it is a more contagious variant. “I mean, the numbers speak for themselves,” she said.
Dr. Chiu also noted that the variant was involved in a number of outbreaks where large numbers of people became infected. “There are worrying signs that this variant could be very transmissible,” he said.
Dr. Chiu and his colleagues are now growing the variant in cells to see how fast they multiply with other variants. The researchers will also look at how well antibodies produced by vaccines work against CAL.20C.
Other scientists are also taking a closer look at the increase in frequency of the variant in California. They are looking for evidence that can determine whether biology or chance is to blame for its emergence.
“This is the work that needs to be done,” said Dr. Vail said. “We just do not have the information.”