In late December, California scientists began to search for coronavirus samples for a new, fast-spreading variant that had just been identified in Britain.
They found it, although in relatively few samples. But in the process, scientists made another undesirable discovery: California had produced its own variant.
This mutant, which belongs to a strain known as CAL.20C, appeared to have appeared in July, but remained hidden until November. Then it started to spread quickly.
CAL.20C was responsible for more than half of the virus genome samples collected in Los Angeles laboratories on January 13, according to a new study that has not yet been published.
“We had our own problem that didn’t come from Europe,” said Jasmine Plummer, a research scientist at Cedars-Sinai Medical Center in Los Angeles, who worked on the new study. “It really originated here and had a chance to start to emerge and increase during the holiday.”
There is no evidence that CAL.20C is more lethal than other variants. And scientists need to conduct more research to determine whether CAL.20C is indeed more contagious than other forms of the virus.
But Eric Vail, director of molecular pathology at Cedars-Sinai, said it is possible that CAL.20C is playing an important role in the increase in cases that has affected hospitals in Southern California. “I am quite confident that this is a more infectious strain of the virus,” said Dr. Vail.
Dr. Charles Chiu, a virologist at the University of California, San Francisco, said that across the state, he and his colleagues are finding the variant in about 20% to 30% of the samples being sequenced. “It just appeared under our noses and is now increasing in several counties,” he said. “Overall, it is safe to say that it will spread outside California.”
Researchers are also looking for CAL.20C in other states, Plummer said, 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 Colombia. It is not yet clear how common it is outside California.
Last week, the Centers for Disease Control and Prevention issued a formal warning about the variant that is flooding Britain. Although this mutant, called B.1.1.7, is still relatively rare in the United States, accounting for less than half a percent of infections, the agency said it could be responsible for most cases in the country by March.
An agency spokesman 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 these differences may have contributed to its appearance or whether this appearance was merely a random event,” he said.
“I will say that this particular variant should be observed,” said 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 not yet clear whether CAL.C20 is becoming more common because it has some biological advantage or just by chance.
If both B.1.1.7 and CAL.C20 are more contagious than other variants, it is not clear how a competition between the two will resolve. “CAL.C20 has a great advantage,” said Dr. Vail. “Even though B.1.1.7 is more infectious in general, we can never see a big increase here in LA”
Since scientists identified the new coronavirus a year ago in China, they have monitored the appearance of new mutations, which appear randomly and are transmitted to new generations of viruses as they replicate in our bodies.
Many mutations are harmful to the virus and worsen its replication. Many others are neutral. But researchers have now discovered several that are of concern because they appear to help the virus infect people more efficiently.
In the early months of the pandemic, a mutation emerged in a strain that then became dominant in much of the world. Known as D614G, it is believed that the mutation makes the virus more easily transmitted from person to person, compared to variants without it.
In December, researchers in Britain discovered B.1.1.7, which is about 50% more transmissible than previous versions of the virus. The variant is a determining factor in the increase in cases and hospitalizations there now.
B.1.1.7 was in the United States in early November, according to a study published online Tuesday by University of Arizona biologists Brendan Larsen and Michael Worobey. This would mean that the variant had been circulating 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 an ear, that decorates the surface of the coronavirus.
“We stumbled upon this really unexpected discovery and continued on from there,” said Vail.
The mutation appeared in different viral strains last year. Scientists have studied L452R because it can help coronaviruses to attach to our cells and infect them.
In California, Dr. Vail, Dr. Plummer and their colleagues found that whenever they encountered a variant with the L452 mutation, it also carried four other distinct mutations. This combination, they said, indicated that they were dealing with a single strain that had emerged somewhere in California. The researchers named any virus carrying all five CAL.C20 mutations.
The California Department of Health gave a news conference on Sunday night to announce that the L452 mutation was becoming more common in California. On Monday night, Cedars-Sinai released a press release about its study, which will soon be published on the pre-press website MedRxiv.
The Cedars-Sinai team is part of a statewide network of researchers who track mutations in the coronavirus. They randomly selected nasal swabs from patients positive for Covid-19 and then collected genetic material from the swabs.
The researchers assembled the fragments to reconstruct the entire virus genome and then looked for distinct mutations. They then compared their own findings with other viral genomes sequenced across the state and country.
The researchers found the first sample of CAL.C20 in July in Los Angeles. They were unable to find another sample until October. The variant became more common in November, reaching 36% of Cedars-Sinai samples in December and 50% last week.
Outside scientists are concerned about the new findings, but say it remains unclear whether mutations in the California variant are giving them an advantage – or whether they are showing up so much by chance.
There may be a bias in the samples that scientists are analyzing, for example. It is also possible that CAL.C20 has become more common thanks to some major over-propagation events.
“I think we need to be careful before concluding that any particular strain is spreading because of a transmission advantage, not because it happened to catch a wave caused by human behavior,” said Dr. Worobey.
If it is more contagious, Plummer said, then CAL.C20 may end up being partly responsible for the recent increase in cases in Southern California hospitals.
As the total number of cases increased, Dr. Plummer and her colleague found out, the percentage of CAL.C20 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 was involved in several outbreaks in which a large number of people were infected. “There are worrying signs that this variant can be highly transmissible,” he said.
Dr. Chiu and his colleagues are now cultivating the variant in the cells to see how quickly they multiply in comparison to other variants. Researchers will also look at how antibodies produced by vaccines work against CAL.C20.
Other scientists are also taking a closer look at the increased frequency of the variant in California. They are looking for evidence that can determine whether biology or chance is to blame for their rise.
“This is the job that needs to be done,” said Dr. Vail. “We just don’t have that information.”