New California variant could lead to increase in virus there, study finds



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At the end of December, scientists in California began to search for coronavirus samples for a new, rapidly spreading variant that had just been identified in Britain.

They found it, but in relatively few samples. But in the process, scientists made another unwelcome discovery: California had produced its own variant.

This mutant, which belongs to a line known as CAL.20C, appears to have arisen in July but remained low until November. Then it started to spread rapidly.

CAL.20C made up more than half of viral genome samples collected from Los Angeles labs on January 13, according to a new study that has yet to be released.

“We had our own problem that didn’t cross Europe,” said Jasmine Plummer, a researcher at Cedars-Sinai Medical Center in Los Angeles, who worked on the new study. “He was really born here, and he was lucky enough to start emerging and soaring during the holidays.”

There is no evidence that CAL.20C is more lethal than the other variants. And scientists need to do more research to determine if CAL.20C is in fact more contagious than other forms of the virus.

But Eric Vail, director of molecular pathology at Cedars-Sinai, said it was possible that CAL.20C could play a significant role in the outbreak of cases that overwhelmed hospitals in Southern California. “I have no doubts that this is a more contagious strain of the virus,” said Dr Vail.

Dr. Charles Chiu, a virologist at the University of California, San Francisco, said that statewide, he and his colleagues found the variant in about 20-30% of the samples sequenced. “It just appeared under our noses, and now it’s increasing in several counties,” he said. “Overall, it’s safe to say it’s going to spread outside of California.”

Researchers are also looking for CAL.20C in other states, Dr Plummer said, and so far have 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 this is outside of California.

Last week, the Centers for Disease Control and Prevention issued a formal warning about the variant overwhelming 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 the majority of cases in the countries by March.

A spokesperson for the agency said the CDC is working with California to learn more about the new variant. “Currently, it is not known if this variant is different from other SARS-CoV-2 viruses, if these differences may have contributed to its emergence, or if this emergence was simply a random event,” he said.

“I will say this particular variant is one to watch out for,” 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’s still unclear whether CAL.20C is becoming more common because it has a biological benefit, or just by chance.

While both B.1.1.7 and CAL.20C are both more contagious than the other variants, it is not known how a competition between the two will work out. “CAL.20C is way ahead,” said Dr. Vail. “Even though B.1.1.7 is more infectious overall, we may never see a big increase here in LA”

Since scientists first identified the novel coronavirus a year ago in China, they have been tracking the emergence of new mutations, which occur at random and are transmitted to new generations of viruses as they replicate. in our body.

Many mutations are harmful to the virus and worsen its replication. Many others are neutral. But researchers have now found several that are worrying because they seem to help the virus infect people more effectively.

In the first few months of the pandemic, a mutation appeared in a lineage which then became dominant in much of the world. Known as D614G, the mutation is now believed to make the virus easier to pass from person to person, compared to variants without it.

In December, British researchers discovered B.1.1.7, which is around 50% more transmissible than previous versions of the virus. The variant is a major 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 uploaded Tuesday by University of Arizona biologists Brendan Larsen and Michael Worobey. This would mean that the variant had circulated for two months before being 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 a peak, which decorates the surface of the coronavirus.

“We stumbled upon this truly unexpected discovery and took it from there,” Dr. Vail said.

The mutation has appeared in different viral lineages over the past year. Scientists have studied L452R because it could help coronaviruses stick 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 distinctive mutations. This combination, they said, indicated that this was a single lineage that had emerged at some point in California. The researchers named any virus that carried the five CAL.20C mutations.

The California Department of Health held a press conference on Sunday night to announce that the L452 mutation is becoming more common in California. On Monday evening, Cedars-Sinai released a press release on their study, which will soon be posted on the MedRxiv pre-print website.

The Cedars-Sinai team is part of a statewide network of researchers who have been tracking 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 together the fragments to reconstruct the virus’s entire genome, then looked for distinctive mutations. They then compared their own findings to other viral genomes sequenced across the state and country.

Researchers found the first CAL.20C sample in July in Los Angeles. They couldn’t find another sample until October. The variant became more common in November, reaching 36% of Cedars-Sinai’s samples in December and 50% last week.

Outside scientists are concerned about the new findings, but say it’s still not clear whether the California variant’s mutations give it an advantage – or if it just happens so by chance.

There may be a bias in the samples that scientists examine, for example. It’s also possible that CAL.20C has become more mainstream thanks to large super-spreader events.

“I think we need to be careful before concluding that a particular lineage is spreading because of a transmission benefit rather than because it has been riding a wave caused by human behaviors,” said Dr Worobey.

If it turns out to be more contagious, Dr Plummer said, then CAL.20C could be partially responsible for the recent crippling outbreak of cases in Southern California hospitals.

As the total number of cases increased, Dr Plummer and his colleague found that the percentage of CAL.20C 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 a number of outbreaks where large numbers of people were infected. “There are worrying signs that this variant may be highly transmissible,” he said.

Dr. Chiu and his colleagues are now growing the variant in cells to see how quickly they multiply compared to other variants. The researchers will also observe how well the antibodies produced by the vaccines work against CAL.20C.

Other scientists are also studying more closely the increase in the frequency of the variant in California. They are looking for evidence that could determine whether biology or chance is behind its rise.

“This is the job that needs to be done,” Dr. Vail said. “We just don’t have that information.”

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