California’s strain of coronavirus looks increasingly dangerous


A variant of the coronavirus that emerged in mid-2020 and became the dominant strain in California not only spreads more easily than its predecessors, but it also evades antibodies generated by COVID-19 vaccines or a previous infection and is associated with serious illness and death, researchers. saying.

In a study that helps explain the dramatic rise in the status of COVID-19 cases and deaths, and heralds more trouble ahead, UC San Francisco scientists said the cluster of mutations that characterizes the local strain should mark it. as a “variant of concern”. on a par with those of the United Kingdom, South Africa and Brazil.

“The devil is here,” said Dr. Charles Chiu, who led UCSF’s team of geneticists, epidemiologists, statisticians and other scientists in a wide-ranging analysis of the new variant, which they call B.1.427 / B.1.429. “I wish it were different. But science is science. “

Californians, along with the rest of the country, have been preparing for the emergence of a more transmissible variant of the UK coronavirus known as B.1.1.7. But they should know that a rival strain that is probably just as worrisome has already taken hold and will likely account for 90% of the state’s infections by the end of next month, said Chiu, an infectious diseases researcher and physician.

The UK and California variants are armed with enhanced capabilities, and the likelihood that they can circulate in the same population raises the specter of a return to infections and deaths, Chiu said. It also opens the door to a “nightmare scenario”: that the two viruses will meet in a single person, swap their mutations and create an even more dangerous strain of the SARS-CoV-2 virus.

New evidence that the California variant could make people sicker and vaccines less effective should prompt more intensive efforts to reduce infections, Chiu said. Those should include both public health measures, such as masking and limits on public activities, such as a rapid vaccination campaign, he added.

The new analysis is currently being reviewed by the San Francisco County and state departments of public health, which collaborated on the new investigation. It is expected to be published later this week on MedRxiv, a website that allows new research to be shared prior to its formal publication.

For five months starting on September 1, the California strain, which is sometimes known as 20C / L452R, emerged from total darkness to represent more than 50% of all coronavirus samples that were subjected to genetic testing in the condition. Compared to the strains that were more prominent here in early fall, the new strain appears to have a greater ability to spread, Chiu said.

Exactly how much more transmissible the California strain is remains an open question, he added. But the evidence that it is more contagious comes from several sources.

Samples collected from a variety of counties, and using a variety of collection methods, suggest that the variant is 19% to 24% more transmissible. But in some circumstances, its advantage was much greater: In an outbreak in a nursing home, B.1.427 / B.1.429 spread at a rate six times faster than its predecessors.

The researchers also discerned uniform patterns of spread of the variant in counties across the state. When infection rates increased, they usually did so in conjunction with mounting evidence for the presence of the California strain.

The greater propensity for the variant to spread was also evident in the laboratory results. An analysis of viral samples from across the state showed that compared to people infected with other strains of SARS-CoV-2, those infected with the California strain had viral loads in the nasopharynx that were twice as high.

That, in turn, made it highly likely that each person infected with the new strain would infect more people.

The genome of B.1.427 / B.1.429 includes three mutations affecting the crucial spike protein, which the virus uses to sneak into human cells and turn them into factories for its own production. One of those three mutations, called L452R, affects the so-called receptor-binding domain, which helps the virus adhere more firmly to target cells.

That adaptation has not been seen in coronavirus variants that have caused concern elsewhere.

In a UCSF lab, scientists found that the L452R mutation alone also made the California strain more harmful. A coronavirus designed to have just that mutation was able to infect human lung tissue at least 40% more easily than circulating variants that lacked the mutation. Compared with so-called wild-type strains, the modified virus was more than three times more infectious.

In the lab, the California strain was also found to be more resistant to neutralizing antibodies generated in response to COVID-19 vaccines, as well as a previous coronavirus infection.

Compared to existing variants, the reduction in protection was “moderate … but significant,” the researchers said.

The coronavirus strain that is now dominant in South Africa, and which has raised concerns about bypassing the immune system’s defenses, has been shown to reduce the effect of neutralizing antibodies by a factor of 6.2. With the California strain, the effect of these antibodies was reduced by a factor of two.

“I anticipate that over time it will have an effect on vaccination,” Chiu said. Although the magnitude of the effect varied from sample to sample and was less pronounced than with the South African strain, “it is still concerning,” he said.

Ominously, the new study also suggested that the California variant might have higher virulence.

That observation is based on the medical records of 324 inpatients at UCSF, a relatively small sample. Still, the researchers found that 21% of these patients who were infected with B.1.427 / B.1.429 were more likely than their counterparts to have been admitted to the ICU, and were 11 times more likely to die. That finding held true even after the researchers adjusted for differences in the patients’ age, gender and ethnicity.

However, Chiu cautioned that this increased risk of death may not be a sign that the variant is inherently more lethal. Rather, it may simply be a reflection that their increased transmissibility caused hospitals to become so overwhelmed and healthcare resources to shrink so much that more deaths were the result, especially in Southern California.

Dr. Marc Suchard, an infectious disease tracking expert at UCLA, said some of the team’s findings will likely be refined as more virus samples are genetically sequenced and more data comes to light.

“It remains vitally important that we actively sequence the virus as cases are diagnosed in our state,” said Suchard, who was not involved in the UCSF work. “I am pleased to see such collaboration between academics and public health departments in California to identify the emergence of a previously unidentified lineage.”



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