December 9, 2023

A variant, first discovered in California in December, is more contagious than previous forms of the coronavirus. Two new studies have shown concerns that emerging mutants like these could hamper the sharp decline in cases across the state and potentially elsewhere.

In one of the new studies, researchers found that the variant had spread rapidly in a neighborhood of San Francisco in the past few months. The other report confirmed that the variant has risen sharply across the state and revealed that it produces twice as many virus particles in a person’s body as other variants. This study also suggested that the variant can bypass the immune system – and vaccines – better than others.

“I wish I had better news for you – that this variant doesn’t matter at all,” said Dr. Charles Chiu, a virologist at the University of California at San Francisco. “But unfortunately we just follow science.”

None of the studies have yet been published in a scientific journal. And experts don’t know how much this variant is public health compared to others that are also spreading in California.

A variant called B.1.1.7 came to the US from the UK, where it quickly became the dominant form of the virus and overloaded hospitals there. Studies of UK medical records suggest that B.1.1.7 is not only more communicable, but also more lethal than previous variants.

Some experts said the new variant in California is of concern, but is unlikely to be as much of a burden as B.1.1.7.

“I’m becoming increasingly convinced that this one transmits more than anyone else in the field,” said William Hanage, an epidemiologist at Harvard TH Chan School of Public Health who was not involved in the research. “But there is no evidence that it is in the same stadium as B.1.1.7.”

Dr. Chiu accidentally stumbled upon the new variant for the first time. In December, he and other researchers in California were concerned about the discovery of B.1.1.7 in the UK. They began screening their samples from positive coronavirus tests in California and sequencing viral genomes to see if B.1.1.7 had made it to their state.

On New Year’s Eve, Dr. Chiu is shocked to find a previously unknown variant that made up a quarter of the samples he and his colleagues had collected. “I thought that was crazy,” he said.

It turned out that researchers at Cedars-Sinai Medical Center in Los Angeles discovered the same variant that soared to high levels in Southern California. Dr. Chiu announced his first finding and the Cedars-Sinai team went public two days later.

Since then, researchers have studied the new variant, known as B.1.427 / B.1.429, in more detail to determine its origin and track its spread. It has performed in 45 states and several other countries so far, including Australia, Denmark, Mexico, and Taiwan. But it has only launched in California so far.

It was initially unclear whether the variant was inherently more transferable than others, or whether it had risen sharply in California due to gatherings that became overarching events.

“Just by chance, poor wedding or choir practice can cause a large frequency difference,” said Joe DeRisi, co-president of the Chan Zuckerberg Biohub, who studied the spread of the variant.

In a new study that will be posted online shortly, Dr. Chiu and his colleagues received 2,172 virus samples from across the state between September and January. In early September, the researchers found no signs of B.1.427 / B.1.429. But by the end of January it had become the predominant variant in California. Dr. Chiu and his colleagues estimate that the cases caused by the variant now double every 18 days.

Dr. Chiu and his colleagues reviewed the medical records of 308 cases of Covid-19 in San Francisco and found that a greater percentage of people had died from the new variant than others. However, this result could be a statistical coincidence: there were only 12 deaths in the group, so the difference in deaths from one subgroup to another in a larger sample may not apply.


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The researchers also conducted experiments in the laboratory to find evidence that the new variant had a biological benefit. In one study, they showed that it was at least 40 percent more effective than previous variants at infecting human cells. When measuring the genetic material of swabs used for coronavirus testing, the researchers found that people infected with the variant produce a viral load twice as high as other variants.

The study also found that the new variant can bypass the immune system better than other variants. Antibodies from people who had recovered from infections with other variants were less effective at blocking the new variant in the laboratory. The same was true when the researchers used blood serum from people who had been vaccinated.

Still, the effect of the variant on immunity appears to be much less than that caused by a variant from South Africa called B.1.351. Dr. Chiu said it was not clear whether the vaccines used against B.1.427 / B.1.429 will be less effective.

“If we can get enough people vaccinated, we can deal with these variants simply because we don’t have ongoing transmission,” he said.

In a separate study that has not yet been published, Dr. DeRisi and his colleagues are carefully investigating how the variant is spreading in the Mission District, a predominantly Latin American neighborhood in San Francisco.

When examining samples in late November, the researchers found that 16 percent of the coronaviruses belonged to B.1.427 / B.1.429. After sequencing 630 genomes in January, they found that they made up 53 percent.

The researchers also looked at the distribution of this and other variants in 326 households. They found that people had a 35 percent chance of getting infected if someone had B.1.427 / B.1.429 in their home. If the person was infected with another variant, the rate was only 26 percent.

“What we see is a modest but significant difference,” said Dr. DeRisi.

Dr. Chiu said the San Francisco study provided a microcosm of how the variant has spread across the state. “The data they have from the mission district really supports our data and vice versa,” he said.

Dr. However, Harvard-based Hanage is not convinced that the variant poses a major threat. Every time B.1.1.7 appeared in a new country, it quickly exploded. In contrast, the variant discovered in California seems to have slowly gained dominance.

Dr. Chiu and his colleagues were able to estimate when B.1.427 / B.1.429 arose by comparing the mutations that have occurred in the viruses since they separated from their common ancestor. This analysis pointed to late spring. If that’s correct, it means the variant may have lurked at extremely low levels in California for four months or more.

“It’s not as big a deal as the others,” said Dr. Hanage. He speculates that if scientists sequence more coronavirus genomes elsewhere, they will find more of these moderately fast-spreading mutants. “Maybe there are variants everywhere, and we only see them where sequencing happens,” he said.

We may soon have new insights into how seriously these new variants should be taken. B.1.1.7 didn’t arrive in California until early December, and although it has doubled about every 12 days, it’s still about 2 percent of the coronaviruses in the state.

Now California is becoming a kind of virus cage match between the two variants. “My suspicion is that the B.1.1.7 will win,” said Dr. Hanage.

Dr. However, Chiu thinks it is possible that B.1.427 / B.1.429 will suppress the newcomer and continue to dominate the state.

“We’ll find out in the next few weeks,” he said.