Studies look at variant of California outbreak and news is not good

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A variant first discovered in California in December is more contagious than earlier forms of the coronavirus, two new studies have shown, fueling concerns that emerging mutants like this could hamper the sharp drop in cases overall state and perhaps elsewhere.

In one of the new studies, the researchers found that the variant had spread rapidly in a neighborhood in San Francisco in the past two months. The other report confirmed that the variant had surged across the state and found that it produced twice as many virus particles inside a person’s body as the other variants. This study also hinted that the variant may be better than others at evading the immune system – and vaccines.

“I wish I had better news for you – that this variant is not significant at all,” said Dr. Charles Chiu, a virologist at the University of California, San Francisco. “But unfortunately, we’re just following the science.”

Neither study has yet been published in a scientific journal. And experts don’t know how much of a threat to public health this variant poses compared to others that are also spreading in California.

A variant called B.1.1.7 arrived in the United States from Britain, where it quickly became the dominant form of the virus and overwhelmed hospitals. Studies of British medical records suggest that B.1.1.7 is not only more transmissible, but more fatal than earlier variants.

Some experts said the new variant in California was concerning, but was not likely to create as much of a burden as B.1.1.7.

“I’m more and more convinced that this one transmits more than others locally,” 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 to suggest that it is in the same stage as B.1.1.7.”

Dr Chiu first came across the new variant by accident. In December, he and other Californian researchers were concerned about the discovery of B.1.1.7 in Britain. They began to scan their positive coronavirus test samples in California, sequencing viral genomes to see if B.1.1.7 had arrived in their condition.

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

It turns out that researchers at Cedars-Sinai Medical Center in Los Angeles separately discovered the same variant reaching high levels in Southern California. Dr Chiu announced his initial discovery and the Cedars-Sinai team went public two days later.

Since then, researchers have taken a closer look at the new variant, known as B.1.427 / B.1.429, to identify its origin and track its spread. To date, it has appeared in 45 states and several other countries, including Australia, Denmark, Mexico, and Taiwan. But so far it has only taken off in California.

It was not clear at first if the variant was inherently more transmissible than others, or if it had exploded in California due to gatherings that have become very widespread events.

“Just by chance, a bad marriage or bad choir practice can create a big difference in frequency,” said Joe DeRisi, co-chair of Chan Zuckerberg Biohub, who has investigated the spread of the variant.

In a new study that will be uploaded soon, Dr Chiu and his colleagues analyzed 2,172 virus samples taken from across the state between September and January. In early September, researchers found no sign 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 cases caused by the variant are now doubling every 18 days.

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

The researchers also conducted laboratory experiments to look for evidence that the new variant had a biological benefit. In one study, they showed it to be at least 40% more efficient at infecting human cells than previous variants. And when they measured the genetic material found on swabs used for coronavirus testing, the researchers found that people infected with the variant produce twice the viral load of other variants.

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

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

“If we can get enough people vaccinated, we’ll be able to treat these variants just because we won’t have continuous transmission,” he said.

In a separate study that has yet to be published, Dr DeRisi and his colleagues took a close look at how the variant has spread in the Mission District, a predominantly Latino neighborhood in San Francisco.

Examining samples from the end of November, the researchers found that 16% of coronaviruses belonged to B.1.427 / B.1.429. In January, after sequencing 630 genomes, they found it was 53 percent.

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

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“What we are seeing is a small but significant difference,” said Dr DeRisi.

Dr Chiu said the San Francisco study offered 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.

But Harvard’s Dr Hanage isn’t convinced the variant poses a major threat. Every time B.1.1.7 appeared in a new country, it exploded quickly. In contrast, the variant discovered in California seems to have slowly gained in dominance.

Dr Chui and his colleagues were able to estimate the origin of B.1.427 / B.1.429 by comparing mutations that have appeared in viruses since they separated from their common ancestor. This analysis indicated the end of spring. If that’s correct, that means the variant has been hiding at extremely low levels in California for perhaps four months or more.

“It’s not as bad as the others,” Dr. Hanage said. He speculates that if scientists sequence more coronavirus genomes elsewhere, they will find more of these moderately fast-spreading mutants. “Maybe the variants are all over the place, and we’re just seeing them where there’s sequencing,” he said.

We may soon have new information on how to take these emerging variants seriously. B.1.1.7 didn’t arrive in California until around the beginning of December, and although it’s doubling every 12 days or so, it still only accounts for about 2% of coronaviruses in the state.

Now California is going to become something of a viral caged match between the two variants. “I suspect that B.1.1.7 will win out,” Dr Hanage said.

Dr Chiu, however, believes it is possible that B.1.427 / B.1.429 will remove the newcomer and continue to dominate the state.

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

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