A variant first discovered in California in December is more contagious than previous forms of the coronavirus, two new studies have found, sparking concern that emerging mutants such as this one are causing the sharp decline in cases across the state and might hinder elsewhere.
In one of the new studies, researchers found that the variant has spread rapidly in a San Francisco neighborhood in recent months. The other report confirmed that the variant has risen through the state and revealed that it produces twice as many viral particles in a person's body as other variants. That study also hinted that the variant may be better than others at evading the immune system – and vaccines.
"I wish I had better news to tell 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 just follow science."
Neither study has been published in a scientific journal so far. And experts don't know how much of a public health threat this variant poses compared to other variants that are also spreading in California.
A variant called B.1.1.7 arrived in the United States from Great Britain, 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 transferable, but also more deadly than previous variants.
Some experts said the new variant in California was a cause for concern, but was unlikely to cause as much of a burden as B.1.1.7.
"I'm increasingly convinced that this one transmits more locally than others," said William Hanage, an epidemiologist at Harvard T.H. Chan School of Public Health who was not involved in the study. "But there is no indication that it is in the same baseball field as B.1.1.7."
Dr. Chiu first encountered the new variant by accident. In December, he and other researchers in California were concerned about the discovery of B.1.1.7 in Britain. They began to sift through their samples of positive coronavirus tests in California and sequence the viral genomes to see if B.1.1.7 had arrived in their state.
On New Year's Eve, Dr. Chiu was shocked to discover 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.
As it turned out, researchers at Cedars-Sinai Medical Center in Los Angeles separately identified the the same variant rises to high levels in Southern California. Dr. Chiu announced his first find 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 determine its origin and track its spread. It has surfaced in 45 states so far and several other countries, including Australia, Denmark, Mexico and Taiwan. But it has only taken off in California so far.
It was initially unclear whether the variant was inherently more transferable than others, or whether it had risen in California due to gatherings that became predominant events.
“Just by chance, a bad wedding or choir practice can create a big frequency difference,” said Joe DeRisi, the co-president of the Chan Zuckerberg Biohub, who has researched the spread of the variant.
In a new study soon to be posted online, Dr. Chiu and his colleagues collected 2,172 virus samples from around the state between September and January. In early September, the researchers found no sign of B.1.427 / B.1.429. But by the end of January, it had become the predominant variety in California. Dr. Chiu and his colleagues estimate that cases caused by the variant now double every 18 days.
Reviewing medical records on 308 cases of Covid-19 in San Francisco, Dr. Chiu and his colleagues reported that a higher percentage of people had died from the new variant than from others. But that result could be a statistical coincidence: There were only 12 deaths in the group, so the difference in deaths from one subgroup to another may not hold up in a larger sample.
The researchers also conducted experiments in the lab to look for evidence that the new variant had a biological benefit. In one study, they showed it was at least 40 percent more effective at infecting human cells than previous variants. And when they determined the genetic material found on cotton swabs used for coronavirus tests, the researchers found that people infected with the variant produce twice the viral load of other variants.
The research also showed that the new variant can avoid the immune system better than 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 of people who had been vaccinated.
Still, the effect of the variant on immunity appears to be much smaller than that caused by a variant from South Africa called B.1.351. Dr. Chiu said it is not clear whether the vaccines used will be less effective against B.1.427 / B.1.429.
"If we can get enough people vaccinated, we will be able to deal with these variants simply because we don't have continuous transmission," he said.
In a separate study that has not yet been published, Dr. DeRisi and his colleagues took a closer look at the variant spread in the Mission District, a predominantly Latino neighborhood of San Francisco.
Looking at samples from late November, the researchers found that 16 percent of the coronaviruses belonged to B.1.427 / B.1.429. In January, after sequencing 630 genomes, they found it accounted for 53 percent.
The researchers also looked at the distribution of this and other variant 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 percentage was only 26 percent.
"What we see is a modest, but meaningful 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.
But Dr. Harvard's Hanage is not convinced that the variant is a major threat. Every time B.1.1.7 popped up 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 originated by comparing the mutations that have evolved in the viruses since they split from their common ancestor. That analysis pointed to late spring. If true, it means that the variant in California may have been lurking at extremely low levels for up to four months or more.
"It's not as important as the others," said Dr. Hanage. He speculates that if scientists sequence more coronavirus genomes in other places, they will find more of these moderately fast-spreading mutants. "Maybe there are variants everywhere, and we just see them in the places where sequencing takes place," he said.
We may soon get new insights on how seriously we can take these emerging variants. B.1.1.7 didn't arrive in California until early December, and while it roughly doubles every 12 days, it's still about 2 percent of the state's coronaviruses.
Now California is becoming sort of a viral cage match between the two variants. "I suspect 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 oppress the newcomer and continue to dominate the state.
"We will find out in the coming weeks," he said.