Virus Variant First Found in Britain Now Spreading Rapidly in U.S.

A new study bolsters the prediction by the Centers for Disease Control and Prevention that the so-called B.1.1.7 variant will dominate Covid-19 cases by March.

People wait to receive a Covid-19 vaccine at a temporary vaccination hub set up at the Colchester Community Stadium in Colchester, Essex, south east England on February 6, 2021.
People wait to receive a Covid-19 vaccine at a temporary vaccination hub set up at the Colchester Community Stadium in Colchester, Essex, south east England on February 6, 2021.Credit…Daniel Leal-Olivas/Agence France-Presse — Getty Images
Carl Zimmer

By Carl Zimmer

Feb. 7, 2021, 11:01 a.m. ET

A more contagious variant of the coronavirus first found in Britain is spreading rapidly in the United States, doubling roughly every 10 days, according to a new study.

Analyzing half a million coronavirus tests and hundreds of genomes, a team of researchers predicted that in a month this variant could become predominant in the United States, potentially bringing a surge of new cases and increased risk of death.

The new research offers the first nationwide look at the history of the variant, known as B.1.1.7, since it arrived in the United States in late 2020. Last month, the Centers for Disease Control and Prevention warned that B.1.1.7 could become predominant by March if it behaved the way it did in Britain. The new study confirms that projected path.

“Nothing in this paper is surprising, but people need to see it,” said Kristian Andersen, a co-author of the study and a virologist at the Scripps Research Institute in La Jolla, Calif. “We should probably prepare for this being the predominant lineage in most places in the United States by March.”

Dr. Andersen’s team estimated that the transmission rate of B.1.1.7 in the United States is 30 percent to 40 percent higher than that of more common variants, although those figures may rise as more data comes in, he said. The variant has already been implicated in surges in other countries, including Ireland, Portugal and Jordan.

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“There could indeed be a very serious situation developing in a matter of months or weeks,” said Nicholas Davies, an epidemiologist at the London School of Hygiene and Tropical Medicine who was not involved in the study. “These may be early signals warranting urgent investigation by public health authorities.”

Dr. Davies cautioned that U.S. data is patchier than that in Britain and other countries that have national variant monitoring systems. Still, he found results from some parts of the United States especially worrisome. In Florida, where the new study indicates the variant is spreading particularly quickly, Dr. Davies fears that a new surge may hit even sooner than the rest of the country.

“If these data are representative, there may be limited time to act,” he said.

Dr. Andersen and his colleagues posted their study online on Sunday. It has not yet been published in a scientific journal.
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Inside the B.1.1.7 Coronavirus Variant

What researchers have learned about the variant first discovered in Britain.

When the British government announced the discovery of B.1.1.7 on Dec. 20, Dr. Andersen and other researchers in the United States began checking for it in American coronavirus samples. The first case turned up on Dec. 29 in Colorado, and Dr. Andersen found another soon after in San Diego. In short order it was spotted in many other parts of the country.

But it was difficult to determine just how widespread the variant was. B.1.1.7 contains a distinctive set of 23 mutations scattered in a genome that is 30,000 genetic letters long. The best way to figure out if a virus belongs to the B.1.1.7 lineage is to sequence its entire genome — a process that can be carried out only with special machines.

The C.D.C. contracted with Helix, a lab testing company, to examine their Covid-19 samples for signs of B.1.1.7. The variant can deliver a negative result on one of the three tests that Helix uses to find the coronavirus. For further analysis, Helix sent these suspicious samples to Illumina to have their genomes sequenced. Last month Helix reached out to Dr. Andersen and his colleagues to help analyze the data.

Analyzing 212 American B.1.1.7 genomes, Dr. Andersen’s team concluded that the variant most likely first arrived in the United States by late November, a month before it was detected.
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The variant was separately introduced into the country at least eight times, most likely as a result of people traveling to the United States from Britain between Thanksgiving and Christmas.

The researchers combined data from the genome sequencing with Helix’s overall test results to come up with an estimate of how quickly the variant had spread. It grew exponentially more common over the past two months.

In Florida, the scientists estimate that more than 4 percent of cases are now caused by B.1.1.7. The national figure may be 1 percent or 2 percent, according to his team’s calculations.

If that’s true, then a thousand or more people may be getting infected with the variant every day. The C.D.C. has recorded only 611 B.1.1.7 cases, attesting to the inadequacy of the country’s genomic surveillance.

In parts of the country where Helix doesn’t do much testing, it is likely delivering an underestimate of the spread, Dr. Andersen cautioned.

“It’s clearly not enough,” he said. “I can guarantee you that there are places where B.1.1.7 might be relatively prevalent by now that we would not pick up.”
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Nathan Grubaugh, a virologist at Yale University who was not involved in the new study, says the data makes it clear that the incidence of B.1.1.7 is increasing just as scientists warned it would. But he does not think the new study reveals exactly how it is growing. “It doesn’t really reveal the cause at this point,” he said.

It’s possible that chains of B.1.1.7 transmission are spreading faster than other viruses. Or it might be that B.1.1.7 was more common among incoming travelers starting new outbreaks.

“I still think that we are weeks away from really knowing how this will turn out,” Dr. Grubaugh said.

The contagiousness of B.1.1.7 makes it a threat to take seriously. Public health measures that work on other variants may not be enough to stop B.1.1.7. More cases in the United States would mean more hospitalizations, potentially straining hospitals that are only now recovering from record high numbers of patients last month.

Making matters worse, Dr. Davies and his colleagues at the London School of Hygiene and Tropical Medicine posted a study online on Wednesday suggesting that the risk of dying of B.1.1.7 is 35 percent higher than it is for other variants. The study has yet to be published in a scientific journal.

Communities can take steps to fight variants like B.1.1.7, as Dr. Grubaugh and his Yale University colleagues recently described in the journal Cell. For instance, they said, health officials should reinforce messaging about wearing effective masks, avoiding large gatherings and making sure indoor spaces are well ventilated.

The scientists also urged governments to require sick leave for people diagnosed with Covid-19 to stop workplace spread. “Such measures could help to significantly reduce community transmission,” Dr. Grubaugh and his co-authors wrote.

Vaccinations can also be part of the strategy to fight B.1.1.7. In Israel, where the variant is now predominant, new cases, severe illnesses and hospitalizations have already dropped significantly in people over 65, a group that was given top priority for vaccines.

“What we need to do with the current vaccines is get them into as many people as we can as quickly as possible,” Dr. Andersen said.

Driving down B.1.1.7 will also reduce the risk that the variant will evolve into something even worse. Already in Britain, researchers have found samples of B.1.1.7 that have gained a new mutation with the potential to make vaccines less effective. It’s not clear whether these viruses will become common. But they demonstrate that the coronavirus has a lot of evolutionary space left to explore.

“We should expect them to crop up here,” Dr. Andersen said. “Whatever was true elsewhere is going to be true here as well, and we need to deal with it.”
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