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 a half-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 B117, since it arrived in the United States in late 2020. Last month, the Centers for Disease Control and Prevention warned that B117 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 virus expert 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."
Andersen's team estimated that the transmission rate of B117 in the United States is 30% to 40% 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, a public health researcher 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."
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, 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.
Andersen and his colleagues posted their study online Sunday. It has not yet been published in a scientific journal.
When the British government announced the discovery of B117 on Dec. 20, Andersen and other researchers in the United States began checking for it in U.S. coronavirus samples. The first case turned up Dec. 29 in Colorado, and 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. B117 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 B117 lineage is to sequence its entire genome -- a process that can be carried out only with special machines.
The CDC contracted with Helix, a lab testing company, to examine its covid-19 samples for signs of B117. 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 Andersen and his colleagues to help analyze the data.
Analyzing 212 U.S. B117 genomes, Andersen's team concluded that the variant most likely first arrived in the United States by late November, a month before it was detected.
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% of cases are now caused by B117. The national figure may be 1% or 2%, according to his team's calculations.
If that estimate proves true, then 1,000 or more people may be getting infected with the variant every day. The CDC has recorded only 611 B117 cases.
VACCINATIONS LOOKING UP
Although more contagious variants are spreading in the United States, top health officials sounded notes of optimism Sunday that both the supply of vaccines and the rate of vaccination will steadily increase.
"The demand clearly outstrips supply right now," Dr. Anthony Fauci, the nation's top infectious disease doctor, said on the NBC program "Meet the Press." "I can tell you that things are going to get better as we get from February into March, into April, because the number of vaccine doses that will be available will increase substantially."
The number of shots administered daily in the United States has increased lately. The CDC reported that more than 2.2 million doses were given Saturday and 1.6 million Friday. That brought the latest seven-day average to 1.4 million a day, which approaches President Joe Biden's new goal of 1.5 million shots per day.
In addition, the supply of vaccines -- though still well below demand -- is growing. Federal officials recently increased shipments to the states to 10.5 million doses a week as Moderna and Pfizer gradually increase production. The two companies have deals to supply the United States with a combined 400 million doses -- enough to vaccinate 200 million people -- by the summer.
Pfizer recently said that it will now deliver its doses two months ahead of schedule, by May, in part because it is now counting an additional dose in each vial it is manufacturing. And Moderna is considering a production change that would allow it to increase the number of doses in its vials to 15 from 10.
Officials are also counting on the Food and Drug Administration authorizing a one-dose vaccine from Johnson & Johnson later this month. Although that company will initially provide the United States with only a few million doses, it is expected to step up output considerably by April.
Although the B117 variant is worrisome because it is more transmissible than earlier variants, vaccine developers are more concerned about a variant discovered in South Africa, known as B1351, because it appears to make current vaccines less effective. Several manufacturers have said they were addressing the problem by developing new versions of their vaccines, which could act as booster shots. The FDA has said it is working on a plan to allow those new vaccine versions to be authorized.
Developers of the AstraZeneca and University of Oxford vaccine said Sunday that they expected to have a modified version of their vaccine available by the fall.
SUPER BOWL FEARS
As the U.S. has seen decreasing numbers in the latest surge in coronavirus cases, public health officials are concerned about Super Bowl Sunday becoming another superspreader date.
Experts worry that football fans gathering Sunday in Tampa, Fla., for the championship game between the Kansas City Chiefs and the Tampa Bay Buccaneers or at watch parties across the country could set back the nascent progress of recent weeks.
The daily reports of new cases and deaths remain high but have fallen somewhat. The seven-day average of new case reports in the U.S. dropped to 125,804 Friday, the lowest level since Nov. 10. Reports of deaths, a lagging indicator because patients who die from covid-19 generally do so weeks after being infected, averaged 2,913 a day, the lowest rate since Jan. 7.
January was the country's deadliest month so far in the pandemic, accounting for about 20% of the more than 460,000 coronavirus deaths the United States has recorded in the past 12 months.
Officials, including Fauci, have warned Americans against gathering for Super Bowl parties with people from other households, especially in places without ideal ventilation.
"You're really putting yourself and your family in danger," Fauci said Friday on MSNBC. "It's the perfect setup to have a mini superspreader event in your house. Don't do that for now."
While health experts worry about a rise in cases after the game, some said they do not anticipate anything as deadly as the post-holiday wave that peaked in January. That is because Thanksgiving and Christmas tend to spur more domestic travel than the Super Bowl does, said Dr. Catherine Oldenburg, an infectious disease public health researcher at the University of California, San Francisco.
DEAL IN CHICAGO
Separately, Chicago Mayor Lori Lightfoot touted a preliminary agreement with the teachers union over covid-19 safety protocols on Sunday, potentially averting a strike in the nation's third-largest school district.
Some students could return to classrooms as soon as Thursday, with the reopening of school phased-in by grade. Also, the city agreed to vaccinate 1,500 teachers and staff weekly at vaccination sites dedicated to Chicago Public Schools. The possible deal -- which still requires approval from the Chicago Teachers Union -- also includes metrics that would trigger school closings when cases spike.
The union and district have been fighting for months over a plan to gradually reopen the roughly 340,000-student district, with talks breaking down in recent days on issues including vaccinations. Lightfoot and school officials had threatened to lock educators out of teaching systems multiple times, which the union said would lead to a strike for the second time in less than two years.
"This agreement was about making sure everyone in our school communities just aren't safe, but also that they feel safe," Lightfoot said, calling the last 11 months a "whirlwind for the entire city."
While she called it a "tentative agreement," the union characterized it as an offer that required further review. Neither side provided comprehensive details of the proposal.
"We do not yet have an agreement with Chicago Public Schools," the union tweeted on Sunday. "We will continue with our democratic process of rank-and-file review throughout the day before any agreement is reached."
It was unclear when the union would begin voting. The union's house of delegates would have to decide whether to send the proposal to the roughly 25,000 members for approval.
A union spokeswoman declined to comment further.
Information for this article was contributed by Carl Zimmer, Katie Thomas, Christina Morales and Ron DePasquale of The New York Times; and by Sophia Tareen of The Associated Press.