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A more contagious variant of the coronavirus first discovered in Britain is spreading rapidly in the United States, doubling about every 10 days, according to a new study.
Analyzing half a million coronavirus tests and hundreds of genomes, a team of researchers predicted that within a month this variant could become predominant in the United States, potentially leading to an outbreak of new cases and an increased risk of death.
The new research offers the first national 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 behaves like it did in Britain. The new study confirms this projected trajectory.
“Nothing in this article is surprising, but people need to see it,” said Kristian Andersen, study co-author and virologist at the Scripps Research Institute in La Jolla, Calif. “We should probably be bracing for the predominant lineage in most places in the United States in March.”
Dr Andersen’s team estimated that the rate of transmission of B.1.1.7 in the United States is 30-40% higher than that of the more common variants, although these numbers may increase as more data is coming, he said. The variant has already been implicated in power surges in other countries, including Ireland, Portugal and Jordan.
“A very serious situation could indeed develop 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 that warrant urgent investigation by public health authorities.”
Dr Davies cautioned that the US data is more patchy than that of Britain and other countries that have national systems for monitoring variants. Still, he found the results for parts of the United States particularly worrying. In Florida, where the new study indicates the variant is spreading particularly quickly, Dr Davies fears a new outbreak may strike even sooner than the rest of the country.
“If these data are representative, the time to action may be limited,” he said.
Dr Andersen and his colleagues published their study online on Sunday. It has not yet been published in a scientific journal.
When the UK government announced the discovery of B.1.1.7 on December 20, Dr Andersen and other researchers in the US began looking for it in US coronavirus samples. The first case appeared on December 29 in Colorado, and Dr. Andersen found another soon after in San Diego. In no time, he was spotted in many other parts of the country.
But it was difficult to determine how widespread the variant was. B.1.1.7 contains a distinctive set of 23 mutations scattered throughout a genome of 30,000 genetic letters. The best way to determine if a virus belongs to the B.1.1.7 lineage is to sequence its entire genome – a process that can only be done with special machines.
The CDC has contracted with Helix, a lab testing company, to examine their Covid-19 samples for signs of B.1.1.7. The variant can give a negative result on any of the three tests 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 them 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 in late November, a month before it was detected.
The variant has been introduced separately into the country at least eight times, likely as a result of people traveling to the United States from Britain between Thanksgiving and Christmas.
The researchers combined genome sequencing data with overall test results from Helix to get an estimate of how quickly the variant had spread. It has become exponentially more common over the past two months.
In Florida, scientists estimate that more than 4 percent of cases are now caused by B.1.1.7. The national figure can be 1 or 2%, depending on the calculations of his team.
If this is true, then a thousand or more people can become infected with the variant every day. The CDC has only recorded 611 B.1.1.7 cases, attesting to the country’s insufficient genomic surveillance.
In areas of the country where Helix doesn’t do a lot of testing, it is likely underestimating the spread, Dr. Andersen warned.
“It is clearly not enough,” he said. “I can assure you that there are places where B.1.1.7 might be relatively prevalent now that we wouldn’t pick up.”
Nathan Grubaugh, a virologist at Yale University who was not involved in the new study, says the data clearly indicates that the incidence of B.1.1.7 is increasing exactly as scientists warned. But he doesn’t think the new study reveals exactly how it’s developing. “It doesn’t really reveal the cause at this point,” he says.
B.1.1.7 chains of transmission may spread faster than other viruses. Or it may be that B.1.1.7 is more common among inbound travelers who start new outbreaks.
“I still think we’re weeks away from really figuring out how this is going to go,” Dr. Grubaugh said.
The contagiousness of B.1.1.7 makes it a threat to be taken seriously. Public health measures that work on other variants may not be sufficient to stop B.1.1.7. More cases in the United States would mean more hospitalizations, which could put a strain on hospitals which are only now recovering from a record number of patients last month.
To make matters worse, Dr Davies and colleagues at the London School of Hygiene and Tropical Medicine published an online study on Wednesday suggesting that the risk of dying from B.1.1.7 is 35% higher than for other variants. The study has not yet been published in a scientific journal.
Communities can take action to combat variants like B.1.1.7, as Dr Grubaugh and colleagues at Yale University recently described in the journal Cell. For example, they said, health officials should reinforce messages about wearing effective masks, avoiding large gatherings and ensuring indoor spaces are well ventilated.
Scientists have also urged governments to demand sick leave for those diagnosed with Covid-19 to stop the spread in the workplace. “Such measures could help significantly reduce community transmission,” wrote Dr. Grubaugh and his co-authors.
Vaccinations can also be part of the control strategy B.1.1.7. In Israel, where the variant is now predominant, new cases, serious illnesses and hospitalizations have already dropped significantly among people over 65, a group that has been given top priority for vaccines.
“What we need to do with the current vaccines is get them to as many people as possible as quickly as possible,” said Dr Andersen.
Reducing B.1.1.7 will also reduce the risk of the variant evolving into something even worse. Already in Britain, researchers have found samples of B.1.1.7 which have acquired a new mutation with the potential to make vaccines less effective. It is not clear if these viruses will become common. But they demonstrate that the coronavirus still has a lot of evolutionary space to explore.
“We should expect them to pop up here,” Dr Andersen said. “What was true elsewhere will also be true here, and we have to face it.”
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