The New York Times, February 1, 2021
A fast-spreading coronavirus variant first observed in Britain has gained a worrisome mutation that could make it harder to control with vaccines, Public Health England reported on Monday. And on Tuesday, a team of researchers reported an experiment suggesting that this mutation might make vaccines somewhat less effective against the variant.
The variant, known as B.1.1.7, first came to light in December. Researchers determined that it had rapidly become more common across Britain in just a couple of months.
Its spread appears to occur because of its improved ability to infect people. Experiments in test tubes suggest that some of its mutations allow the B.1.1.7 variant to hold on to cells more tightly than other coronaviruses.
Since B.1.1.7’s discovery in Britain, the variant has been reported in 72 other countries. The United States confirmed its first case of the B.1.1.7 variant on Dec. 29, but is conducting little of the genomic sequencing necessary to track the spread of new variants that have caused concern. Since then, the Centers for Disease Control and Prevention has recorded 467 samples of the variant in 32 states. Officials in New York City said on Tuesday that they had identified 13 cases of the variant and were ramping up testing capacity to detect more.
In its latest analysis, Public Health England estimated that the variant’s rate of infection is 25 percent to 40 percent higher than that of other forms of the coronavirus. Some preliminary evidence suggests that it may also cause more deaths.
Several lines of evidence suggest that vaccines will work against the B.1.1.7 variant. On Thursday, the vaccine maker Novavax announced that its British trial found no evidence that B.1.1.7 could evade the vaccine’s defenses.
But in South Africa, where a variant called B.1.351 has surged to dominance, the Novavax and Johnson & Johnson vaccines have both been less effective in trials.
That variant has been reported in 31 countries so far. In the United States, it has turned up in Maryland and in South Carolina.
Scientists suspect that the B.1.351 variant’s partial escape from vaccines is largely thanks to a single mutation, called E484K. Experiments indicate that the E484K mutation makes it harder for antibodies to grab onto the virus and prevent it from entering cells.
Now it turns out that some B.1.1.7 coronaviruses in Britain also have the E484K mutation.
To search for new mutations, British researchers reviewed the 214,159 genomes of coronaviruses that the United Kingdom has sequenced as of Jan. 26. In its report, Public Health England said that they found 11 samples of the B.1.1.7 variant that also had the E484K mutation.
Since that analysis, more of these viruses have come to light. NextStrain, a website where scientists gather and analyze coronavirus genomes, now identifies 16 B.1.1.7 variants that carry the E484K mutation.
These B.1.1.7 coronaviruses gained the mutation thanks to random copying errors as they multiplied inside of people. The evolutionary tree of the coronaviruses suggests that 15 of the variants descend from one common ancestor that gained the E484K mutation. Meanwhile the sixteenth variant seems to have gained the same mutation on its own.
Commenting on Monday’s report, Kristian Andersen, a virologist at Scripps Research Institute in La Jolla, Calif., said that it was impossible yet to say whether the E484K mutation would make these coronaviruses not only more contagious but more resistant to vaccines. “It’s much too early to speculate whether it will, so we’ll have to wait for data,” he said.
Just because the E484K mutation helps the B.1351 variant, the one initially found in South Africa, evade antibodies doesn’t mean it will do the same in other variants. That’s because mutations don’t have a fixed effect. The impact of a single new mutation to a virus depends on the other mutations that the variant already carries.
But in a report posted online Tuesday, Ravi Gupta, a virologist at the University of Cambridge, and his colleagues reported an experiment they ran to address exactly this question. They combined the E484K mutation with other key mutations found in the B.1.1.7 variant, the one initially found in Britain. The addition of the E484K mutation made it difficult for antibodies to block the viruses. The researchers wrote that they “observed a significant loss of neutralizing activity.”
However, Dr. Gupta and his colleagues used antibodies taken from people who had received just the first of two doses of the Pfizer-BioNTech vaccine. It remains to be seen whether the B.1.1.7 variant with the new mutation, E484K, can evade antibodies after a full vaccination.
Nicholas Davies, a mathematical biologist at the London School of Hygiene and Tropical Medicine, cautioned that with so few of these new coronaviruses, it’s hard to say whether they will become more common than ordinary B.1.1.7 variant.
But it is striking that the same mutation, E484K, has now been documented arising several times in Britain, as well as in South Africa. Meanwhile, in Brazil, yet another variant has also gained the same E484K mutation on its own.
Dr. Davies speculated that the mutation may give the virus an advantage when it is spreading in populations where a lot of people have already been sick with Covid-19. It may be able to evade their antibodies to other variants. “E484K may well convey a fitness advantage in settings where there is existing immunity,” Dr. Davies said.
If so, the virus may be providing the world with a dangerous new example of a common theme in evolution. A good solution can arise more than once — such as flight, which evolved in birds, bats, and insects. Evolutionary biologists call this repeated pattern convergence.
“It’s not great to see this mutation in the B.1.1.7 lineage, although I think it’s no surprise at all,” said Dr. Andersen. “We should expect that to happen.”
Dr. Gupta argued on Twitter that the best defense against this convergence is vaccination. By making it harder for coronaviruses to get from person to person, they will have fewer chances to gain the E484K mutation or other dangerous changes.
“We need to continue vaccinating and drive down transmission,” Dr. Gupta wrote.
Copyright 2021 The New York Times Company. Reprinted with permission.