Scientists in Oregon have discovered a local version of a fast-spreading variant of the coronavirus that first appeared in Britain, but is now being combined with a mutation that may make the variant less susceptible to vaccines.
Researchers have so far found only one case of this formidable combination, but genetic analysis suggested that the variant was acquired in the community and did not arise in the patient.
“We didn’t import this from anywhere else in the world, it happened spontaneously,” said Brian O’Roak, a geneticist at Oregon Health and Science University who led the work. He and his colleagues are involved in the Centers for Disease Control and Prevention effort to track down variants, and have deposited their results in databases shared by scientists.
The variant originally identified in Britain, called B.1.1.7, has spread rapidly across the United States, accounting for at least 2,500 cases in 46 states. This form of the virus is more contagious and more deadly than the original version, and is expected to account for the majority of infections in the United States within a few weeks.
The new version that appeared in Oregon has the same backbone, but also a mutation, E484K, or “Eek,” which is seen in variants of the virus circulating in South Africa, Brazil, and New York City.
Laboratory studies and clinical trials in South Africa indicate that the Eek mutation makes current vaccines less effective in attenuating the body’s immune response. (The vaccines still work, but the findings are concerning enough that Pfizer-BioNTech and Moderna have begun testing new versions of their vaccines designed to beat the variant found in South Africa.)
The B.1.1.7 variant with Eek has also emerged in Britain, designated as a “variant of concern” by scientists. But the virus identified in Oregon appears to have evolved independently, Dr. O’Roak said.
Dr. O’Roak and his colleagues found the variant among coronavirus samples collected by the Oregon State Public Health Laboratory across the state, including some from an outbreak in a healthcare setting. Of the 13 test results they analyzed, 10 turned out to be just B.1.1.7 and one the combination.
Other experts said the discovery was not surprising, because the Eek mutation has emerged in forms of the virus around the world. But the occurrence of the mutation in B.1.1.7 is worth watching, they said.
In Great Britain, this version of the variant accounts for a small number of cases. But when the combination evolved there, B.1.1.7 had already spread across the country.
“We’re at the point where B.1.1.7 has just been introduced” in the United States, said Stacia Wyman, an expert in computational genomics at the University of California, Berkeley. “As it slowly evolves and becomes dominant, it could accumulate more mutations.”
Viral mutations can enhance or weaken each other. For example, the variants identified in South Africa and Brazil contain many of the same mutations, including Eek. But the Brazilian version has a mutation, K417N, which is not present in the South African version.
In a study published Thursday in Nature, researchers compared antibody responses to all three variants of concern, those identified in Britain, South Africa and Brazil. Consistent with other studies, they found that the variant that struck South Africa is more resistant to antibodies produced by the immune system.
But the variant that circulated in Brazil was not so resistant, despite the fact that it carried the Eek mutation. “If you have the second mutation, you don’t see such a bad effect,” said Michael Diamond, a viral immunologist at Washington University in St. Louis, who led the study.
It is too early to tell if the Oregon variant will behave like the South African or Brazilian ones. But the idea that other mutations could weaken Eek’s effect is “excellent news,” Dr. Wyman said.
Above all, he said, the Oregon finding reinforces the need for people to continue to take precautions, such as wearing a mask, until a substantial portion of the population is immunized.
“People should not be scared, but remain alert,” he said. “We cannot lower our guard just yet as long as these more communicable variants continue to circulate.”