Scientists in Oregon have discovered a native version of a fast-spreading variant of the coronavirus that first appeared in the UK – but now combined with a mutation that may make the variant less susceptible to vaccines.
The researchers have only found a single case of this formidable combination to date, but genetic analysis revealed that the variant was community-acquired and did not occur 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 participate in the Centers for Disease Control and Prevention efforts to track variants and have posted their results in databases shared by scientists.
The variant originally identified in the UK, named B.1.1.7, has quickly spread throughout the United States, accounting for at least 2,500 cases in 46 states. This form of the virus is both more contagious and deadly than the original version and is expected to be responsible for most infections in America in a few weeks.
The new version, which surfaced in Oregon, shares the same backbone, but also has a mutation – E484K or “Eek” – seen in variants of the virus circulating in South Africa, Brazil and New York City.
Laboratory studies and clinical studies in South Africa show that the Eek mutation makes current vaccines less effective by weakening the body’s immune response. (The vaccines are still working, but the results are worrying enough that Pfizer-BioNTech and Moderna have started testing new versions of their vaccines to defeat the variant found in South Africa.)
The B.1.1.7 variant with Eek has also appeared in the UK and has been described by scientists as a “worrying variant”. But the virus identified in Oregon appears to have evolved independently, said Dr. O’Roak.
Dr. O’Roak and colleagues found the variant among coronavirus samples collected by the Oregon State Public Health Lab across the state, including some from a health care outbreak. Of the 13 test results they analyzed, 10 turned out to be B.1.1.7 alone and one as a combination.
Other experts said the discovery wasn’t surprising given that the Eek mutation appeared in forms of the virus around the world. However, the occurrence of the mutation in B.1.1.7 is worth seeing, they said.
In the UK, this version of the variant makes up a small number of cases. By the time the combination developed there, B.1.1.7 had already spread across the country.
Updated
March 6, 2021, 10:48 p.m. ET
“We’re at the point where B.1.1.7 is just rolling out in the US,” said Stacia Wyman, a computational genomics expert at the University of California at Berkeley. “As it evolves and slowly becomes the dominant thing, it could accumulate more mutations.”
Viral mutations can reinforce 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, that is not present in the South African version.
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In a study published Thursday in Nature, the researchers compared antibody responses with all three affected variants – those identified in the UK, South Africa and Brazil. In line with other studies, they found that the variant that beat South Africa was the most resistant to antibodies produced by the immune system.
But the variant circulating in Brazil was not as resistant, despite carrying 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 say whether the Oregon variant will behave like it did in South Africa or Brazil. But the idea that other mutations might weaken Eek’s effects is “excellent news,” said Dr. Wyman.
Overall, she said, the finding in Oregon reinforces the need for people to continue taking precautions, such as wearing a mask, until a significant portion of the population is vaccinated.
“People don’t have to freak out, they just have to be vigilant,” she said. “We cannot give up our vigilance as long as these more transferrable variants are still in circulation.”
