The U.S. Has Its Own New Worrisome Variants

A new study identifies seven variants with the same concerning mutation. Lebanon, enmeshed in overlapping crises, begins its vaccination program.

A new study identifies seven U.S. virus variants with the same worrying mutation

As Americans anxiously watch the spread of coronavirus variants that were first identified in Britain and South Africa, scientists are finding a number of new variants that seem to have originated in the United States — and many of them may pose the same kind of extra-contagious threat.

In a study posted on Sunday, a team of researchers reported seven growing lineages of the coronavirus, spotted in states across the country. All have gained a mutation at the exact same spot in their genes.

“There’s clearly something going on with this mutation,” said Jeremy Kamil, a virologist at Louisiana State University Health Sciences Center and a co-author of the new study.

It’s not clear yet whether this shared mutation makes the variants more contagious, but because it appears in a gene that influences how the virus enters human cells, the scientists are highly suspicious.

“I think there’s a clear signature of an evolutionary benefit,” Dr. Kamil said.

It’s not unusual for different genetic lineages to independently evolve in the same direction. Charles Darwin recognized convergent evolution in animals. Virologists have found that it  happens with viruses too. As the coronavirus branches into new variants, researchers are observing Darwin’s theory of evolution in action every day.

It’s difficult to answer even basic questions about how prevalent the new variants are in the United States because the country sequences genomes from less than 1 percent of coronavirus test samples. The researchers found examples scattered across much of the country, but they can’t tell where they first arose.

It’s also hard to say whether the variants are spreading now because they are more contagious, or for some other reason, like holiday travel or superspreader events.

Scientists say the mutation could plausibly affect how easily the virus gets into human cells. But Jason McLellan, a structural biologist at the University of Texas at Austin who was not involved in the study, cautioned that the way that the coronavirus unleashes its harpoons was still fairly mysterious.

“It’s tough to know what these substitutions are doing,” he said of the mutations. “It really needs to be followed up with some additional experimental data.”

U.S. governors are easing restrictions, but the virus-variant news keeps getting worse.

Robert Jennings taking a saliva sample for a coronavirus test last month in Davis, Calif.
Robert Jennings taking a saliva sample for a coronavirus test last month in Davis, Calif.Credit…Max Whittaker for The New York Times

Vaccinations are picking up pace. The spread of the coronavirus in the United States has slowed drastically. The Centers for Disease Control and Prevention is urging K-12 schools to reopen safely and as soon as possible.

But just as states are again lifting mask-wearing mandates and loosening restrictions, experts fear that more contagious variants could undo all that progress.

That threat seems only to grow as researchers learn more. British government scientists now believe the more contagious variant that is ravaging Britain is also “likely” to be deadlier than earlier versions of the virus, according to a document posted on a government website on Friday. An earlier assessment on a smaller scale warned last month that there was a “realistic possibility” the variant was more lethal.

The variant, also known as B.1.1.7, is spreading rapidly in the United States, doubling roughly every 10 days, another recent study found.

In line with an earlier warning from the C.D.C., the study predicted that by March the variant could become the dominant source of coronavirus infection in the United States, potentially bringing a surge of new cases and increased risk of death.

Beyond that, scientists reported on Sunday that they have begun to spot more new variants that seem to have emerged in the U.S. and are concerned that they may spread more readily than earlier versions.

Vaccine distribution is accelerating — the U.S. is now averaging about 1.66 million doses a day, well above the Biden administration’s target of 1.5 million — but B.1.1.7 has a worrisome mutation that could make it harder to control with vaccines, a Public Health England study found this month.

The variant has spread to at least 82 countries, and is being transmitted 35 percent to 45 percent more easily than other variants in the United States, scientists recently estimated. Most people who catch the virus in Britain these days are being infected by that variant.

The British research on B.1.1.7’s lethality did come with caveats, and the reasons for the variant’s apparently elevated death rate are not entirely clear. Some evidence suggests that people infected with the variant may have higher viral loads, a feature that could not only make the virus more contagious but also potentially undermine the effectiveness of certain treatments.

But government scientists were relying on studies that examined a small proportion of overall deaths. They also struggled to account for the presence of underlying illnesses in people infected with the new variant, and for whether the cases originated in nursing homes.

Bill Hanage, an epidemiologist at Harvard University, said that although “we do need to have a degree of caution” in looking at the findings, “it’s perfectly reasonable to think that this is something serious — I am certainly taking it seriously.”

“It’s pretty clear we have something which is both more transmissible and is more worrying if people become infected,” he said.

Angela Rasmussen, a virologist at Georgetown University, said relaxing restrictions now would be “courting disaster.” She urged Americans to “be extra vigilant” about mask wearing, distancing and avoiding enclosed spaces.

“You don’t want to get any variant,” Dr. Rasmussen said, “but you really don’t want to get B.1.1.7.”

The United States confirmed its first case of the B.1.1.7 variant on Dec. 29. Unlike Britain, it has been conducting little of the genomic sequencing necessary to track the spread of new variants that have caused concern, though the Biden administration has vowed to do more.

On Friday, for the fifth time in six days, the number of new virus cases reported in the United States dipped below 100,000 — far less than the country’s peak of more than 300,000 reported on Jan. 8.As the numbes and hospitalizations has fallen, the Republican governors of Montana, Iowa, North Dakota and Mississippi have recently ended statewide mask-wearing mandates. In New York, Gov. Andrew M. Cuomo, a Democrat, has allowed indoor dining to resume at 25 percent capacity, though experts have repeatedly warned that maskless activities, such as eating, in enclosed spaces are high-risk.

Although virus case numbers are moving in the right direction, the loosening of restrictions has unnerved experts like Saskia Popescu, an epidemiologist at George Mason University in Virginia.

“Now more than ever, with novel variants, we need to be strategic with these reopening efforts and be slow and not rush things,” she said.Coronavirus Variants and MutationsTracking recent mutations, variants and lineages.

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