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CDC: No sign of homegrown U.S. coronavirus variant, but scientists need to look harder

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Infectious-disease experts say there is no evidence the massive winter surge that is killing thousands of people a day in the United States is linked to the U.K. variant or to a homegrown strain. But they acknowledge their battlefield awareness is limited.

Some states have minimal capacity to conduct genomic sequencing that allows scientists to trace the random mutations that could give a virus variant some advantage over other strains. Like any virus, this one mutates randomly, and countless variants are in circulation.

The increase in the rate of new infections in the United States has been so rapid in recent weeks that scientists cannot rule out the possibility that an undetected variant is accelerating the spread. Other factors may be behind the surge, including holiday gatherings and the lack of adherence in some communities to public health guidelines designed to limit transmission, such as social distancing and wearing masks.

“It could be — a possibility — that we have our own mutant that’s being more easily transmissible,” Anthony S. Fauci, director of the National Institute of Allergy and Infectious Diseases, said Monday. “We don’t know. We’re looking for it. . . . If you look at the slope of our curve, which is very steep, it looks a bit like the curve in the U.K.”

Nearly 198,000 new coronavirus cases and more than 1,600 deaths were reported Monday in the United States. The seven-day running average for daily deaths has topped 3,200. Nearly 375,000 people have died of the virus in the nation since the beginning of the pandemic.

Officials in Indiana announced that the U.K. variant has been identified in their state. More than 60 cases of the variant strain have been identified across nine states since it was first detected stateside two weeks ago in Colorado.

Indiana State Health Commissioner Kristina Box said in a statement Monday that viruses commonly mutate and that the best defense is to practice good hygiene and social distancing.

“Because this strain of the virus can be transmitted more easily, it’s more important than ever that Hoosiers continue to wear their masks, practice social distancing, maintain good hygiene and get vaccinated when they are eligible,” Box said.

The Centers for Disease Control and Prevention said Monday its strain surveillance program and its partners are on track to more than double by week’s end the number of genomic sequences being uploaded to public databases compared with the sequencing rate in December. The CDC has organized virtual meetings with scientists and public health experts in an attempt to share information about variants of the virus in circulation.

“The general consensus is there’s no single variant driving current U.S. cases. That said, we need to be on the lookout for these variants of concern,” Duncan MacCannell, chief science officer with the CDC’s Office of Advanced Molecular Detection, said Monday.

Other scientists share that view.

“We don’t see any evidence of a particular variant ‘out running’ others,” Kristian Andersen, an immunologist at the Scripps Research Institute, said in an email. “That’s not to say there isn’t one, but we haven’t seen any evidence of it so far and we are looking, just not enough.”

William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health, said in an email that “surveillance is such that we’d not detect any such variant until it was already emerged and well established.”

MacCannell estimated that less than 0.5 percent of current transmission in the United States involves the U.K. variant, known as B.1.1.7. It has a suite of 17 mutations, including eight that affect the spike protein on the surface of the virus. British scientists believe it could be roughly 50 percent more transmissible than the more common coronavirus, which itself contains a mutation that appears to have boosted infectivity.

MacCannell said he expects that B.1.1.7 in coming weeks will make up a greater proportion of cases but said the pace and scale of that emergence is impossible to predict.

Scientists emphasize that these mutations do not appear to change the severity of covid-19, the disease caused by the virus. There are multiple lines of evidence supporting the theory that this variant is more transmissible, but no evidence it is deadlier. One study published in Britain found no statistically significant difference in the rate of hospitalization among people infected with the new variant as opposed to the more common coronavirus strain.

But even if the variant doesn’t make an individual sicker, its increased transmissibility could result in more people becoming infected and, thus, increase deaths overall.

“Are the variants that are out there escaping the protection of the vaccine? Yes or no? That’s what they’re working on right now,” Fauci said, referring to scientists funded by his institute. “I need that answer and I need it very quickly.”

Another uncertainty is whether monoclonal antibodies used as therapeutic treatments will be effective against viruses that contain alterations to the portion of the spike protein targeted by those antibodies.

The maker of another medication used by some doctors to treat the coronavirus, remdesivir, said it is likely to be effective against variant strains, the CEO of that company said Monday.

Gilead Sciences is testing the drug on variants first detected in Britain and South Africa to determine its efficacy. Gilead has already found in laboratory tests that remdesivir maintains its effectiveness against 2,000 coronavirus strains, chief executive Daniel O’Day said.

“Remdesivir works at the source in the cell where the virus replicates, and what we know is, in these new variants, that part of the cell is not changing at all, in fact,” O’Day said Monday during an interview on CNBC’s “Squawk Box.”

Hospitalized patients with covid-19 can receive remdesivir, which may shorten their recovery time. The Food and Drug Administration approved the drug last year, under an emergency use authorization.

The virus will continue to mutate and, through natural selection, evolve, a fact that does not surprise the scientific community but has taken on new salience amid the recent bulletins about problematic variants.

“I think there is a high level of concern,” MacCannell said, referring to the views of the scientific community. “We don’t know fully the functional implications of these mutations. . . . I would suspect a lot of the mutations that we’re seeing are helping to optimize the virus for increased transmission.”

The rollout of vaccines, he said, “will be another set of pressures on the virus. That is one of the critical reasons why we need to get large-scale national monitoring up and running.”

Andersen said the U.K. variant and another identified initially in South Africa probably will become dominant in the United States within months. “Our mitigation efforts are woefully insufficient to deal with those,” he warned.

That’s a conundrum for policymakers. There are few officials with any appetite for greater restrictions on businesses and personal mobility, even with variants posing a new challenge. But what has happened in the United Kingdom — where much of the country is locked down — is sobering.

There are more than 1 million new infections every week in the United States, and scientists at scattered universities and research institutions are looking at only a few thousand genomic sequences weekly. The CDC is putting out contracts to academic and research institutions in an effort to push that to a goal of 6,500 weekly sequences.

“This is a brand-new virus. We’re learning as we go. There are the unknown unknowns that we have to acknowledge,” said Jeremy Luban, a virologist at the University of Massachusetts Medical School. “We’re all working on this around-the-clock.”

Fauci said it is critical to suppress the spread of the virus, given that a high number of infections leads to a greater number of chances for mutations.

“The race is to suppress the virus before it mutates to the point where it’s actually going to give you trouble,” Fauci said. “I don’t worry about these things, I just take them very seriously.”

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