NEW YORK -- Despite its world-class medical system and its vaunted Centers for Disease Control and Prevention, the U.S. fell behind in the race to detect dangerous coronavirus mutations. And it's only now beginning to catch up.
The problem has not been a shortage of technology or expertise. Rather, scientists say, it's an absence of national leadership and coordination, plus a lack of funding and supplies for overburdened laboratories trying to juggle diagnostic testing with the hunt for genetic changes.
"We have the brains. We have the tools. We have the instruments," said Ilhem Messaoudi, director of a virus research center at the University of California, Irvine. "It's just a matter of supporting that effort."
Viruses mutate constantly. To stay ahead of the threat, scientists analyze samples, watching closely for mutations that might make the coronavirus more infectious or more deadly.
But such testing has been scattershot.
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Less than 1% of positive specimens in the U.S. are being sequenced to determine whether they have worrisome mutations. Other countries do better -- Britain sequences about 10% -- meaning they can more quickly see threats coming at them. That gives them greater opportunity to slow or stop the problem, whether through more targeted contact tracing, possible adjustments to the vaccine, or public warnings.
On Thursday, coronavirus deaths in the United States surpassed 455,000, and daily deaths remain stubbornly high at more than 3,000 a day, despite falling infections and the arrival of multiple vaccines.
Infectious disease specialists expect deaths to start dropping soon, after new cases hit a peak right around the beginning of the year. New covid-19 deaths could ebb as early as next week, said the new director of the CDC.
But there's also the risk that improving trends in infections and hospitalizations could be offset by people relaxing and coming together -- including this Sunday, to watch football, she added.
"I'm worried about Super Bowl Sunday, quite honestly," Dr. Rochelle Walensky said Thursday.
Walensky said one reason cases and hospitalizations are not rising as dramatically as they were weeks ago is because the effect of holiday gatherings has faded.
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The effect on deaths is delayed. The daily toll amounts to 50,000 new fatalities in the past two weeks alone.
"We're still in quite a bad place," she said.
CDC officials say variants have not driven recent surges in overall U.S. cases. But experts worry that what's happening with variants is not clear and say the nation should have been more aggressive about sequencing earlier in the epidemic.
"If we had evidence it was changing," said Ohio State molecular biologist Dan Jones, "maybe people would've acted differently."
U.S. scientists have detected more than 500 cases of a variant first identified in Britain and expect it to become the cause of most of this country's new infections in a matter of weeks. Another troubling variant tied to Brazil and a third discovered in South Africa were detected last week in the U.S. and also are expected to spread.
The British variant is more contagious and is believed to more deadly than the original, while the South Africa one may render the vaccines somewhat less effective. The ultimate fear is that a variant resistant to existing vaccines and treatments could eventually emerge.
Potentially worrisome versions may form inside the U.S., too. "This virus is mutating, and it doesn't care of it's in Idaho or South Africa," Messaoudi said.
But the true dimensions of the problem in the U.S. are not clear because of the relatively low level of sequencing.
"You only see what's under the lamppost," said Kenny Beckman, director of the University of Minnesota Genomics Center, which started analyzing the virus's genetics last spring.
A JUMBLE OF APPROACHES
After the slow start, public health labs in at least 33 states are now doing genetic analysis to identify emerging coronavirus variants. Other states have formed partnerships with university or private labs to do the work. North Dakota, which began sequencing last week, was the most recent to start that work, according to the Association of Public Health Laboratories.
The CDC believes a minimum of 5,000 to 10,000 samples should be analyzed weekly in the U.S. to adequately monitor variants, said Gregory Armstrong, who oversees the agency's advanced molecular detection work. And it's only now that the nation is hitting that level, he acknowledged.
Still, it is a jumble of approaches: Some public health labs sequence every positive virus specimen. Some focus on samples from certain outbreaks or certain patients. Others randomly select samples to analyze.
On top of that, labs continue to have trouble getting needed supplies -- like pipette tips and chemicals -- used in both gene sequencing and diagnostic testing.
President Joe Biden, who inherited the setup from the Trump administration, is proposing a $1.9 trillion covid-19 relief package that calls for boosting federal spending on sequencing of the virus, though the amount has not been detailed and other specifics have yet to be worked out.
"We're 43rd in the world in genomic sequencing. Totally unacceptable," White House coronavirus response coordinator Jeff Zients said.
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For more than five years, U.S. public health labs have been building up their ability to do genomic sequencing, thanks largely to a federal push to zero in on the sources of food poisoning outbreaks.
At the pandemic's outset, some labs began sequencing the coronavirus right away. The Minnesota Department of Health, for example, started doing so within weeks of its first covid-19 cases in March, said Sara Vetter, an assistant lab director. "That put us a step ahead," she said.
The CDC likewise worked with certain states to sequence close to 500 samples in April, and more than a thousand samples in May and June.
But many labs didn't do the same -- especially those overburdened with ramping up coronavirus diagnostic testing. The CDC's Armstrong said that at the time, he couldn't justify telling labs to do more sequencing when they already had their hands full and there wasn't any evidence such analysis was needed.
"Up until a month ago, it wasn't on the list of things that are urgently necessary. It was nice to have," said Trevor Bedford, a scientist at the Fred Hutchinson Cancer Research Center in Seattle. "There was definitely lack of federal resources assigned to doing exactly this."
ONE-SHOT VACCINE SEEKS OK
Separately, Johnson & Johnson asked U.S. regulators Thursday to clear the world's first single-dose covid-19 vaccine, an easier-to-use option that could boost scarce supplies.
J&J's vaccine was safe and offered strong protection against moderate to severe covid-19, according to preliminary results from a massive international study.
It didn't appear quite as strong as the two-dose competitors made by Pfizer and Moderna -- a finding that may be more perception than reality, given differences in how each was tested.
But the Food and Drug Administration is asking its independent advisers to publicly debate all the data behind the single-dose shot -- just like its competitors were put under the microscope -- before it decides whether to green-light a third vaccine option in the U.S. The panel will meet Feb. 26.
Overall, the single-dose vaccine was 66% effective at preventing moderate to severe covid-19, according to early findings from a study of 44,000 people in the U.S., Latin America and South Africa.
But it was 85% protective against the most serious symptoms -- and starting 28 days after their shot, researchers found no one who got the vaccine needed hospitalization or died.
The one-dose option worked better in the U.S. -- 72% effective against moderate to severe covid-19 -- compared with 66% in Latin America and 57% in South Africa.
Also Thursday, a CDC study found that gay, lesbian and bisexual Americans are more prone to have underlying health conditions that could put them at higher risk of severe covid-19.
Researchers had difficulty collecting data on those groups, and the CDC is now recommending that public health departments begin tracking the effects of covid-19 on what the study refers to as sexual minority populations.
In November, the CDC gathered advocacy and health care organizations in listening sessions across the United States and discovered "major concern" was widespread throughout the LGBT community that information about sexual orientation and gender identity is not standard in covid-19 data collection systems.
"This data gap underscores the need to extend covid-19 surveillance and other studies to include measures of sexual orientation and gender identity," the study concludes.
The analysis found that multiple underlying conditions -- including asthma, cancer, heart disease, COPD, hypertension, kidney disease, smoking, obesity and stroke -- are more prevalent among lesbian, gay and bisexual individuals than heterosexual men and women, in the overall population as well as within specific racial and ethnic groups.
Researchers looked at 11 underlying conditions that could lead to more severe cases of covid-19. "None of the 11 conditions studied was more prevalent among heterosexual persons than among members of sexual minority groups," the study said.
Underlying health conditions among sexual minorities within the Black and Hispanic populations -- communities that have already been disproportionately affected by the coronavirus pandemic -- "is of particular concern," the study said.
"Persons who are members of both sexual minority and racial/ethnic minority groups might therefore experience a convergence of distinct social, economic, and environmental disadvantages that increase chronic disease disparities and the risk for adverse covid-19-related outcomes," the study said.
MASKS STILL AT ISSUE
Meanwhile, Wisconsin Gov. Tony Evers issued a new statewide mask order Thursday, an hour after the Republican-controlled Legislature voted to repeal his previous mandate saying he didn't have authority to make such a decree.
Evers and the Legislature have been at odds throughout the pandemic but the latest moves created an unprecedented level of whiplash. Republican lawmakers last year persuaded the state Supreme Court to scrap Evers' stay-at-home order and a state appeals court halted the limits he placed on indoor gatherings.
As the Legislature moved to repeal the order, many cities and counties rushed to enact or extend local mask ordinances. Milwaukee and Dane County, where Madison is located, are among those with orders in place.
The Democratic governor said in a video message that his priority is keeping people safe and that wearing a mask is the most basic way to do that.
"If the Legislature keeps playing politics and we don't keep wearing masks, we're going to see more preventable deaths, and it's going to take even longer to get our state and our economy back on track," Evers said.
Republican state Sen. Steve Nass, who led the push to repeal the order, accused Evers of being a "lawless governor." Nass said he was drafting another resolution to repeal the new order and was considering asking the Wisconsin Supreme Court to take emergency action.
The Supreme Court could end the legislative back-and-forth with a ruling in a pending case that says Evers must secure lawmakers' approval every 60 days. The court could also say he doesn't need approval, forcing the Legislature to repeal every order Evers issues if it wants to stop him.
The attorney who argued in the case to undo Evers' order, Rick Esenberg, said, "It is now incumbent upon the courts to rein in this abuse of power."
Information for this article was contributed by Mike Stobbe, Marion Renault, Michelle R. Smith, Amy Taxin, Tamara Lush, Lauran Neergaard and Scott Bauer of The Associated Press; and by Michael Wilner of the McClatchy Washington Bureau.
