NEW YORK (AP) – Despite its world-class medical system and renowned Centers for Disease Control and Prevention, the United States has lagged behind in the race to detect dangerous mutations in the coronavirus. And only now is it starting to catch up.
The problem has not been the lack of technology or expertise. Rather, scientists say, it is a lack of national leadership and coordination, in addition to a lack of funding and supplies for overloaded labs trying to juggle diagnostic testing with the search for genetic changes.
“We have the brain. We have the tools. We have the tools, ”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 constantly mutate. To stay ahead of the threat, scientists analyze the samples, watching closely for mutations that could make the coronavirus more infectious or deadly.
But these tests have been scattered.
Less than 1% of positive specimens in the U.S. are being sequenced to determine if they have worrying mutations. Other countries do better (UK sequences around 10%), which means they can see threats more quickly. This gives them more opportunities to slow down or stop the problem, either through more specific contact tracking, possible vaccine adjustments, or public notices.
CDC officials say the variants have not caused recent growth in general cases in the U.S. But experts worry that what is happening with the variants is unclear and say the nation should have been more aggressive about the previous sequencing of the epidemic that has now killed more than 450,000 Americans.
“If we had evidence that it was changing,” said Dan Jones, a molecular biologist from the state of Ohio, “maybe people would have acted differently.”
U.S. scientists have detected more than 500 cases of a variant first identified in Britain and expect it to be the cause of most of the country’s new infections in a matter of weeks. Another worrying variant linked to Brazil and a third discovery in South Africa were detected last week in the US and are also expected to spread.
The British variant is more contagious and is thought to be more deadly than the original, while the South African one may make the vaccines a little less effective. The ultimate fear is that a variant resistant to existing vaccines and treatments may eventually emerge.
Potentially troubling versions may also be formed in the United States. “This virus is mutating and it doesn’t matter in Idaho or South Africa,” Messaoudi said.
But the true dimensions of the problem in the US are unclear due to the relatively low level of sequencing.
“You just see what’s under the lantern,” said Kenny Beckman, director of the University of Minnesota Genomics Center, which began analyzing the virus’s genetics last spring.
After the slow start, public health labs in at least 33 states are doing genetic testing to identify emerging variants of coronavirus. Other states have established partnerships with university or private labs to do the work. North Dakota, which began sequencing last week, was the most recent to begin this 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 properly monitor variants, said Gregory Armstrong, who oversees the agency’s advanced molecular screening work. And it is only now that the nation reaches this level, he acknowledged.
Still, it’s a mix of approaches: some public health labs sequence all specimens of positive viruses. Some focus on samples from certain outbreaks or from certain patients. Others select samples at random for analysis.
In addition, laboratories continue to have trouble obtaining the necessary supplies, such as pipette tips and chemicals, which are used in both gene sequencing and diagnostic testing.
President Joe Biden, who inherited the Trump administration’s setup, is proposing a $ 1.9 trillion COVID-19 relief package calling for increased federal spending on virus sequencing, though the amount is not ‘detailed and no other specific data has been worked out yet. out.
“We are 43rd in the world in genomic sequencing. Totally unacceptable, “said Jeff Zients, White House coronavirus response coordinator.
For more than five years, U.S. public health labs have been consolidating their ability to do genomic sequencing, thanks in large part to a federal push toward zero in the sources of food poisoning outbreaks.
At the beginning of the pandemic, some laboratories began sequencing the coronavirus immediately. The Minnesota Department of Health, for example, began doing so within weeks of the first COVID-19 cases in March, said Sara Vetter, assistant laboratory director. “That moved us forward,” he said.
The CDC also worked with certain states to sequence about 500 samples in April and more than a thousand samples in May and June.
But many labs did not do the same, especially those with an overload of coronavirus diagnostic tests. Armstrong, of the CDC, said that at the time, he could not justify the laboratories doing more sequencing when they already had their hands full and there was no evidence that it was necessary.
“Until a month ago, it was not on the list of things that were urgently needed. It was nice to have that, ”said scientist Trevor Bedford at the Fred Hutchinson Cancer Research Center in Seattle. “There was definitely a lack of allocated federal resources to do exactly that.”
At the same time, due to home stay orders imposed during the outbreak, researchers at some labs were told not to go to work, Messaoudi said.
“Instead of making a call to arms,” he said, “they sent everyone home.”
But during the summer, a group of scientists sounded the alarm on the state of genomic surveillance in the US and began to push for something more systematic.
In November, the CDC began rolling out a national program to remove and more methodically review specimens to better determine which strains are circulating. In December, the United States received a wake-up call when British researchers announced that they had identified a variant that appears to be spreading more easily.
The CDC reacted by announcing that its surveillance program would increase to processing 750 samples nationwide per week. The agency also hired three companies – LabCorp, Quest Diagnostics and Ilumina – to sequence thousands more each week. State labs make thousands of them.
Meanwhile, the outbreak is almost certain to sow more COVID-19 mutations.
“Wherever you have free income from the site, there will be significant variants that will evolve,” said Dr. Eric Topol, a scientist at the Scripps Research Institute. “The more genomic sequencing, the more we can stay ahead of the virus.”
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The Associated Press Health and Science Department is supported by the Howard Hughes Medical Institute’s Department of Science Education. The AP is solely responsible for all content.