NEW YORK (AP) – Despite its world-class medical system and its vaunted Centers for Disease Control and Prevention, the United States has lagged behind in the race to detect dangerous coronavirus mutations. And it is only now beginning to recover.
The problem was not a lack of technology or experience. Instead, say the scientists, it is the lack of national leadership and coordination, as well as the lack of funding and supplies for overworked laboratories that try to reconcile diagnostic tests 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 is just a matter of supporting this effort.”
Viruses mutate constantly. To stay ahead of the threat, scientists analyze samples, watching closely for mutations that can make the coronavirus more infectious or more deadly.
But these tests have been dispersed.
Less than 1% of positive samples in the USA are being sequenced to determine whether they have worrying mutations. Other countries do better – Britain sequences about 10% – which means they can see threats reaching them more quickly. This gives them more opportunity to lessen or stop the problem, whether through more targeted contact tracking, possible adjustments to the vaccine or public warnings.
CDC officials say the variants have not sparked recent outbreaks in general US cases. But experts fear that what is happening with the variants is unclear and say the country should have been more aggressive about sequencing at the beginning of the epidemic that has killed more than 450,000 Americans.
“If we had evidence that he was changing,” said Ohio state molecular biologist Dan Jones, “maybe people would have acted differently.”
American scientists have detected more than 500 cases of a variant first identified in Britain and expect it to become the cause of most new infections in the country in a matter of weeks. Another worrying variant linked to Brazil and a third discovery in South Africa were detected last week in the United States and are also expected to spread.
The British variant is more contagious and is believed to be more deadly than the original, while that of South Africa may make vaccines a little less effective. The final fear is that a variant resistant to existing vaccines and treatments may eventually emerge.
Potentially worrisome versions may also form within the United States. “This virus is mutating and does not care about it in Idaho or South Africa,” said Messaoudi.
But the real dimensions of the problem in the US are unclear due to the relatively low level of sequencing.
“You only see what’s under the pole,” said Kenny Beckman, director of the Genomics Center at the University of Minnesota, who started analyzing the virus’s genetics last spring.
After the slow start, public health laboratories in at least 33 states are now carrying out genetic analyzes to identify emerging variants of the coronavirus. Other states have entered into partnerships with universities or private laboratories to do the job. North Dakota, which started sequencing last week, was the most recent to begin this work, according to the Association of Public Health Laboratories.
The CDC believes that 5,000 to 10,000 samples should be analyzed weekly in the United States to properly monitor the variants, said Gregory Armstrong, who oversees the agency’s advanced molecular detection work. And only now is the nation reaching that level, he acknowledged.
Still, it is a confusion of approaches: some public health laboratories sequence each positive virus sample. Some focus on samples from certain outbreaks or from certain patients. Others select samples at random to analyze.
In addition, laboratories continue to struggle to obtain the necessary supplies – such as pipette tips and chemicals – used for both gene sequencing and diagnostic testing.
President Joe Biden, who inherited the configuration of the Trump administration, is proposing a $ 1.9 trillion COVID-19 aid package that calls for increased federal spending on virus sequencing, although the figure has not been detailed and other details have yet to be worked out.
“We are in 43rd place in the world in genomic sequencing. Totally unacceptable, ”said Jeff Zients, White House coronavirus response coordinator.
For more than five years, public health laboratories in the United States have been developing their ability to perform genomic sequencing, largely thanks to a federal effort to zero out sources of food poisoning outbreaks.
At the beginning of the pandemic, some laboratories began to sequence the coronavirus immediately. The Minnesota Department of Health, for example, started doing this weeks after its first COVID-19 cases in March, said Sara Vetter, assistant director of the lab. “It put us a step ahead,” she said.
But other labs have not done the same – especially those overwhelmed by the intensification of coronavirus diagnostic tests. Armstrong of the CDC said that at the time, he could not justify telling the labs to do more sequencing when they were already busy and there was no evidence that such an analysis was necessary.
“Until a month ago, it was not on the list of things that are urgently needed. It was nice to have, “said Trevor Bedford, a scientist at Fred Hutchinson Cancer Research Center in Seattle.” There was definitely a lack of federal resources assigned to do just that. “
At the same time, because of home stay orders imposed during the outbreak, researchers at some laboratories were told not to work, said Messaoudi.
“Instead of having a call to arms,” she said, “they sent everyone home.”
During the summer, however, a group of scientists raised the alarm about the state of genomic surveillance in the United States and began to push for something more systematic.
In November, CDC began to launch a national program to methodically extract and verify samples to better determine which strains are circulating. Then, in December, the United States was alerted when British researchers announced that they had identified a variant that appears to spread more easily.
The CDC responded by announcing that its surveillance program would increase to process 750 samples per week across the country. The agency also signed a contract with three companies – LabCorp, Quest Diagnostics and Ilumina – to sequence thousands more each week. State laboratories are making thousands on their own.
Meanwhile, the outbreak is almost certainly sowing more COVID-19 mutations.
“Where there’s free rein in the place, there will be significant variants that evolve,” said Scripps Research Institute scientist Dr. Eric Topol. “The more genomic sequencing, the more we can stay ahead of the virus.”
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The Associated Press Department of Health and Science receives support from the Howard Hughes Medical Institute’s Department of Science Education. The AP is solely responsible for all content.
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