NEW YORK (AP) – Despite its world-class medical system and the acclaimed Centers for Disease Control and Prevention, the US was left behind in the race to detect dangerous mutations in the coronavirus. And it is only now starting to catch up.
The problem is not a lack of technology or expertise. Rather, scientists say it’s a lack of national leadership and coordination, plus a lack of funding and supplies for overburdened labs trying to combine diagnostic testing with the hunt for genetic changes.
‘We have the brains. 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 are constantly mutating. To stay ahead of the threat, scientists are analyzing samples and watching closely for mutations that could make the coronavirus more contagious or deadly.
But such tests have been scattered.
Less than 1% of positive specimens in the US are sequenced to determine if they have mutations of concern. Other countries are doing better – Britain strings about 10% – meaning they can spot threats more quickly. That gives them a better chance to slow down or stop the problem, be it more targeted contact tracking, possible vaccine modifications, or public alerts.
CDC officials say variants have not led to recent spikes in general US cases. But experts worry that it’s not clear what’s happening with variants, saying the nation should have been more aggressive about sequencing earlier in the epidemic that now killed more than 450,000 Americans.
“If we had evidence that it was changing,” said Ohio state molecular biologist Dan Jones, “maybe people would have acted differently.”
US scientists have discovered more than 500 cases of a variant first identified in Britain and expect it to become the cause of most of the new infections in this country within weeks. Another disturbing variant related to Brazil and a third discovered in South Africa was discovered in the US last week and is also expected to spread.
The British variant is more contagious and believed to be more deadly than the original, while the South African variant can make the vaccines slightly less effective. The ultimate fear is that a variant may eventually emerge that is resistant to existing vaccines and treatments.
Versions of concern can also occur in the US. “This virus is mutating, and he doesn’t care if it’s in Idaho or South Africa,” Messaoudi said.
But the true dimensions of the problem in the US are not clear due to the relatively low sequence level.
“You only see what’s under the lamppost,” said Kenny Beckman, director of the University of Minnesota Genomics Center, which began analyzing the genetics of the virus last spring.
After the slow start, public health laboratories in at least 33 states are now conducting genetic analyzes to identify emerging coronavirus variants. Other states have partnerships with university or private laboratories to do the work. According to the Association of Public Health Laboratories, North Dakota, which began sequencing last week, was the most recent to begin that work.
The CDC believes that in the US, a minimum of 5,000 to 10,000 samples should be analyzed weekly to monitor variants adequately, said Gregory Armstrong, who oversees the agency’s advanced molecular detection work. And it is only now that the nation is reaching that level, he acknowledged.
Still, it’s a jumble of approaches: Some public health labs sequence every positive virus sample. Some focus on samples from specific outbreaks or specific patients. Others randomly select samples to analyze.
In addition, laboratories continue to struggle to obtain the necessary supplies – such as pipette tips and chemicals – that are used in both gene sequencing and diagnostic testing.
President Joe Biden, who inherited the Trump administration’s setup, proposes a $ 1.9 trillion COVID-19 aid package calling for an increase in federal spending on sequencing the virus, although the amount is not detailed and there are other details to be worked out. from.
“We are 43rd in the world in genomic sequencing. Absolutely unacceptable, ”said Jeff Zients, White House coronavirus coordinator.
For more than five years, U.S. public health laboratories have been building their ability to perform genomic sequencing, thanks in large part to a federal push to seek out the sources of food poisoning.
At the start of the pandemic, some laboratories immediately started sequencing the coronavirus. The Minnesota Department of Health, for example, started doing this within weeks of the first COVID-19 cases in March, said Sara Vetter, an assistant laboratory director. “That took us a step forward,” she said.
The CDC also worked with certain states to sequence nearly 500 samples in April and more than a thousand samples in May and June.
But many labs didn’t do the same – especially those labs that were overloaded with speeding up diagnostic tests for the coronavirus. The CDC’s Armstrong said at the time he couldn’t justify telling labs to do more sequencing if they already had their hands full and there was no evidence that such analysis was needed.
“Until a month ago, it was not on the urgent need list. It was nice to have, ”said Trevor Bedford, a scientist at the Fred Hutchinson Cancer Research Center in Seattle. “There was definitely a lack of federal resources to do just this.”
At the same time, researchers from some labs were told not to go to work because they ordered to stay home during the outbreak, Messaoudi said.
“Instead of being summoned,” she said, “they sent everyone home.”
But during the summer, a group of scientists raised the alarm about 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 more methodically collect and monitor samples to better determine which strains are circulating. In December, the US was shaken when British researchers announced they had found a variant that appears to spread more easily.
The CDC responded by announcing that its surveillance program would scale up to process 750 samples per week nationally. The agency also contracted three companies – LabCorp, Quest Diagnostics and Ilumina – to add thousands every week. State laboratories do thousands of their own.
Meanwhile, the outbreak is almost certainly seeding more COVID-19 mutations.
“Where it has free rein, there will be significant variants that evolve,” said scientist Dr. Eric Topol from the Scripps Research Institute. “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 is supported by the Science Education Department of the Howard Hughes Medical Institute. The AP is solely responsible for all content.