NEW YORK (AP) – Despite its world-class medical system and prestigious 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 he starting to catch up.
The problem was not the lack of technology or expertise. Rather, scientists say, there is a lack of national leadership and coordination, plus a lack of funding and supply for overloaded labs trying to juggle diagnostic tests for genetic modification.
“We have a 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 this effort.”
Viruses move constantly. To stay ahead of the threat, scientists are analyzing the evidence, looking closely for mutations that could make the coronavirus more infectious or deadly.
But such tests have disappeared.
Less than 1% of positive specimens in the US are sequenced to determine if they have worrying mutations. Other countries are doing better – the UK sequence is around 10% – which means they can see threats coming at them faster. This gives them more opportunities to slow down or stop the problem, either by tracking contacts more closely, possible vaccine adjustments, or public warnings.
CDC officials say the variations have not led to recent increases in all cases in the United States. But experts worry that what is happening with the variants is not clear and say the nation should have been more aggressive in sequencing earlier the epidemic that has 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.”
U.S. scientists have detected more than 500 cases of a variant first identified in the UK and it is expected to become the cause of most of the country’s new infections in a few weeks. Another worrying variant related to Brazil and the third discovered in South Africa were detected last week in the USA and are also expected to spread.
The British version is more contagious and is thought to be more deadly than the original, while the South African version may make vaccines somewhat less effective. The ultimate fear is that a variant resistant to existing vaccines and treatments could eventually emerge.
Potentially worrying versions may also be formed in the US. “This virus is mutant and doesn’t care if it’s in Idaho or South Africa,” Messaoudi said.
But the true dimensions of the US problem are unclear due to the relatively low level of sequencing.
“You just see what’s under the traffic light,” said Kenny Beckman, director of the University of Minnesota’s Genomics Center, which began analyzing the virus’s genetics last spring.
After a slow start, public health laboratories in at least 33 states are now doing genetic testing to identify emerging variants of coronavirus. Other states have formed partnerships with university or private laboratories to do the job. North Dakota, which began sequencing last week, was the most recent to begin that work, according to the Association of Public Health Laboratories.
The CDC estimates that a minimum of 5,000 to 10,000 samples should be analyzed weekly in the United States to adequately monitor variants, said Gregory Armstrong, who oversees the activity of the advanced molecular detection agency. And only now is the nation reaching that level, he acknowledged.
However, it is a mixture of approaches: Some public health laboratories sequence each virus specimen positively. Some focus on samples from certain outbreaks or from certain patients. Others randomly select samples for analysis.
In addition, laboratories continue to have problems obtaining the necessary consumables – such as pipette tips and chemicals – used in both gene sequencing and diagnostic testing.
President Joe Biden, who inherited the setting from the Trump administration, is proposing a $ 1.9 trillion COVID-19 aid package calling for increased federal spending on virus sequencing, although the amount has not been detailed and no other plans have been developed specificities. outside.
“We are 43 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 strengthened their ability to perform genomic sequencing, largely due to zero federal action on food poisoning sources.
At the beginning of the pandemic, some laboratories immediately began sequencing the coronavirus. The Minnesota Department of Health, for example, began doing so within weeks of its first cases of COVID-19 in March, said Sara Vetter, assistant laboratory director. “That took us one step further,” she said.
The CDC also worked with some states to sequence nearly 500 samples in April and more than a thousand samples in May and June.
But many labs have not done the same – especially those overloaded with accelerating coronavirus diagnostic tests. CDC’s Armstrong said at the time, he couldn’t justify telling labs to do more sequencing when they already had their hands full and there was no evidence needed for such an analysis.
“Until a month ago, it was not on the list of things that are urgently needed. It was fun, “said Trevor Bedford, a scientist at the Fred Hutchinson Cancer Research Center in Seattle. “The federal resources allocated to do just that have certainly been lacking.”
At the same time, because of house arrest orders imposed during the outbreak, researchers in some laboratories were told not to go to work, Messaoudi said.
“Instead of using weapons,” she said, “they sent everyone home.”
During the summer, however, a group of scientists sounded the alarm about the state of genomic surveillance in the US and began to push for something more systematic.
In November, the CDC began launching a national program to shoot and check samples more methodically to better determine which strains are circulating. Then, in December, the US received a wake-up call when British researchers announced that they had identified a variant that seems to be spreading more easily.
The CDC responded by announcing that its surveillance program would expand to 750 samples nationwide per week. The agency has also contracted with three companies – LabCorp, Quest Diagnostics and Ilumina – to sequence thousands more each week. State laboratories make their own thousands.
Meanwhile, the outbreak is certainly seeded several COVID-19 mutations.
“Where there is free rein, there will be significant variations that will evolve,” said Dr. Eric Topol, a scientist at the Scripps Research Institute. “The more genomic the sequencing, the more we can stay in front of the virus.”
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