U.S. is rushing to catch up with competition to detect mutant COVID-19 mutant

Despite its world-class medical system and its pride Centers for Disease Control and Prevention, U.S. lags behind competition to detect danger Coronavirus mutation. And it’s just starting to catch up.

The problem was not a lack of skill or expertise. Rather, scientists say it is a lack of funding and supply for overloaded laboratories trying to reconcile the search for genetic changes with diagnostic tests, in addition to the lack of national leadership and coordination. I will.

“We have the brain, we have the tools, we have the equipment,” said Ilhem Messaoudi, director of the Virus Research Center at the University of California, Irvine. “It’s a matter of supporting that effort.”

The virus is constantly mutating. To stay ahead of the threat, scientists analyze the sample and carefully monitor for mutations that can make the coronavirus more infectious or deadly.

However, such tests are scattered.

Less than 1% of positive samples in the United States are sequenced to determine if there are mutations of interest. Other countries work better — United Kingdom The sequence is about 10%. In other words, you can see more quickly that a threat is imminent. This gives you more opportunities to delay or stop the problem through more targeted contact tracing. vaccine, Or a public warning.

On Tuesday, February 2, 2021, a man wearing a mask against coronavirus passed an NHS advertisement for COVID-19 in London. (AP photo / Alastair Grant)

CDC officials say variants have not caused a recent surge in cases across the United States. But experts are concerned that it’s unclear what’s happening in the variant, and the country is more aggressive about sequencing early in the epidemic, which is currently killing more than 450,000 Americans. It says it should have been.

“People would have behaved differently if there was evidence that it was changing,” said Dan Jones, a molecular biologist at Ohio State University.

US scientists have detected more than 500 cases of the first identified variant in the UK and expect it to be the cause of most of the country’s new infectious diseases within a few weeks.Another nasty variant associated with Brazil And the third was found in South Africa It was detected in the United States last week and is expected to spread again.

The British variant is highly contagious and is considered more deadly than the original variant, but in South Africa the vaccine may be slightly less effective. The ultimate fear is that mutants that are resistant to existing vaccines and therapies may eventually emerge.

Potentially interesting versions may form in the United States as well. “The virus is mutated and I don’t care if it’s in Idaho or South Africa,” said Mesaoudi.

However, the relatively low level of sequencing makes the true side of the US problem unclear.

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“We can only see what’s under the streetlight,” said Kenny Beckman, director of the University of Minnesota Genomics Center, who began analyzing the genetics of the virus last spring.

After the slow start, public health laboratories in at least 33 states are currently conducting genetic analysis to identify new coronavirus variants. Other states have partnerships with universities and private laboratories to do their jobs. North Dakota, which launched the sequence last week, was the latest to begin its work, according to the Association of Public Health Institutes.

The CDC believes that 5,000 to 10,000 samples need to be analyzed weekly in the United States to properly monitor variants, said Gregory Armstrong, who oversees the agency’s advanced molecular detection work. And he admitted that the country has only reached that level now.

Still, it’s a mess of approaches: some public health laboratories sequence all positive virus specimens. Some people focus on samples from specific outbreaks or specific patients. Others randomly choose a sample to analyze.

What’s more, laboratories continue to have problems getting the necessary consumables such as pipette tips and chemicals used in both genetic sequencing and diagnostic testing.

President Joe BidenProposing, inheriting the setting from the Trump administration $ 1.9 Trillion COVID-19 Relief Package The amount has not been explained in detail and other details have not yet been elucidated, but it demands increased federal spending on virus sequencing.

“We are the 43rd in the world on genomic sequencing. It is totally unacceptable.” White House Coronavirus response coordinator Jeff Seients Said.

For over five years, the US Institute of Public Health has built the ability to perform genomic sequencing, primarily thanks to federal promotion to eliminate sources of food poisoning.

When the pandemic began, some laboratories soon began sequencing coronavirus. For example, the Minnesota Department of Health began doing so within a few weeks of the first COVID-19 case in March, said Assistant Lab Director Sarabetter. “It took us one step further,” she said.

But other labs didn’t do the same — especially those that were overloaded by enhancing the coronavirus diagnostic tests. CDC’s Armstrong cannot justify instructing the lab to perform further sequences if the lab was already full at the time and there was no evidence that such an analysis was needed. Said.

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“Until a month ago, it wasn’t on the list of urgent needs. I’m glad I had it,” said Trevor Bedford. the scientist At the Fred Hutchinson Cancer Research Center in Seattle. “There was definitely a shortage of federal resources allocated to do just this.”

At the same time, researchers in some laboratories were told not to go to work because of a stay-at-home order imposed during the outbreak, Mesaudi said.

“Instead of demanding weapons, they sent everyone home,” she said.

But during the summer, a group of scientists Sounded an alarm We have begun to promote something more systematic about the status of genome surveillance in the United States.

In November, the CDC launched a nationwide program to systematically pull and check specimens to more accurately determine which strains are circulating. Then, in December, the United States received a wake-up call when British researchers announced that they had identified a variant that appeared to spread more easily.

The CDC responded by announcing a surveillance program and scaled up to process 750 samples nationwide per week. The agency also signed contracts with LabCorp, Quest Diagnostics, and Illumina to create thousands more sequences each week. State laboratories carry out thousands of unique studies.

In the meantime, outbreaks are almost certainly planting more COVID-19 mutations.

Dr. Eric Topol, a scientist at the Scripps Research Institute, said, “Where you can freely control the place, there will be important variants that evolve.” “The more genomic sequences, the more we can stay ahead of the virus.”