US Virus Variant Tracking Improved After Slow Start

After a slow start, the United States has improved its surveillance system to track new coronavirus variants like omicron, increasing its capabilities by tens of thousands of samples per week since the beginning of this year.

Viruses are constantly mutating. To find and track new versions of the coronavirus, scientists analyze the genetic makeup of some of the samples that test positive.

They are studying the chemical letters of the virus’ genetic code to find new and troubling mutants like omicron and trace the spread of known variants like delta.

This is a global effort, but until recently the US has made very little contribution. Using uncoordinated and scattered tests earlier this year, less than 1% of positive samples were sequenced in the United States. He now runs these tests on 5-10% of the samples.

The timing of the tests remains uneven, almost two years after the start of the pandemic.

“Genomic surveillance is a strong system,” said Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories.

This is facilitated by nearly 70 state and local public health laboratories, which sequenced from 15,000 to 20,000 samples weekly. In other laboratories, including those at the Centers for Disease Control and Prevention and its contractors, the total is between 40,000 and 80,000 each week.

Nine months ago, about 12,000 samples were analyzed in this way every week.

“We are in a much better place than a year ago or even six or nine months ago,” said Kenny Beckman of the University of Minnesota, who listed federal dollars allocated to public and private labs. He runs the university’s genomics lab, which now sequences about 1,000 samples a week from Minnesota, Arkansas, and South Dakota. A year ago, no sequencing was performed in the laboratory.

Building on the $ 1.7 billion contributed to President Joe Biden’s Coronavirus Relief Bill, the United States is building a national network to better track coronavirus mutations.

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However, about two dozen countries are sequencing more positive samples than the United States, said Dr William Moss of the Bloomberg Johns Hopkins School of Public Health. The emergence of Omicron could “incentivize the United States to do it better.”

“I think we still have a long way to go,” Moss said.

In addition to surveillance efforts, standard PCR tests using nasal swabs sent to laboratories can detect an indication that someone likely has an omicron variant. If the PCR test only tests positive for two of the three target genes – the result of the so-called S-dropout test – is an omicron marker even before the additional genetic sequencing step to prove it.

“It’s an accident,” said Trevor Bedford, a biologist and geneticist at the Fred Hutchinson Cancer Research Center. “If you need to perform sequencing to determine a variant, you will always be a little behind and it will cost more. If you just rely on this S-dropout for identification, then it’s easier. “

He said that the other variants also caused this quirk in the PCR test results, but not the delta variant. With the currently dominant delta in the United States, Bedford said the S-dropout would be noticeable. (Bedford receives funding from the Howard Hughes Medical Institute, which is also supported by the Associated Press’s Department of Health and Science.)

Dr. Anthony Fauci, a leading national expert on infectious diseases, said the infiltration of the omicron into the United States was “inevitable.”

Many experts said he was probably already here and would soon be detected by a surveillance system. But the question is, what then?

University of Wisconsin AIDS researcher David O’Connor said: “We have no interstate travel restrictions that would allow the virus to be contained anywhere.”

Instead, genomic surveillance will tell officials if the omicron is spreading unusually fast somewhere and whether more resources need to be directed to those places, he said.

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When the omicron does appear, public health authorities will have to consider other variables in their triage efforts, such as the rate of infection already present in this community and the rate of vaccination. Serious outbreaks in highly vaccinated areas may be of particular concern.

Still, Beckman of the University of Minnesota sees little benefit in dramatically expanding sequencing.

“You don’t need to order more than a few percent of positive cases to understand how fast they are growing,” he said.

Unlike some other countries, US government officials have not exercised the right to force quarantine if they test positive for worrying options. With this in mind, sequencing is basically a surveillance tool to track the spread of mutations.

“I think it’s important to track variations, but I don’t think it’s practical to think that we can trace the sequence quickly and broadly enough to stop a variation from emerging,” Beckman said.

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