U.S. Labs Able to Spot Omicron Through Current COVID Swab Tests When Variant Arrives

When the newly identified Omicron variant of COVID-19 arrives in the U.S., labs should be able to detect a sign that someone is infected with the strain through the nasal swabs used in standard PCR tests, the Associated Press reported.

Being able to effectively identify the variant is especially important as Dr. Anthony Fauci, the top infectious disease expert in the nation, warns that its emergence in the U.S. is "inevitable."

If a PCR test finds that someone is positive for just two of the three target genes, in what is called the S-dropout test result, it can indicate that that individual is positive for the variant before genetic sequencing confirms it, AP reported. Trevor Bedford, a biologist and genetics expert at Fred Hutchinson Cancer Research Center, said that this ability to spot the marker before sequencing is "fortuitous."

"If you need to do sequencing to identify the variant, you're always going to be lagged a bit and it's going to be more expensive. If you just rely on this S-dropout as identification, then it's easier," Bedford said.

Bedford added that other variants have also caused the S-dropout result, but the Delta variant was not among them. Therefore, any S-dropout indicators are sure to be flagged because Delta is currently so prevalent in the U.S., he said.

Omicron emerged as the U.S. is amplifying its surveillance efforts for new variants by increasing its capacity by tens of thousands of samples per week since early in 2021, according to AP.

Though it is still not clear just how dangerous and infectious Omicron is compared to past variants, the highly mutated strain has set the world on edge amid fears that it will prolong the lingering pandemic even further.

For more reporting from the Associated Press, see below.

Omicron Tracking
When the newly identified Omicron variant of COVID-19 arrives in the U.S., labs should be able to detect a sign that someone is infected with the strain through the nasal swabs used in standard PCR tests. Above, James Robson, a biomedical engineering graduate student, holds a swab and specimen vial in the new COVID-19 on-campus testing lab on July 23, 2020, at Boston University. Charles Krupa/AP Photo

Viruses mutate constantly. To find and track new versions of the coronavirus, scientists analyze the genetic makeup of a portion of samples that test positive.

They're looking at the chemical letters of the virus's genetic code to find new worrisome mutants, such as Omicron, and to follow the spread of known variants, such as Delta.

It's a global effort, but until recently the U.S. was contributing very little. With uncoordinated and scattershot testing, the U.S. was sequencing fewer than 1 percent of positive specimens earlier this year. Now, it is running those tests on 5 percent to 10 percent of samples.

"Genomic surveillance is strong," said Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories.

Contributing to the effort are nearly 70 state and local public health labs, which are sequencing 15,000 to 20,000 specimens each week. Other labs, including those run by the Centers for Disease Control and Prevention and its contractors, bring the total to 40,000 to 80,000 weekly.

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

"We're in a much, much better place than a year ago or even six or nine months ago," said Kenny Beckman of the University of Minnesota, who credited federal dollars distributed to public and private labs. He directs the university's genomics laboratory, which now sequences about 1,000 samples a week from Minnesota, Arkansas and South Dakota. A year ago, the lab did no sequencing.

Relying on $1.7 billion in President Joe Biden's coronavirus relief bill, the U.S. has been setting up a national network to better track coronavirus mutations.

Still, about two dozen countries are sequencing a larger proportion of positive samples than the U.S., said Dr. William Moss of the Johns Hopkins Bloomberg School of Public Health. Omicron's emergence could "stimulate the United States to do this better."

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

Many experts said it's probably already here and will be picked up by the surveillance system soon. But the question is, then what?

University of Wisconsin AIDS researcher David O'Connor noted: "We don't have the sorts of interstate travel restrictions that would make it possible to contain the virus in any one place."

Instead, genomic surveillance will tell officials if Omicron is spreading unusually fast somewhere and whether more resources should be sent to those places, he said.

When Omicron does surface, public health authorities will have to consider other variables in their triage efforts, such as the level of infection already present in that community and the vaccination rate. Serious outbreaks in highly vaccinated areas would be particularly concerning.

Still, the University of Minnesota's Beckman sees little upside in vastly ramping up sequencing.

"You don't need to sequence more than a few percent of positive cases to get a feel for how quickly it's growing," he said.

Unlike in some other countries, U.S. government officials haven't exercised the authority to force people to quarantine if they test positive for worrisome variants. Given that, sequencing is mainly a surveillance tool for tracking mutations' spread.

"I think it's important to track variants, but I don't think it's practical to think that we're going to be able to sequence quickly and broadly enough to stop a variant in its tracks," Beckman said.

COVID-19 Testing Sign
Being able to effectively identify the Omicron variant is especially important as Dr. Anthony Fauci, the top infectious disease expert in the nation, warns that its emergence in the U.S. is “inevitable.” Above, a COVID-19 testing facility is advertised at Newark Liberty International Airport on November 30, 2021, in Newark, New Jersey. Spencer Platt/Getty Images