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How Minnesota monitors for coronavirus variants

Testing for variants like the newly identified omicron variant is a more complicated process than a basic COVID-19 test.

The process of genetic analysis, known as sequencing, reveals any mutations that may indicate a variant of the virus is present.
The process of genetic analysis, known as sequencing, reveals any mutations that may indicate a variant of the virus is present.
REUTERS/Brendan McDermid

Minnesota confirmed the second-known U.S. case of the omicron variant of COVID-19 this week.

The new COVID-19 variant was first discovered in South Africa last month, but subsequent analysis of samples revealed it was in Europe before that. Given the rapid spread of the variant in countries around the world, health officials say it’s no surprise to find the variant in Minnesota.

The Minnesota case involves an adult male and resident of Hennepin County who traveled to New York City to attend a large anime convention last month. The man developed symptoms on Nov. 22 and tested positive for COVID-19 back in Minnesota after getting tested Nov. 24  — the same day the variant’s discovery was reported to the World Health Organization and two days before the WHO declared it a “variant of concern.”

The man had been fully vaccinated against COVID-19  and received a booster dose in early November, per the Minnesota Department of Health. His symptoms were mild and have resolved.

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Health officials credit the state’s variant surveillance system with the detection of omicron in Minnesota just one day after the first U.S. omicron case was detected in San Francisco. (Additional cases have since been detected in California, Colorado, Hawaii and New York.)

Health Commissioner Jan Malcolm
Christine T. Nguyen/MPR News/Pool
Health Commissioner Jan Malcolm
“Having this robust virus surveillance system allowed us to quickly identify omicron once it was in our state, and frankly made it more likely that we would be among the first states to find the variant,”  Health Commissioner Jan Malcolm said in a COVID-19 media briefing Thursday.

The process for detecting coronavirus variants is a complicated one involving days of lab work. It would be impractical to check every positive COVID-19 test in Minnesota for variants; instead, the state relies on a sampling technique. Here’s how Minnesota’s variant surveillance system works.

Sampling the samples

The sample that turned out to be Minnesota’s first confirmed omicron case came from a saliva test conducted at one of the state’s community testing sites.

Each lab running PCR, or molecular, COVID-19 tests is being asked to send a subset of positive samples to MDH each week to have their genetic code analyzed, said Sara Vetter, assistant MDH lab director. Sequencing, the process of analyzing a living thing’s genetic code, can reveal any mutations that may indicate a variant of the virus is present.

Currently, roughly 2,000 positive cases from Minnesota per week are being sequenced. (Overall, Minnesota has been seeing 20,000 to 30,000 new cases per week recently.) The labs doing the work are MDH’s public health lab, the University of Minnesota’s Genomics Center, CDC-funded labs and commercial labs.

When samples arrive at the MDH lab, they are tested to double-check that they are, in fact, positive COVID-19 cases, Vetter said. The lab also checks to make sure there’s enough virus in the sample to be sequenced.

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Then, the sample is run through a sequencer, which reads the virus’ genetic code. Once that data is gathered, a sophisticated computer process compares sequences of the virus sample’s DNA to sequences in a database, allowing mutations to be detected.

Algorithms determine whether the sample matches a previously identified strain, like the delta variant, or the new omicron variant.

Only sequencing can confirm whether a specimen is omicron or not, but some tests commercial labs run can hint at the variant. One of the telltale signs that a sample might be omicron is an s gene dropout, or s gene target failure, result on some commonly used tests. This stems from a mutation of the spike protein that is prevalent in omicron (and the alpha strain of COVID-19 for that matter), but is less prevalent in the delta variant samples that make up almost all the cases in Minnesota right now.

Vetter said that after learning of the omicron variant, MDH asked Infinity BiologiX, a lab in the state that uses tests that can identify this result, to send them any samples that exhibit this trait for expedited sequencing. Health officials said Thursday they are awaiting sequencing results from fewer than 10 other specimens that show s-target dropout. All-told, the sequencing process typically takes four to five days, but can be expedited to one or two.

An omicron surge?

Because Minnesota has experienced a surge as cases in other states subside in recent months, some have hypothesized that omicron could be partly responsible.

MDH officials dispelled that theory.

“Besides the one omicron we just detected, we’ve been 100 percent delta for weeks, if not months, now,” Vetter said, adding that given the rate of samples sequenced, it would likely be statistically impossible to miss a variant prevalent enough to cause an ongoing wave like Minnesota’s been seeing.

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“Could you have missed a single case? Maybe. But could you have missed the entire peak? No, not at all,” said Kris Ehresmann, MDH’s infectious disease director.

Vetter said had omicron been found in Minnesota before it was identified in South Africa, the state’s variant surveillance system likely would have identified it as something new. The only big limitation to identifying concerning new variants, she said, is that there are so many small mutations that it isn’t always clear what’s a significant new strain.

As soon as news came out that a new variant had been identified, MDH was able to quickly look back through data to see if any with the same number had been found. Anything that wasn’t delta would have stood out quickly, Vetter said.

Health officials have been lauding Minnesota’s variant surveillance system as one of the more advanced in the country.

“We were fortunate enough to go into this pandemic with a lot of sequencing capacity in the first place, and then we’ve been able to really build it up during the past year. So we have just a lot of capacity in our public health lab,” Vetter said.

She also listed collaboration with the University of Minnesota and good relationships with commercial labs as assets to the state’s variant detection program.

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Omicron ahead

Health officials are urging patience and caution — not panic — as we learn how the emergence of omicron will affect the ongoing pandemic. It’s still not clear how transmissible the variant is, whether or not it causes more severe disease and how effective vaccines are against it.

Still, a surge in cases in South Africa — reminiscent of an early surge related to the delta variant in India — suggests that the variant may be highly transmissible.

“Over the course of the next two to four weeks, we’ll learn whether the omicron variant will out-compete delta or not. It’s basically survival of the fittest for these viruses,”said Matthew Binnicker, vice Chair of practice in the department of laboratory medicine and pathology at the Mayo Clinic, in a media availability Thursday.