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Minnesota labs screening for omicron variant as COVID wave persists

No cases of newly-identified omicron variant had been reported in the U.S. as of Monday, though public health officials agree it is only a matter of time before it emerges.

Photo: Unsplash/Fusion Medical Animation

ST. PAUL — While no cases of the omicron variant of the coronavirus had been detected in the U.S. as of Monday afternoon, Nov. 29, Minnesota health officials said they continue to monitor for the newly identified strain.

In a statement, Health Commissioner Jan Malcolm said the state has a system in place to detect new strains of the virus and will report if the omicron variant is detected.

New variants are expected to occur, Malcolm said, adding that the best course of action anyone can take to protect themselves from COVID-19 is to get vaccinated.

"Fortunately, Minnesota has built one of the nation's strongest genomic sequencing and variant surveillance systems," the statement said. "If an Omicron variant infection is found in Minnesota, we will share that information as soon as possible."

Minnesota monitors some but not all COVID-19 tests for new variants at the state public health lab. Labs running testing for the virus spot suspected positive samples with potential markers of a variant and pass them along to the state, according to Minnesota Department of Health spokesman Doug Schultz.


The process of detecting variants involves sequencing the entire genome of the specimen and takes longer to complete than running a typical test for COVID-19 — up to 42 hours to run 100 tests, according to MDH. The state does not release those results to doctors or patients.

The World Health Organization last week labeled the omicron variant a "variant of concern" due to a large number of mutations and steep increase in infections in South Africa, where the strain was first identified. Scientists are still working to determine if the variant is more infectious or causes worse illness than previous coronavirus variants. It also remained unclear early this week whether the vaccine is less effective in protecting against the new strain.

While the omicron variant's impact remains uncertain, many countries have already taken steps to prevent its spread, including travel restrictions on southern African countries. As of Monday, the strain had been found in countries including the Netherlands, Canada, Germany, Portugal and Spain. Public health officials say the variant will likely appear in the U.S.

With a new strain looming, Minnesota's seven-day average COVID-19 case rate led the nation Sunday, with 426 cases per 100,000 people, according to data from the Centers for Disease Control and Prevention. The level the CDC considers high risk is 100 or more per 100,000.

MDH reported 44 deaths and 4,511 new cases of COVID-19 Monday as hospitalizations for the virus remained at highs not seen since late 2020.

Daily average case numbers and test positivity rates remain in the high-risk category of community spread set by the CDC. The seven-day rolling average case rate per 100,000 people as of Nov. 19, the most recently available data from MDH, was 76, more than seven times higher than the lower threshold of high risk of 10 per 100,000 people. The rolling average test positivity rate as of Nov. 19 was 10.9%, slightly down from the 11% reported a few days before.

The state's most recent count of hospitalizations for COVID-19 was 1,467. The ongoing surge in cases has strained the state's hospitals, leaving 72% without intensive care unit beds for adults. Monday's hospitalization numbers come from Friday counts as the Thanksgiving holiday delayed data processing.

The Monday case number update includes data from 4 a.m. Wednesday through 4 a.m. Friday. Officials plan to release weekend case data on Tuesday. The state did not update vaccination numbers on Monday.


Following are the Minnesota Department of Health COVID-19 case rates, deaths, hospitalizations and vaccinations as of Monday. Because all data is preliminary, some numbers and totals may change from one day to the next.

Statewide case rates

  • NEW CASES: 4,511


Hospitalizations, deaths




  • TOTAL DEATHS: 9,125


  • FIRST DOSE ADMINISTERED: 3,631,472 or 69.7% of ages 5 and up

  • COMPLETED SERIES (2 doses): 3,346,984 or 64.2% of ages 5 and up

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