COVID test used in Minnesota may offer clues about new strain

The U.S. Food and Drug Administration is alerting lab managers that several COVID-19 tests, including one used in Minnesota's free public testing, carry a slight risk of returning inaccurate results because of recent genetic mutations in the virus.

But there's an upside. Thermo Fisher Scientific, which makes the TaqPath COVID test used at community testing sites across the state, says the test not only remains accurate, but it may offer an important clue that a more infectious COVID strain is present.

And the technique has already worked in Minnesota.

Department of Health officials say three of Minnesota's first confirmed cases of a more infectious variant of COVID-19, announced Jan. 9, were found after analyzing samples that returned a specific test result in the lab called an "S-gene drop out."

Then state epidemiologists saw that one of the three people who had the new more infectious variant shared a street address in Minnesota with someone else who recently tested positive for regular COVID at a different lab.

So officials pulled that sample and expedited a deeper analysis, ultimately finding that it, too, contained the more infectious strain whose spread in the United Kingdom and Europe led to travel restrictions in Europe late last year.

"That [fourth case]was not a TaqPath assay, so there was no reason for the lab to even question it. It just came up positive like any other test," said Sara Vetter, interim assistant director of the state public health lab in St. Paul.

In other words, careful examination of S-gene drop outs allowed contact tracers to spot a transmission of the more infectious version of the virus in Minnesota that would have been missed otherwise.

Vetter and Dr. Andrew Brooks — chief executive of Infinity Biologix, which operates Minnesota's private saliva test-processing lab in Oakdale — said the technique isn't written into any formal process. But lab employees will keep doing it.

All viruses develop genetic mutations as they reproduce over time, which is a key reason why molecular tests for SARS-CoV-2 and other viruses are designed to detect several different targets in the pathogen.

Like other COVID tests, the TaqPath assay reacts to small snippets of three genes in the virus. Only two of three are needed for a diagnosis, so the tests work even if a mutation makes it impossible to detect the third gene. The gene that goes missing is called a "drop out" or a "target failure."

"If you have three shots on goal from different angles, you are more likely to make sure at least one of the shots gets in, to use a hockey analogy," said Dr. Tim Stenzel, director of the FDA's Office of In Vitro Diagnostics and Radiological Health.

Tracking variants of the SARS-CoV-2 virus will be important over time, public health officials say.

While many genetic changes will make the virus less effective, some will help it, such as the mutations discovered last year in the U.K. The CDC is also tracking variants that have been found in South Africa and Brazil.

State Health Commissioner Jan Malcolm said confirmation of the U.K. variant in Minnesota is a clear sign that precautions like distancing, masking and staying home when sick remain important, despite falling numbers of case counts here.

"While our trends have stabilized, we are still in a high-risk situation and the variant is a major new unknown," Malcolm said last week.

The total number of confirmed cases of COVID-19 in Minnesota rose by 1,333 on Sunday, bringing the state's total to over 446,000. The seven-day average number of new cases per day has been declining since Jan. 8.

Minnesota recorded 40 additional deaths from complications of COVID-19 on Sunday, bringing the state tally to 5,927. New cases per day and new deaths per day peaked between late November and mid-December.

Nearly 185,000 Minnesotans have received a first dose of COVID vaccine, and nearly 36,000 have completed vaccination by getting their second dose. While state statistics show 43% of the state's doses had been used as of Sunday, tens of thousands of doses are being held in reserve for those who need their second shot.

Of the 31,567 diagnostic test results reported by the Health Department on Sunday, about 4% were positive for the virus that causes COVID.

While private hospitals and clinics around the state use a variety of COVID tests, the state lab in St. Paul and the private lab in Oakdale that processes the state's saliva samples both use the Thermo Fisher TaqPath test.

It was one of three mentioned by name in the FDA's Jan. 8 alert to lab managers warning of a small potential for the tests to incorrectly return negative test results because of genetic changes in the virus over time.

The alert noted two of the tests — TaqPath, and another one called the Linea COVID-19 Assay — may produce a "signature" that is evidence for the U.K. variant.

At the molecular level the U.K. variant has 17 mutations, one of which deletes amino acids in the genetic sequence that tells the virus how to build its signature surface spikes.

The TaqPath and Linea tests are designed to react specifically to that section of the virus' spike gene, often called the S-gene. That's why a drop out of the S-gene target, combined with positive detection for the other two genes, is a good clue.

"There is a signature, a pattern, with both of these assays that alerts labs to the potential that that sample could have the U.K. variant," FDA's Stenzel said.

S-gene target failure isn't definitive proof of the variant, but it can be a cue to conduct deeper analysis with a machine that can read the virus' entire genome.

Of the two dozen S-gene target failures the state lab examined in early January, three were positive for the U.K. variant, the Department of Health's Vetter said. The department has found that the test has 99% analytical sensitivity overall in detecting the virus.

Minnesota's fourth case of the variant was discovered through contact tracing, and a fifth case was confirmed after one of the major commercial lab companies alerted the state, Vetter said.

Dr. William Morice, president of Mayo Clinic Laboratories in Rochester, said researchers should expect continued mutation — especially in the spike gene, which encodes the part of the virus needed to invade a host cell.

To date, FDA officials have not seen a COVID test rendered totally obsolete by viral mutations — but they are looking. Stenzel said the agency is vigilant in comparing known variants with the genetic targets in existing tests.

If molecular tests one day need to be recalibrated, it won't take nearly as long as it did to design the first few COVID tests last year, because so much more is known about the virus today, said Ryan Lang­lois, associate professor of immunology at the University of Minnesota Medical School.

"If the virus evaded all three TaqPath assay targets, I would predict people would have a new test in one to two weeks," Langlois said.

Joe Carlson • 612-673-4779