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Minnesota among top states for COVID variant screening

Identification of new strains through whole-genome sequencing is a process far more complex than the standard lab tests used to clinically diagnose a patient with COVID-19.

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Samples are loaded into a sequencer at the Minnesota Department of Health Public Health Laboratory. Some but not all positive COVID-19 tests have their entire genome analyzed in order to determine their variant.
Contributed / Minnesota Department of Health
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ST. PAUL — Vaccines, masking and testing are visible, everyday parts of the fight against COVID-19, but one of the most crucial tools is a sophisticated process largely out of public view.

In ongoing international efforts to identify new strains of the virus that causes COVID-19, scientists in Minnesota process genetic data from thousands of test specimens each week. The process marshals multiple laboratories, experienced scientists and supercomputing power from the University of Minnesota.

When Minnesota confirmed the presence of the omicron variant of SARS-CoV-2, it’s likely that the state was among the first to do so in the U.S. because of its strong disease surveillance capacity. That capacity was there well before the arrival of COVID-19, said Jessie Cavazos, a health educator with the state health department.

"Our public health laboratory was really at the forefront of a lot of the science and technology when it came to food-borne illness outbreaks and viruses," Cavazos said. "If you hear that Minnesota has a lot of food-borne outbreaks ... we have the same amount, Minnesota just finds them and reports them."

Identification of new strains is a process far more complex than the standard lab tests used to clinically diagnose a patient with COVID-19, Cavazos said. It’s done through a process called genomic sequencing, where the entire genome of the virus is analyzed molecule-by-molecule to determine its structure.

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Each week, the state Public Health Laboratory, the University of Minnesota, the Mayo Clinic and a private lab partner fully sequence 15-20% of all positive PCR tests in the state, or about 2,500 specimens, according to Minnesota Department of Health spokesman Doug Schultz.

PCR, or polymerase chain reaction, is a genetic material detection process used to confirm cases of COVID-19. Sequencing takes PCR to the next step by fully mapping the genome of a sample.

In November, Minnesota ranked third in the U.S. for total number of fully sequenced specimens, according to data from the Centers for Disease Control and Prevention. In the four weeks leading up to Nov. 27, Minnesota fully sequenced 13,955 specimens, behind Massachusetts at 14,239 and California at 18,424. Neighboring North Dakota and South Dakota ranked fifth and fourth lowest in the U.S. respectively, sequencing just over 200 cases each.

The sequencing process is painstaking and complex. Minnesota's public health lab can take up to 42 hours to run roughly 100 tests, according to MDH. Some labs report the process taking about one week.

Sean Wang, Sequencing and Bioinformatics Supervisor at the Public Health Laboratory, says partner labs ship positive tests for sequencing for full sequencing if they bear markers of a particular variant of the virus, such as delta or omicron.

Lab staff extract the genetic material from the specimens. The virus that causes COVID-19 stores its genetic material as single-stranded RNA which is converted into double-stranded DNA before it is sequenced. DNA is then amplified, or made into more copies, so the sequencing machine has more material to analyze.

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A public health laboratory worker prepares specimens for whole-genome sequencing.
Contributed / Minnesota Department of Health

The sequencing machine processes 96 different specimens at a time, and to ensure the machine can distinguish samples, each strand of DNA gets a molecular “bar code” at each end.

One at a time, the machine converts nucleotides, the building blocks of DNA, into data. Cavazos compares the process to DNA being strung through a hole like a beaded necklace.

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The process generates millions of short fragments of the virus’ genome in digital format. The University of Minnesota Supercomputing Institute then processes gigabytes of raw data to produce a map of each viral specimen, which the public health lab can compare to variants of SARS-CoV-2 for confirmation.

Through this process, at least 65 cases of the omicron variant had been identified so far in Minnesota on Dec. 22. Based on laboratory data, MDH estimates omicron is now the dominant strain in the state, according to Schultz.

The World Health Organization declared omicron a variant of concern in late November, citing numerous mutations in the virus that raised questions about whether the variant was more infectious or if it could elude the COVID-19 vaccine.

So far, scientists have found the vaccine may not offer as much protection against omicron, though one South African study indicated the variant may not cause as severe of illness as previous strains.

As of late December, the omicron variant of COVID-19 had grown to become the dominant strain in the U.S., according to the CDC. The variant's rise has prompted renewed international travel restrictions, event cancellations, and President Joe Biden to direct further federal resources to address its spread.

Follow Alex Derosier on Twitter @xanderosier or email aderosier@forumcomm.com .

Alex Derosier covers Minnesota breaking news and state government for Forum News Service.
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