MDH uses variant surveillance program to monitor how COVID mutates in population

Through the variant surveillance program, the Minnesota Department of Health was able to identify one of the first cases of omicron in the United States. The program is an extension of what they were already doing to monitor the flu but on a much bigger scale.

Long before COVID-19, MDH had a surveillance laboratory and program in place to monitor mutation in the flu virus and food-borne illnesses. Since March 2020, they’ve expanded the program to test thousands of COVID-19 samples every month.

"We used to sequence 6,000 samples a year and that would include all of the food-borne illness samples, now we’re sequencing 6,000 samples in two months, with just COVID-19, that’s not counting all of the other sequencing work we’re doing," MDH epidemiologist and director of the Public Health Laboratory Dr. Sara Vetter said.

Vetter explains MDH collects a portion of positive COVID-19 tests from labs around the state and examines those samples to learn more about how COVID-19 is changing on a genetic, molecular level.

"We are looking for variants so we can understand when and how a new introduction of a variant comes into Minnesota and starts circulating in our communities," Vetter said.

That monitoring can be on a small scale, like learning about how an outbreak could have happened at a nursing home or testing samples from people who are hospitalized. By looking at the genetic sequencing of the virus, they can learn more about where it potentially came from, how it compares to other strains or variants, and study how these changes could impact how infectious or contagious the virus is.

"We can look at those individual sequences themselves and learn a little bit more about what that means," Vetter said.

On a larger scale, Vetter explains, MDH works with national and global public health partners to contribute information and learn more about how variants like Omicron and Delta are spreading, mutating, and impacting infected people.

"It’s all the data together, not just Minnesota, but nationwide, and some extent worldwide, that we’ll be able to make more conclusions," Vetter said.

"We are looking for things like are there different rates of vaccine breakthrough?" Kathy Como-Sabetti, Section Manager Epidemiologist for the COVID-19 epidemiology section, said.

Como-Sabetti says regardless of the variant or genetic mutations, the people landing in the hospital are largely unvaccinated. Because genetic sequencing takes a few weeks to complete, she said they do not have numbers yet on if any patients in Minnesota hospitals have the Omicron variant.

These health officials from MDH say they’ll continue the COVID-19 monitoring program for the foreseeable future, like their flu program, to continue watching how COVID-19 mutates in the future.