Minnesota has stepped up its genomic sequencing of COVID-19 patient samples to more quickly identify emerging viral variants amid the state's plans to phase out its pandemic restrictions, including the indoor mask mandate.
While Gov. Tim Walz is scheduled at noon Thursday to announce a three-phase plan to eliminate business and social restrictions because of improving case numbers, state health officials said close monitoring of more infectious variants of the virus that causes COVID-19 is needed to prevent any resurgence in pandemic activity. The B.1.1.7 variant found in England largely caused Minnesota's latest wave of infections.
B.1.1.7 got a head start when it surfaced in Minnesota in January, because sequencing activities to identify it were limited and the state's COVID-19 vaccination campaign was just starting, said Kris Ehresmann, state infectious disease director. The more infectious variant first spread in smaller groups, including in youth sports activities centered in suburban Carver County, but now makes up 68% of all new infections in Minnesota.
"In this race, the variant won," Ehresmann said.,"though we did have success in avoiding a large surge due to the expansion of vaccination in February, March and April — which was points for our side. We are hoping that with the increased vaccination we have seen … that we will win future races with variants."
Walz's plan is for a graduated elimination of remaining COVID-19 mitigation strategies, including the mask mandate for public indoor spaces, that will be somewhat tied to Minnesota's ability to advance from a vaccination rate of 59% among eligible people to 70%.
The plan follows a week of meetings for Walz with business and health leaders, as well as Republican lawmakers who have been eager for the governor to reduce COVID-19 restrictions and the emergency powers he has used to authorize them.
Broad vaccination can inhibit the spread of the SARS-CoV-2 virus, which also prevents its constant mutations from creating a variant that is more infectious or that causes more severe illness.
However, vaccination within Minnesota only offers partial protection from variants, which can rise in other states or countries. Health officials this week identified six Minnesota infections involving a variant from India — although it remains unclear whether it is a "variant of concern" that presents more of a threat than others.
Sequencing of the unique genetic signatures of viral samples will remain an important monitoring tool — especially for the arrival in Minnesota of any variants that show vaccine resistance.
The technology also has been used to track the geographic lineage or spread of SARS-CoV-2, and to link transmission chains together. Minnesota health officials, for example, tracked how an infected participant of the Sturgis Mortorcycle Rally in South Dakota brought the virus back to Minnesota last summer and spread it.
"We're now sequencing for clinical purposes, but also just for surveillance, so we can keep a handle on and keep an eye on what is circulating in our communities," said Dr. Bobbi Pritt, head of microbiology at Mayo Clinic in Rochester, which is contributing to surveillance in Minnesota.
Minnesota's public health lab and several private and public partner labs have increased sequencing from 300 samples per week earlier this year to more than 2,500. Identification of B.1.1.7 in the Carver outbreak was slowed by the analysis of samples collected three to four weeks earlier. Now sampling is happening at a real-time pace, Ehresmann said.
Samples for sequencing are selected at random, but also from cases linked to broader outbreaks at schools, restaurants, workplaces or other group locations.
Mayo also is launching a study of 22,000 samples from southeastern Minnesota to chart the course of viral spread and the type of variants involved in that region.
Comparative data of 25 states posted by the U.S. Centers for Disease Control and Prevention showed that Minnesota sequenced 6,064 samples in a four-week period ending April 10 — the highest number behind Florida and California. The CDC also found that Minnesota in that period had one of the highest rates, at 67.5%, of samples containing the B.1.1.7 variant.
State health officials said that doesn't necessarily mean that Minnesota had more of a B.1.1.7 problem than other states — only that it was looking for it more aggressively.
"You know how there are always news stories about how Minnesota has the most foodborne outbreaks in the country or the most in the Midwest — we come off looking like we have terrible restaurants," said Stephanie Meyer, an epidemiology and data supervisor for the Minnesota Department of Health's COVID-19 Section. "What we really have are well-tuned systems that can find things that others haven't. … I believe [the B.1.1.7 rate] to be fairly representative of what other states would see if they had the capacity to do what we are doing."
There is little question, though, that the latest B.1.1.7-driven wave has been more severe in Minnesota. The most recent White House COVID-19 state report showed that Minnesota still had the third-highest rate of new infections for the week ending April 29.
Seventeen COVID-19 deaths were reported in Minnesota on Wednesday along with 1,267 more infections, raising the state's pandemic totals to 7,191 fatalities and 582,576 diagnosed infections. The deaths reported Wednesday included a Ramsey County resident in the 25 to 29 age range — only the 14th COVID-19 death of someone younger than 30 in Minnesota.
Deaths didn't increase in the latest wave at the same pace as infections and hospitalizations, and health officials believe that is because of broad vaccination in senior citizens and other high-risk individuals.
Fourteen of the 17 COVID-19 deaths involved people who lived in private residences. At the end of 2020, long-term care residents made up 64% of Minnesota's total COVID-19 deaths. After prioritizing them for initial supplies of vaccine, the proportion of COVID-19 deaths involving long-term care residents in 2021 dropped to 51%.
Nearly 2.6 million people in Minnesota have at least received a first dose of vaccine, and Walz on Wednesday celebrated that more than 2 million people have completed the one- or two-dose series.
"Every Minnesotan who gets a shot in their arm brings us closer to closing this chapter," the governor said, "and getting back to all the things we love in life.
Jeremy Olson • 612-673-774