Minnesota only has three counties with high COVID-19 community levels this week, but a 70% increase in U.S. counties with that federal designation has some health officials concerned.

The fast-spreading BA.5 variant and a high rate of breakthrough infections in people with immunity is causing COVID-19 surges in Southern and Western states. BA.5 is also the dominant variant in Minnesota. Genomic sequencing found BA.5 in 40% of samples from COVID-positive patients in late June and the rate has likely increased.

Coronavirus infections have fallen steadily from 2,100 per day in mid-May to less than 1,300 in Minnesota, but those numbers are likely undercut by the decline in publicly reported COVID-19 tests and the increase in private at-home tests, said Michael Osterholm, director of the University of Minnesota's Center for Infectious Disease Research and Policy. The closure of several state testing sites in late June could have hastened that switch.

"Those [case] numbers are no longer giving us what we once had," he said. "I look at hospitalizations and I look at deaths. Those are still relatively stable here. I think the next two to four weeks are going to tell us a lot."

COVID-19 hospitalizations in Minnesota have declined from 482 on May 31 to 407 on Wednesday. While only 48 of those patients required intensive care, that number hasn't improved this summer. Minnesota also has been stuck at about five COVID-19 deaths per day for two months, although that is far below the 39 deaths per day at the peak of the winter delta pandemic wave.

The current level of risk remains greatest among seniors, who made up 18 of 21 COVID-19 deaths in the first week of July, according to the Minnesota Department of Health's situation update on Thursday. Minnesota's total COVID-19 death toll is now 12,872.

HealthPartners is urging people to stay up to date with COVID-19 vaccinations, because immunity has at least made a difference in the severity of illness even if it isn't preventing all infections, said Dr. Mark Sannes, an infectious disease specialist with the Bloomington-based health system.

"We continue to see an illness that is much less severe than it was early in the pandemic or even in 2021," he said.

Minnesota ranks 18th among states for vaccinations, with nearly 70% of its population completing the initial COVID-19 vaccine series, according to the Centers for Disease Control and Prevention. It ranks second among states for boosters, with nearly 60% of people eligible for first booster doses receiving those shots.

However, the state only considers 30% of its population up to date with vaccines, because many vaccinated people have skipped boosters.

The CDC last week had only reported three Minnesota counties with moderate COVID-19 levels — a hybrid measure of local infection and hospitalization rates. This week, it reported 22 counties with moderate levels and Renville, Olmsted and Wabasha counties at high levels — meaning that indoor mask-wearing is recommended to reduce viral transmission.

Olmsted and Wabasha have spent more time in the CDC high risk range than other counties, partly because they are in the health care region including the Mayo Clinic in Rochester that draws patients from a large referral region.

This week's national risk map is a flip-flop from the winter, when most counties in Minnesota and northeastern states such as New York were at moderate or high COVID-19 levels. Now, most of Florida is at the high level and none of its counties are at the low level. Most of the California coast has high COVID-19 levels as well.

Osterholm said he doesn't have a lot of confidence in the CDC county designations, and instead looks closely at wastewater sampling to see how much virus is spreading.

Results were mixed through July 10 from sewage sampling at 40 wastewater plants statewide, according to the latest results reported by the University of Minnesota. The viral load in wastewater was flat or declining in five of the state's seven regions. It increased in the southwest and northwest corners of Minnesota, but those results were based on a small number of plants where results can swing up and down from week to week.

Osterholm said Friday's separate sewage sampling data from the Metropolitan Wastewater Treatment Plant in St. Paul would be telling, because it would indicate the prevalence of BA.5 in the Twin Cities.

The variant already made up 60% of the viral load from that plant's sampling last week, Osterholm said, when he encountered more infections among people he knew than he could recall in the entire pandemic. Some already had COVID-19 this winter, but the variant is "basically eating your immune protection's lunch from four months ago," he said.

Osterholm agreed that immunity by vaccine or recent infection is playing an important role by reducing the number of infections that result in hospitalizations. But some people are just below that level of severity of illness.

"I think we are seeing a lot of those cases right now — really quite ill but not enough to be hospitalized," he said. "People who are in bed for 10 to 15 days."