Minnesota at the forefront of surveillance for COVID-19 variants – .

Minnesota at the forefront of surveillance for COVID-19 variants – .

Minnesota began testing more COVID-19 patient samples this fall than almost any state, stepping up its search for new coronavirus variants that could worsen the disease or compromise vaccination.

About 8% of Minnesota’s 920,000 coronavirus infections have been sequenced to identify their DNA fingerprints, but public and private labs are now testing 20% ​​to prevent troubling variants from arising undetected.

At 2,000 genetic sequences per week, Minnesota is likely to detect a significant variant even if it exists in 0.1% of samples, said Sara Vetter, director of the state’s public health laboratory. “If something circulates in 1 in 1000 [samples], we will find it. “

The tighter safety net helps explain why Minnesota was the second state to identify an infection involving the omicron variant a week after its discovery in South Africa. The infection involved a Hennepin County man who exhibited mild symptoms of COVID-19 on November 22 after attending a convention in New York City.

Minnesota has submitted the third genomic sequencing results of coronavirus samples in the past 90 days to the open access database GISAID, allowing a broader search for trends among the results. Colorado was also among the first five states to discover omicron infections, and it placed second.

“It might be a coincidence… but I don’t think so,” said Kenny Beckman, director of the University of Minnesota Genome Center, which is part of the state’s sequencing group.

This summer’s genomic sequencing has shown the shocking speed at which the fast-spreading alpha variant has been swept away by the faster-spreading delta variant. Monitoring was trivial in comparison this fall when the delta appeared in 99% of the samples.

“In three weeks, we went from no delta to almost the entire delta,” Beckman said.

Omicron has been called a “variant of concern” after its discovery on November 24 in South Africa because it appeared to be spreading even faster than delta. He also exhibited genetic characteristics suggesting that he might escape immunity from a previous infection or vaccination.

The increase in sequencing this fall allowed Minnesota to quickly search all of its samples to find out if omicron was already in the state.

Minnesota’s sequencing partnership includes the state public health lab and the U’s Genomics Center, as well as Infinity BiologiX, a New Jersey company that processes samples from state saliva testing centers. Fortunately, they had a good idea where to start, as some variants, including alpha and omicron, react unexpectedly to testing, Beckman said.

Standard PCR diagnostic tests look for multiple genetic targets to identify a coronavirus, and the goal is to find them all and leave little doubt about the results, Beckman said. With omicron, some tests fail to identify the S gene target even though they find other targets and confirm infections.

“You actually have a clue, which is pretty cool, that comes from failing certain commercial tests” in a way that produces useful information, said Beckman, whose center is also sequencing samples from Arkansas. , Missouri and South Dakota.

Eight samples have been identified, including one from the Hennepin County man whose infection proved omicron was in the United States before it was announced in South Africa. Sequencing of at least four other samples did not find the omicron variant.

Omicron is not the first variant to raise concerns about a mutation that could allow the coronavirus to evade immunity. The beta and gamma variants found earlier this year in Brazil and South Africa, respectively, raised similar concerns and were eventually detected in Minnesota. But delta was found to be the strongest variant, and sequencing in Minnesota found only 262 infections involving beta and 552 involving gamma.

It is not known whether omicron can overtake delta as the dominant strain, but sequencing should provide answers in four weeks, said Matthew Binnicker, vice president of practice in the Mayo Clinic’s department of laboratory medicine and pathology. .

“Delta showed us that he was the king of the hill. It could supplant other variants and has become 99% of the virus in the country, ”he said. “We’ll have to see… if the omicron is better at transmitting than the delta. “

Genomic sequencing has long been used by epidemiologists in Minnesota, particularly in the search for sources of foodborne illness. During the pandemic, sequencing identified how participants in the 2020 Sturgis Motorcycle Rally in South Dakota brought the virus back to Minnesota.

The sequencing also made it possible to establish a detailed map this spring that linked coronavirus infections among several schools and sports teams in Carver County and surrounding areas of the South Metro.

No variant labeled as special concern was first discovered in Minnesota. Beckman said such variations are usually found where they occur. A variant of interest was identified earlier this year in California, but limited genomic sequencing at the start of the pandemic reduced the discovery of other variants in the United States, he said.

“I think the United States is now doing the sequencing at such a frequency that if there are any variants of concern here, they will be detected,” he said.

Even sequencing 20% ​​of the specimens, state health officials said they had to choose which ones were selected in order to increase the chances of finding variants of concern. Random sampling of specimens is selected from across Minnesota for geographic surveillance, but epidemiologists may also recommend sequencing of suspicious clusters, for example in communities with increasing transmission rates. Sequencing also attempted to identify the variants most likely to cause hospitalization or breakthrough infection in fully vaccinated people.

The corresponding genomic sequences “help connect the dots,” Vetter said. “So if we see something in a school, if we see something in a geographic area, we can see how [the virus] has been featured and disseminated in the community.


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