Minnesota at the forefront of COVID-19 variant surveillance

Minnesota will begin analyzing samples from more COVID-19 patients than most states this fall, searching for new coronavirus variants that may exacerbate the disease or undermine vaccination. Was strengthened.

Approximately 8% of Minnesota’s 920,000 coronavirus infections have been sequenced to identify genetic fingerprints, but public and private laboratories have now detected problematic variants. We are analyzing 20% ​​to prevent a surge without.

Minnesota is likely to detect significant mutations in 2,000 gene sequences per week, even if they are present in 0.1% of the sample, said Sara Vetter, director of the state’s public health laboratory. .. “If something is circulating in 1 in 1,000 people [samples], We will find it. “

A closer safety net helps explain why Minnesota was the second state to identify an infection involving the Omicron mutant a week after it was discovered in South Africa. The infection was associated with a man in Hennepin County who experienced mild COVID-19 symptoms on 22 November after attending a convention in New York.

Minnesota has submitted the third most abundant genomic sequencing results of coronavirus samples over the last 90 days to the GISAID Open Access Database. This allows for a wide range of research on outcome trends. Colorado was also one of the first five states to discover Omicron infection and was ranked second.

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

Genome sequencing this summer showed a shocking rate at which the rapidly spreading alpha mutants were wiped out by the faster spreading delta mutants. Surveillance was mediocre compared to this fall when Delta appeared in 99% of the samples.

“In three weeks, we moved from no delta to almost every delta,” Beckman said.

Omicron was labeled a “variant of concern” because it appeared to spread even faster than the Delta after it was discovered in South Africa on November 24th. There were also genetic features suggesting that it may avoid immunity from previous infections and vaccinations.

With more sequences this fall, Minnesota is now able to quickly search the width of the sample to see if Omicron is already in the state.

The Minnesota Sequence Partnership includes Infinity BiologiX, a New Jersey company that processes samples from the state’s Public Health Institute and the US Genomics Center, as well as the state’s saliva testing center. Fortunately, some variants, including Alpha and Omicron, react unexpectedly to the test, so they were wondering where to start, Beckman said.

Standard PCR diagnostic tests look for multiple genetic targets to identify the coronavirus. The goal is to find them all and leave little doubt about the results, Beckman said. Some tests at Omicron cannot identify the S gene target by finding other targets and confirming the infection.

“In fact, there are clues from the failure of some commercial tests,” said Beckman, who also sequences samples from Arkansas, Missouri, and South Dakota.

Eight samples were identified, including a man from Hennepin County, whose infection proved that Omicron was in the United States before it was announced in South Africa. No omicron variants were found in the sequence of at least 4 other samples.

Omicron is not the first variant to raise concerns about mutations that may allow the coronavirus to evade immunity. Beta and gamma variants found in Brazil and South Africa earlier this year raised similar concerns and were eventually detected in Minnesota. However, Delta proved a more potent variant, and the sequence in Minnesota found only 262 infections, including beta, and 552 infections, including gamma.

It is unclear whether Omicron can cross the delta as the predominant strain, but sequencing should provide an answer in four weeks, said Matthewby, Vice-Chair of the Mayo Clinic’s Department of Laboratory Medicine and Pathology. Nicker says.

“Delta has shown us that it is the king of the hills, which can defeat other variants and has become 99% of the country’s virus,” he said. “We need to see if Omicron is better at transmitting than Delta.”

Epidemiologists in Minnesota have long used genomic sequencing, especially to look for causes of food poisoning. During the pandemic, the sequence identified how participants in the 2020 Sturgis Motorcycle Rally in South Dakota returned the virus to Minnesota.

Sequencing also enabled a detailed map of coronavirus infections associated with multiple schools and sports teams in the area surrounding Carver County and the South Metro this spring.

In Minnesota, no variants labeled as of concern were first discovered. According to Beckman, such varieties are usually found where they occur. Although mutants of interest were identified earlier this year in California, early limited genomic sequencing of the pandemic reduced the discovery of other mutants in the United States, he said.

“I think the United States is currently sequencing the variants of concern here as often as they are detected,” he said.

Even with 20% of the specimens sequenced, state health officials said the specimens must be strategically selected to increase the likelihood of finding mutant strains of concern. While choosing random sampling of specimens from across Minnesota to provide geographic monitoring, epidemiologists can also recommend sequences of suspicious clusters, such as communities with spiked transmission speeds. Sequencing also sought to identify mutations that are likely to cause hospitalization or breakthrough infections in fully vaccinated people.

Matching genomic sequences “help connect the dots,” Better said. “So if you look at something at school, you can see what it looks like if you look at something in a geographic area. [the virus] Introduced and spread throughout the community. “