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Montana Researchers Use Gene Sequencing To Identify COVID-19 Variants

A PCR testing machine at the University of Montana Genomics Core lab in Missoula, Montana.
Aaron Bolton
Montana Public Radio
A PCR testing machine at the University of Montana Genomics Core lab in Missoula, Montana.

Montana Researchers Use Gene Sequencing To Identify COVID-19 Variants

As health officials continue to roll out COVID-19 vaccines, making sure those vaccines remain effective against new variants of the virus is an important part of controlling the pandemic. Montana’s state health department and universities are working to stay on top of the virus evolution.

At the University of Montana Genomics Core lab in Missoula, one machine is capable of extracting RNA particles from COVID-19 nasal swabs.

“This kind [of machine] can work on 96 samples at once,” lab manager David Xing says.

Xing explained that the RNA from these samples will be run through another machine that gives positive or negative test results. In the near future, Xing’s lab will also be able to sequence the genes of the viruses from COVID-19 tests.

Genetic sequencing allows scientists to identify known COVID-19 variants that federal health officials say are concerning. It also helps them keep an eye out for new variants that could be more infectious, more deadly or able to evade vaccines altogether.

“We just did a trial run. We did the sequencing of around 20 positive samples. We know it’s the worst concern,” Xing says.

The state health department, Xing’s lab and Montana State University have done limited sequencing work so far, identifying about 260 variant cases statewide. A more systematic sequencing effort is in the works so health officials can stay on top of how the virus is changing.

The Montana Department of Public Health and Human Services is using $11.5 million in federal funding to contract with Xing’s lab at the University of Montana, labs at Montana State University and Fyr Diagnostics, a private lab in Missoula.

A machine extracts RNA particles from COVID-19 nasal swabs at the University of Montana Genomics Core lab in Missoula, Montana.

The state lab is also bolstering its own sequencing capacity by more than sixfold, according to the state health department’s Jim Murphy.

“I think we’ll have a good network in Montana that should be able to spot anything new that is circulating around here,” Murphy says.

Murphy says the cost of this work makes it impossible to sequence every positive test in Montana, even as case numbers go down. Instead, the state has set its sights on sequencing 10%-15% of all positive samples.

Last week, the state was able to sequence 12% of the positive PCR tests. 

Andrew Pekosz, a virologist with Johns Hopkins Bloomberg School of Public Health, says that “12% is a great number to be at.”

He says federal health officials haven’t offered firm guidance on what percentage of positive COVID-19 tests should be sequenced in order to stay on top of emerging variants.

“But there have been modelers and others that have suggested that if you do that 10%-15% range, you should get a good idea of when something is becoming more dominant in your population,” Pekosz says.

He explained that the more people that become infected, the greater the chance new variants will crop up. That means rural states like Montana, with low populations and smaller case numbers, are more likely to see variants imported from elsewhere - versus finding a homegrown strain. Pekosz says that doesn’t mean it can’t still happen. 

“That’s why the surveillance efforts are really, really important. I’ll also add that there’s, on top of that, we are starting to see variants that have different disease severity.”

That means identifying the arrival of more severe variants early can help hospitals prepare for sicker patients, allow health officials to inform the public and push the pandemic-related precautions. 

Pekosz and other experts say much of the country is just beginning to hit that 10%-15% sequencing goal, namely because labs have to sequence fewer positives as COVID-19 cases are going down.

He added that maintaining that coverage will get harder if cases increase, and it will be important for Montana and other states to continue building their sequencing capacity through the summer months.

“Now is the time that we all prep and get ready for what we expect to be a bit of a surge in the fall, once the weather becomes cooler and people move inside and transmission is much more likely.”

Capacity building is already happening at Missoula’s Fyr Diagnostics, says CEO Chris Booth, in anticipation of finalizing the company’s contract for sequencing work with the state. According to Booth, Fyr is buying new equipment and doubling the size of its lab.

“So as long as we have all the infrastructure set up, we’d be able to do a lot of samples every week, which is great.”

Booth says the lab could sequence 300 samples per week — and maybe even more. He added it has been tough to hire enough lab technicians to boost sequencing capacity. There has been a spike in sequencing demand as labs across the country try to prepare for a potential fall surge of COVID-19 cases.
Copyright 2021 Montana Public Radio. To see more, visit Montana Public Radio.

Aaron is Montana Public Radio's Flathead reporter.