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Missoula lab working on front lines as omicron COVID-19 variant emerges

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Posted at 10:08 AM, Dec 08, 2021
and last updated 2021-12-08 12:08:14-05

MISSOULA — The race is on in the US to chase down cases of omicron -- the new COVID-19 variant of concern now showing up around the globe and popping up in more states across the country. 

“That was a tough question to answer because I think it just depends on your perspective on the situation. As a scientist and somebody in my position, to me, it's a public health issue,” noted Chris Booth who is the CEO of FYR Diagnostics in Missoula.

He added that it’s especially important when the variants are emerging so that communities can react accordingly.  

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“Compared to earlier this year, when we were sequencing about 8,000 samples per week, we have increased our genomic sequencing capability,” explained US Centers for Disease Control and Prevention (CDC) Director Dr. Rochelle Walensky. “And we are now sequencing approximately 80,000 samples per week -- about 1 in every 7 PCR-positive cases.  And that’s more than any other country. 

"And that's how we're also going to catch something when something new starts to come out. If they didn't have the surveillance capabilities -- and that they did in South Africa, which are really great -- they might not have caught it as early on,” Booth said. “It might have been a couple of weeks before somebody would have noticed it because again, we're only sequencing 10 to 15% of these things.” 

Sequencing catches new variants like omicron — which is a strain health experts worry could pose a double threat of increased transmissibility and potentially evading immunity.  

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“When you see the alignment, when you’re looking at the sequence -- and you see all the mismatches, all the mutations -- there hasn’t been anything like it. Like not even close,” Booth explained. “Sequencing is very time-consuming. And it's also pretty expensive in comparison to PCR testing.”

That’s why before sequencing, FYR re-deployed a PCR test that actually screens for variants in all positive samples they process. “We’re very proud of our test,” Booth said. “It works really, really well. And we continue to make improvements.   

It helps them prioritize what runs through the sequencer. 

“If we do this quick screening -- and it literally takes an hour and a half -- and we can screen everything, we can identify if any of the positives might be omicron,” Booth said. “Then we can make sure that those are at the front of the line for the next sequencing run and make sure that we catch it.”

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Booth says they look for something called an s-gene dropout in omicron, “s-g69, s-g70—minus minus.”

PCR tests target genes in the genome to look for the virus, including the s-gene. But omicron has many alterations in that gene that make it hard to detect using PCR.  Think of it as a molecular clue that labs across the country are now searching for -- including the University of Washington.  

“So, we're in a much better place in terms of just our ability to find these in our lab. And I think this is similarly true for labs across the country and across the world,” said UW School of Medicine Laboratory acting instructor Pavitra Roychoudhury.

It’s how Minnesota scientists found the state’s first case of omicron — by going back over recently positive samples.     

Booth is confident any omicron case that comes through FYR Diagnostics will be caught through that screening. But a different tool in the fight against COVID-19 spread could mean a blind spot. 

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“So, all of the rapid tests -- the point of care tests like the  Abbott ID now or any of the antigen testing that's being done -- that might be able to indicate that somebody is a positive,” Booth said. “There's no way for us to be able to sequence that sample “

Once those rapid test samples are run, they are spent.  

“There is a push right now to increase the amount of rapid test being used, which is fine, but at the same time for epidemiological reasons, and really getting a grasp and understanding of the virus I mean, it's not just like, catching it early,” Booth explained. “We're still as a globe trying to understand the severity of this virus. “

Booth recommends getting a secondary PCR Test or a second sample for a lab like his to sequence. As for the question of when omicron could appear on the computer, "Not very long I don’t think. Unfortunately,” Booth noted.

Once it does show up it will be entered into a global database to give scientists a better idea of omicron-- including how it spreads, if it evades immunity and exactly what we’re up against.