MUSC looks for Omicron in local COVID cases

Scientists at the Medical University of South Carolina are sequencing almost 400 local COVID cases this week to see if any involve the new Omicron variant. Sequencing involves looking at each virus sample’s genetic makeup. That shows any mutations and lets the scientists identify variants. They expect to have results this Thursday or Friday. 

“We have talked about how important it is to do real-time or as close to real-time analysis as possible,” said Julie Hirschhorn, Ph.D., director of Molecular Pathology at MUSC. “And this is a perfect example of when we know that we're looking for something new, to try to do our sequencing runs more frequently. And so for the next couple of weeks, we're going to try to do a run a week.”

The virus samples came from people who tested positive for COVID-19 at MUSC Health. Each run takes three to four days to complete. MUSC sends its results to the South Carolina Department of Health and Environmental Control and shares them online with the public.

 

Hirschhorn and her team feel a sense of urgency as the world watches to see if Omicron becomes a serious problem. Scientists announced the new coronavirus variant’s discovery in South Africa just last week. Since then, it has shown up in several other countries. No cases have been announced in the United States, but experts say it’s likely already here.

Bailey Glen, Ph.D., who works with Hirschhorn, did a retroactive search for Omicron the day after Thanksgiving – the day the World Health Organization designated Omicron a variant of concern. “I got up and looked at a good chunk of our recent data,” Glen said. 

 

He knew what to watch for, thanks to a site for scientists that shows what Omicron looks like. Glen was able to compare Omicron’s genetic sequence with that of the MUSC samples. None matched. The Delta variant, which became the dominant strain in the U.S. last summer, was still king.

But some experts, including Glen, are worried about Omicron because of its high number of mutations. It’s been described as “almost Frankensteinish.”

“It has many more mutations in the spike protein – like three, three-and-a-half times as many as we were seeing in the previous round of variants of concern,” Glen said. “The amount of change that represents and the amount of uncertainty it brings is another big reason there's a lot of concern, along with the way it seemed to come out of nowhere.”

It’s unclear how contagious the new variant is. Scientists say it will take two or three weeks to get a better picture of how easily it spreads, how well vaccines work against it and whether antibodies can beat it back. 

It’s also unclear how sick Omicron may make people – and whether it will fizzle like some previous variants, Hirschhorn said. “There's always the possibility that these new variants pop up, but for one reason or another, they just don't take hold in, in our population or in our state. So we can cross our fingers.”

But we can also prepare, she said. “It's probably a good idea to treat it like it's going to be bad, even though we don't know yet. I don't want to scare people, but at the same time, we've seen these things go both ways. With Mu and Lambda, we were concerned – rightly so – but they never took hold. It's important to think about as we go into another holiday season: How do we keep the people we love safe?”

MUSC has been playing a key role in South Carolina’s response to the pandemic from its early days, and Hirschhorn said the Omicron sequencing is a continuation of that. “MUSC is a health care leader in South Carolina, and as part of that team, I feel an obligation to the state to help monitor this public health situation. And I think that a service like sequencing variants brings comfort to people in some ways, because they know what's going on,” she said,

“So often during this pandemic, we have all felt helpless – like we didn't know what was happening. And so to me, and to our lab, it's very important that we try and provide as much information as we can, so that way, people can at least feel a little bit of control.”