Omicron now 97% of cases sequenced by MUSC

January 14, 2022
Bar chart shows Omicron accounts for almost all cases sequenced at MUSC.
The Omicron variant, whose discovery was announced less than two months ago, has quickly taken over.

The Omicron variant now accounts for 97% of all COVID cases sequenced at the Medical University of South Carolina. Data scientist Bailey Glen, Ph.D., an assistant professor in the College of Medicine, wasn’t surprised by the development. 

“Like most of the country and the world, we're seeing Omicron very rapidly take over as not just the dominant variant but perhaps displacing other variants entirely,” he said. 

As you can see in the chart above, Omicron first showed up at MUSC in early December 2021. By Christmas, it had outpaced the Delta variant. In the most recent sequencing run, which looked at COVID samples from Dec. 27 to Jan. 2, it was found in almost all of the 120 cases that scientists tested. Sequencing involves looking at a COVID sample’s viral genome to check for variants. 

Julie Hirschhorn, Ph.D., directs the Molecular Pathology Lab doing the sequencing. “We've been trying to perform a sequencing run every week or every two weeks in order to get out as many samples as we can in close to real time,” she said.  

That’s in addition to the regular COVID testing her team of more than 15 technicians performs 24/7. But those diagnostic COVID tests don’t look for variants, just whether the sample is positive or negative. Sequencing to check for Omicron and other strains can be done afterward on samples that test positive. 

Hirschhorn said now that Omicron has been around for about a month and a half globally, scientists have the chance to get a better idea of how it affects people. “I know we've been saying for a long time, we need to collect more data for the outcomes and hospitalizations, but we're starting to enter that window where we can start collecting that information,” she said. 

Glen said so far in the U.S., some of the data has been less encouraging than in other areas such as South Africa and the United Kingdom. “This may be related to differences in, say, the percentage of the population that’s boosted or vaccinated. But it's the question of how mild it is and how it’s going to affect the U.S. that remains to be seen. The very early data doesn't look great, but it hasn't been long.” 

The Centers for Disease Control and Prevention says current vaccines are expected to keep most vaccinated people from ending up in the hospital with Omicron. It recommends booster shots for everyone 16 and up.  

But the number of unvaccinated people in South Carolina is relatively high. Only about half of all eligible South Carolinians are considered fully vaccinated by the Department of Health and Environmental Control.  

And when you combine that with a variant that spreads easily, creating what public health scientist Michael Sweat, Ph.D., recently called a “massive explosion of cases,” hospitalizations are on the rise. At MUSC Health’s Charleston hospitals, the number of COVID patients is around its previous pandemic peak. Not as many are in the intensive care unit as at the peak in July 2021, according to MUSC Health System’s chief quality officer, but they’re still sick enough to be in the hospital. 

Meanwhile, Hirschhorn and her team are keeping an eye on something that could tell them when the current surge begins to take a turn for the better: the positivity rate. That gauges the percentage of COVID tests that are positive. Right now, it’s really high.  

“Around Christmas, they were 13% and then last week, they were 35%. The numbers still seem to be rising, but not as quickly,” Hirschhorn said. “I am hopeful that soon we may start seeing a bit of a plateau.” 

It’s another period of uncertainty as a variant that caught a lot of people off guard gains ground, and scientists look ahead. “I'd say that Omicron put us in a situation where the future’s harder to predict, perhaps. A lot of times you see viruses move in a stepwise evolution — the next strain comes off of the previous strain. So far with COVID, that hasn't been the case,” Glen said.  

“The evolution of Omicron goes back much earlier. It came from a very early strain that had already been outcompeted by bunches of other strains from Alpha to Delta. I feel like the relatively milder nature of Omicron is encouraging, but it’s left us with a lot of uncertainty over what's next.” 

Hirschhorn said her team will be ready for whatever lies ahead, whether it’s a shift from a pandemic to endemic state — meaning we live with a low level of COVID — or whether we have to contend with more variants.

“They have such a commitment to making sure that as many people as possible get tested and people can feel confident in the system. I think that's what drives us to all support each other in this effort and prop each other up when we're starting to feel a little dragged down — the need to provide good, accurate results really drives what we do.” 

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About the Author

Helen Adams

Keywords: COVID-19