Omicron represents more than 60% of recent COVID cases sequenced at MUSC

A Christmas Eve release of new data from the Medical University of South Carolina shows Omicron accounts for more than 60% of all COVID cases in scientists’ most recent sequencing run. Julie Hirschhorn, Ph.D., leads the molecular pathology lab that made that finding.

“You can tell that our experience is consistent with what other places are seeing and also it points to the incredible increase in transmissibility with the Omicron variant,” she said. “This pattern of increase is consistent with a doubling every two to three days, as reported by other countries.”

As you can see on the chart above, Omicron went from 3% of all cases sequenced at MUSC the week of Dec. 1 through Dec. 6 to 11% of all cases the following week, and then that stunning jump to 61% the week after that.

“Careful monitoring carefully the number of cases that we're seeing is going to help us plan for the more immediate future. There are multiple ways that even mild disease can have a pretty significant impact on day-to-day operations,” Hirschhorn said.

As she noted, at this point, early evidence suggests that Omicron may cause milder illness than earlier versions of the virus. But its rapid rise could still cause problems.

“People have talked about overwhelming the hospital system. And I think we need to be cognizant that when we talk about overwhelming the health care system, if we have a disease like this that may have milder symptoms, but it's so much more transmissible, we might see an overwhelmed health care system just from the absence of sick care team members.”

That would be similar to the scenario playing out in the travel industry. Airlines are short on staff this Christmas Eve because so many employees have contracted the coronavirus, leading to some flight cancellations.

With that in mind, the Centers for Disease Control and Prevention updated it guidelines just yesterday to try to prevent health care staff shortages. Health care workers who test positive for COVID-19 but don’t have any symptoms can go back to work after seven days with a negative test. That isolation time can be even shorter if needed. And health care workers who have had a booster shot don’t need to quarantine after high-risk exposures.

Hirschhorn said everyone, whether they work in health care or not, can benefit from knowing that Omicron is living up to its reputation as a speedy spreader. While many cases may be mild, the variant could still send people to the hospital. Whether that’s likely to be a small number of patients or a large one is still being discussed. Either way, it’s an important thing to consider as people gather for the holidays.

“We've been told over and over again what keeps us safe. Being vaccinated and getting boosted is a great way to try and reduce your risk of being hospitalized or worse. Try to limit your exposure and limit other people's exposure. The CDC recommends smaller gatherings,” Hirschhorn said.

The CDC also recommends wearing a mask indoors if you aren’t fully vaccinated or you’re in an area with high COVID transmission, staying six feet apart from people who don’t live with you, avoiding crowds, washing your hands and getting tested if you think you might have the virus or you’re about to be around other people, indoors, who aren’t in your household.

But Hirschhorn said Omicron won’t ruin her holidays. “Despite everything that's happening, I'm happy to be here with my family. I'm lucky because right now my kids are healthy and we're going to have a wonderful Christmas celebration with this in the background. It always kind of stays in the background, but we're doing everything we can to be safe and enjoy our Christmas.”

Her team, which is working through the holidays, has shared its data with the South Carolina Department of Health and Environmental Control. “They can also use this information for their contact tracing, if needed. The data really does help with the huge task that our DHEC epidemiology team has as of monitoring the state.”

Brannon Traxler, M.D., is DHEC’s director of public health. “MUSC’s sequencing data, which they immediately shared with DHEC, demonstrates what we anticipated would occur in South Carolina with Omicron’s increased transmissibility. We are seeing the Omicron surge in South Carolina beginning with these cases in the Lowcountry, but expect it to quickly become the dominant variant statewide just as it has elsewhere.”

Hirschhorn said her team is pleased to work with DHEC to get the latest data about the virus out to the public as quickly as possible. “I think some people are anxious to know - just to have that knowledge and be armed with it. And so, to me, even though it's Christmas Eve, it's very important that we work on this and get this information out to the people who care and that want to know about it.”