MUSC lab finds coronavirus 'variants of concern' in samples from this month

March 25, 2021
Bar chart shows changes in coronavirus variants from December 2020 to March 2021.
This graph, created by Dr. Julie Hirschhorn, shows the fluctuation in coronavirus variants from December through March.

About 40% of the coronavirus samples analyzed in March by scientists at the Medical University of South Carolina are “variants of concern” or “variants of interest,” as defined by the Centers for Disease Control and Prevention. The number of samples analyzed so far at MUSC this month is small, just 54, but scientists say the findings give some insight into what the bigger picture may look like.

Julie Hirschhorn, Ph.D., assistant director of the Molecular Pathology Laboratory, leads MUSC’s variant sequencing efforts. “This is a bit of forecasting, but there's certainly a risk. Even though the COVID-19 positive numbers are down right now, there's the potential for more contagious variants to cause another surge. You can see that across the world, and we’re starting to see that in our country already.”

Dr. Julie Hirschhorn talks with Kristen Maurer, a medical technologist who is indexing each coronavirus-positive sample so 384 samples can be sequenced at the same time. 
Dr. Julie Hirschhorn, left, talks with medical technologist Kristen Maurer as they prepare to sequence coronavirus-positive samples for possible variants. Photo by Sarah Pack

In particular, Hirschhorn noted an uptick in the number of B.1.1.7 cases in South Carolina. B.1.1.7, also known as the U.K. variant, may be about 50% more transmissible and can make people sicker than the coronavirus strain that started the pandemic. It’s also the variant that the CDC predicted would become dominant in the U.S. by March.

The CDC has three categories for coronavirus variants. The most serious category is “variant of high consequences.” Fortunately, there are no variants in that category yet, in South Carolina or anywhere else.

But the next category down is “variant of concern,” and it does include several variants that spread more easily, make people sicker and are more resistant to antibodies. B.1.1.7 (U.K.), P.1 (Brazil), B.1.351 (South Africa), B.1.427 (California) and B.1.429 (California) make up that group. All showed up in MUSC’s March analysis.

And the lowest category is “variant of interest.” It includes B.1.525 (New York) and P.2 (Brazil), both of which also showed up in the MUSC March analysis. Variants in this category may have genetic markers that might affect the virus’ spread, diagnosis, treatment or immunity.

MUSC’s molecular pathology lab began analyzing, or sequencing, coronavirus samples in December 2020. It wants to give people an idea of what variants have cropped up in the past, testing samples gathered from earlier in the pandemic, and which ones are gaining ground. It also wants to help scientists, hospitals and government leaders prepare for what may lie ahead.

“I feel like we, as a state, don't have a lot of data out there. So it’s important for MUSC to share this information. I'm not aware of any other facility in the state that’s doing surveillance testing, except for DHEC,” Hirschhorn said, referring to the South Carolina Department of Health and Environmental Control.

A plate of indexes used to identify individual samples during the process of sequencing for variants. 
Technologists are careful in identifying each sample during the sequencing process. Photo by Sarah Pack

Her team’s variant analysis is the latest in a series of pandemic-driven advancements at MUSC. Last April, it became the first hospital/medical center in the state capable of doing its own COVID-19 testing. An MUSC team was also first in the nation to report early success with an experimental therapy for MIS-C, multisystem inflammatory syndrome in children.

Like testing for and treating COVID-19, sequencing for variants at MUSC has the potential to help people across the state – and beyond.

“For March, we were trying to pull all the positives that meet sequencing criteria. You have to have a pretty decent viral load in order to be sequenced. Moving forward, we're going to be collecting as many positives as we can. We're also going to try and get the positives from MUSC Health’s Regional Health Network to come in for sequencing as well."

Hirschhorn said that should give everyone an even better idea of what’s happening as variants ebb and flow. “We have a lot of clinicians who are very interested in this. There are no variants that appear to really have any high impact consequences for treating patients clinically. But if those do develop, we want to make sure that we are able to detect them. Getting into the sequencing at this point in time will help us build our level of expertise as variants of concern emerge across the country.”