The highly transmissible coronavirus subvariants BA.4 and BA.5 have taken over in the latest COVID results from the Medical University of South Carolina as the number of people getting tested goes up.
“We’ve seen a pretty rapid increase in the number of BA.4 and BA.5s and the expected increase in the number of samples we can sequence. And there’s definitely some subtype information that may be relevant,” said Bailey Glen, Ph.D. He’s a scientist who specializes in analyzing biological data and part of the team looking at the genetic makeup of COVID samples collected at MUSC Health test sites. They call that process sequencing.
Any subvariant that starts with the letter B is a mutation of the Omicron variant. As you can see on the graph above, all of the COVID samples sequenced in June and July at MUSC were Omicron’s offspring. In June, out of 220 COVID samples sequenced, about half were BA.2.12.1 and BA.2 and half BA.4 and BA.5. By July, out of the 79 cases sequenced so far, BA.5 was the most common subvariant, followed by BA.4, BA.2.12.1 and BA.2.
Glen, an assistant professor in the College of Medicine, said he also saw something new pop up – that subtype he mentioned. “We see a BA.4.6 that we haven’t seen until now. There’s still lots of change going on. From a genetic perspective, it’s still rapidly adapting. It’s still just kind of wild how much it’s able to change and adapt.”
BA.4.6 is a mutation of BA.4, the latest change for the Omicron variant. It’s unclear what the new mutation’s impact will be or whether it will even stick around, Glen said. But Omicron sure has. It burst onto the scene at MUSC in December 2021 and became dominant the next month. It has mutated to become more and more transmissible.
Julie Hirschhorn, Ph.D., directs the Molecular Pathology Lab at MUSC and serves as an associate professor in the College of Medicine. “I think that we’re surging again. We’re either heading into it or in it. It’s a little hard to tell because there’s not as much reporting of positive tests as before to make it as clear what’s going on. But it does appear that we’re surging again. It’ll be interesting to see how long this wave lasts. We definitely have seen higher sustained positivity rates than previous waves.”
Positivity rate is the percentage of all reported tests that turn out to be COVID positive. That higher sustained positivity rate adds to the sequencing team’s sense of urgency. “Our plan is to try and collect samples as quickly as we can and do the next run sooner rather than later,” Hirschhorn said.
MUSC started sequencing COVID samples in early 2021, tracking the coronavirus’s evolution to show health officials and the public how it’s changing and what the changes mean. The work has been funded by the federal Coronavirus Aid, Relief and Economic Security Act, or CARES Act. But Hirschhorn said that funding is about to come to an end. “We won’t be able to continue to sequence.”
They will keep doing COVID tests to see if people are positive or negative – they just won’t be able to tell which variants are showing up. It’s another challenge in tracking a virus that many people now test for at home.
“It’s intriguing as we move forward to think about having to use the different tools that we have such as wastewater testing in conjunction with individual surveillance testing, to try and gather a broader picture of what’s going on. And I think that’s part of why the CDC is trying to make such an effort to do more wastewater surveillance across the U.S. So that way, we can pair that information together,” Hirschhorn said.
And at a time when many people have quit paying attention to the coronavirus, Hirschhorn encouraged them to tune back in. “COVID still exists. Hospitalizations are a little bit up. For the most part, people that are vaccinated are seeing good protection from hospitalization, but still be careful for the people around you and get tested if you think you have symptoms.”