Delta variant mutations show up in MUSC testing

August 26, 2021
Illustration of the Delta variant. Red background with a ball that has triangles coming out of it to represent Delta.
The blue triangles represent the Greek letter for Delta. iStock

As COVID-19 testing ramps up in the Charleston area amid the biggest case surge of the pandemic, scientists at the Medical University of South Carolina are finding mutations of the Delta variant. One known as AY.4 has become so prevalent that they say it may end up getting a new name.

“It’s clearly blowing up much faster than the original Delta strain,” said Bailey Glen, Ph.D., a bioinformatics scientist in the College of Medicine. Bioinformatics uses technology to analyze biological data.

Julie Hirschhorn, Ph.D., directs the Molecular Pathology Laboratory at MUSC. She said AY.4 is one of more than 20 Delta sub-lineages. “Delta is proving to be a crazy mutator. It’s mutating in a step-wise manner, which may provide one of these variants a selective advantage.”

Delta already spreads easily. “When you talk about original SARS-CoV-2, the transmissibility for that was every person who had it on average transmitted it to two to three people. And when we're talking about Delta, every person who has Delta on average transmits it to five to seven people,” Hirschhorn said.

“So getting Delta under control is really important. And that brings into scale how much Delta is out there and how much mutation can happen because of that.”

Dr. Julie Hirschhorn, associate director of molecular pathology laboratory. 
Dr. Julie Hirschhorn, director of the Molecular Pathology Lab, at work in the early days of the pandemic. Photo by Sarah Pack

Glen said that has implications for public health. “The more we allow Delta to run rampant, the more chances it has to turn into a worse version.”

They’re not saying that AY.4 is making people sicker than other variants, just that it’s part of a pattern that could lead to bigger problems than we’re already facing.

To track that pattern, Hirschhorn and her team use a process called sequencing to see which variants are showing up in people who test positive for COVID-19. “Sequencing takes about four days to complete and evaluates the entire genome of the virus,” she said.

The results show how quickly things change. In April, the Alpha variant ruled. Delta emerged in June, and within a couple of weeks became the dominant strain. It’s blamed for the current surge in cases.

Dr. William Bailey Glen 
Dr. William "Bailey" Glen

Since the number of tests has gone way up in recent weeks, MUSC has started to sequence more frequently, giving a closer to real-time look at what’s happening. That can help guide public health decision-making.

It can also help scientists studying breakthrough infections in vaccinated people, Hirschhorn said. “You can't look for a loss of efficacy in vaccines without knowing what variant those patients have. It's hard to do the research without staying on top of the latest information on what those variants are and combining your data across the country and across the world using the same nomenclature.”

AY.4 is not unique to the Charleston area, Glen said. “This is primarily what the U.K. had by the end. They were primarily AY.4. They don't have as much of this distribution - we have more of this proportionally than most places - but it may come out differently in the end.”

The sequencing team, which includes not only Hirschhorn and Glen but also Darek Pytel, Ph.D., will post its results via the MUSC COVID-19 Epidemiology Intelligence Project. “This is a small group that provides a large amount of data,” Hirschhorn said.

It’s all part of MUSC’s effort to analyze COVID-19 trends and make science-based predictions to help leaders and the public understand what’s happening and what may lie ahead.

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