A collaboration among UNC-Chapel Hill clinicians and researchers is leading the way in how we think about tracking viral variants.
By Angela Harwood
Photos by Jen Hughey and Megan May
t seems like every other month we hear about the emergence of a new variant of the virus that causes COVID-19. In order to make decisions that improve public health outcomes, policymakers, health officials and epidemiologists need to know how quickly and easily these variants spread and whether or not they’re able to break through vaccines.
But where do these data come from? And who can health officials rely on for the most immediate information?
With support from the UNC COVID-19 Research Accelerator Fund, Jeremy Wang, Ph.D., assistant professor of genetics in the UNC School of Medicine, and his team are identifying and tracking the variants emerging in our state and sharing their findings with the public from right here at UNC-Chapel Hill.
Serving the state
The process includes clinical experts from UNC Medical Center and researchers from across Carolina — all working together to support the greater public health effort to quash the pandemic.
“It’s important to know how the virus is changing in as close to real time as possible so that we can get interpreted data out to people as quickly as possible,” Wang said.
Wang, whose research focuses on bioinformatics, metagenomics and genomic epidemiology, gets deactivated samples from COVID-19 tests processed by the Clinical Microbiology Laboratory at UNC Medical Center. Through a process known as genomic sequencing, he identifies which variants are apparent and shares the aggregate data through a public database.
“The transparency of the data on this public facing website is critical,” stressed Professor Melissa Miller, Ph.D., director of the Clinical Microbiology and Molecular Microbiology laboratories at UNC Medical Center. “Our clinicians look at it daily; I get emails about it. It is definitely a service to our professional community and to public health and the community at large.”
Beyond its clinical use, Miller uploads the data to the state’s communicable disease branch, providing state health officials with accurate, up-to-the-week snapshots of what’s going on in North Carolina.
“As a component of a broad health care system, we have specimens coming from hospitals across the state, so our data represent more than just our surrounding counties,” she said. “Policymakers and epidemiologists can link those data to GPS or community specific data, like zip codes, and they know the vaccination rates in counties across the state. They can then take action, really target those areas where a variant of concern is spreading.”
For example, as the state is starting to see more of the Delta variant, which is of concern because it is more highly transmissible, one excellent intervention that Miller mentioned is to try to improve the vaccination rates in the areas most affected.
“As you’d expect, we’re seeing more COVID in the areas that have lower vaccination rates, and it’s important to look at what the variants are,” Miller said. “The more you have transmission of the virus, the more likely it is for a new variant of concern to emerge. When you increase vaccination rates, you decrease the potential for emerging variants.”
Responding to the moment
Wang and his team started sequencing genomes and sharing their findings in January 2021 in response to the need for more information about emerging variants.
“There just wasn’t a lot of publicly available data out there from North Carolina at the beginning of the year,” Wang said. “There were several entire states that had not released a single genome, so there were these huge blind spots in the world’s view of what the variants were, where they were, and how quickly they were spreading.”
Since then, Wang and colleagues have sequenced and shared more genomes of the virus than anyone else in North Carolina, tracking which variants appear to spread more quickly in as close to real time as possible.
“When you go back and look at the data from January, you’ll see that variants in North Carolina were virtually nonexistent,” Wang noted. “It was all the standard COVID-19 strain that launched the pandemic. What’s happened over time is that as new variants come in, we’re able to see which ones are dominating in North Carolina.”
It’s important to know which variants are dominant as some variants may be more or less transmissible and/or easier or more difficult for our immune systems or vaccines to handle than others.
“Tracking these variants helps us know whether or not we are winning or losing the time game on vaccinations,” said Corbin Jones, Ph.D., a biology professor in the UNC College of Arts & Sciences working with Wang and his team. “If we could vaccinate enough people well enough and fast enough, we’d be able to squelch the virus.”
When Wang started genomic sequencing in January, 7-8% of the genomes were mutations of the original strain of the virus. Now the data reflect that almost 95% are variants, with the Delta variant starkly on the rise. Because of Wang’s efforts, policymakers can see these shifts quickly, allowing them to make better policy decisions.
“We are getting these data to health officials just a week removed from the patients appearing in the hospital,” Jones said. “That gives you some predictability or targetability to where the critical spots are going to be.”
Making a difference
This entire project, and the development of the fund that supports it, reflects how the Carolina community has pivoted throughout the pandemic.
The UNC Office of the Vice Chancellor for Research launched the UNC COVID-19 Research Accelerator Fund in April of 2020 to provide critical, unrestricted support to Carolina’s world-renowned COVID-19 research teams. Since then, more than 200 donors have contributed to the fund. Collectively, these gifts — which range from $5 to $20,000 — have made a significant difference.
“If it hadn’t been for the Research Accelerator Fund, these data would not exist,” Jones stressed. “We spend the bulk of these funds on purchasing the reagents and primers necessary to get samples processed and sequenced as quickly and smoothly as we can. But most importantly, the funding gives Jeremy the freedom to do this work, as we are not charging anyone for this service.”
The funding also allowed the research team to hire Brianna de la Houssaye ’20 to help with the RNA extractions and sequencing. Houssaye volunteered in Jones’ lab as an undergraduate student studying biology at Carolina. Together, she and Wang process around 100 samples a week, and Houssaye is gaining valuable experience in the field of genetics.
“I’m actually able to apply knowledge from the classroom into action in the lab,” said Houssaye. “It’s definitely made me want to do more in population genetics. I’m glad to have this opportunity to work on this research that is so important to so many people.”
The collaboration among Carolina’s clinical and academic researchers continues to evolve to best meet the needs of patients and the community.
Wang and Jones stepped up to fill the void when this service didn’t exist. They had the equipment and expertise to pivot to sequencing and genomic analysis of SARS-CoV-2 because of their previous work in genome assembly and phylogenetic analysis for a wide variety of organisms — including fruit flies, pupfish and E. coli.
Wang continues to interpret data and provide the bioinformatics to the public, but the sequencing now takes place in the UNC Medical Center Clinical Microbiology Lab under Miller’s clinical microbiology fellow Shawn Hawken, Ph.D., M.P.H.
This collaborative approach to tracking viral variants has implications beyond the state’s borders.
“Jeremy’s work displays the power of the partnership you can have among health care systems, academic labs and corporate labs to address a public health problem,” said Miller. “This partnership and process is a model on how we can do this going forward with influenza seasons or to be ready for the next pandemic.”