Lumen Scholar Grace Carter ’20 examining evolution of retroviruses

Grace Carter '20 and Assistant Professor of Biology Alfred Simkin are analyzing the chimpanzee genome in hopes of better understanding viruses like HIV.

Grace Carter ’20 set her sights on the Lumen Prize during her very first year on campus.

“I was like, ‘I want to do this. This sounds so cool,'” Carter said about the chance to join Elon’s prestigious program for undergraduate research.

Now, midway through her senior year, Carter is deep into her Lumen Prize research into how retroviruses evolve. Her work has identified thousands of retroviruses that appear to have been previously unknown to researchers. It’s work that could eventually contribute to a better understanding of retroviruses like the Human Immunodeficiency Virus, or HIV.

“Lumen has definitely changed the course of my Elon career,” she said.

As a Lumen Scholar, Carter received a highly competitive, $20,000 award as a rising junior. Lumen Prize applicants construct a proposal and interview with a committee of faculty members from across the university, who determine the cohort of Lumen Scholars each year, based on the students’ merit, proposals and passion for their projects. Lumen Scholars work closely with a mentor during the course of their research, which often produces conference presentations and publications.

For Carter, the search for a research topic was a journey unto itself. As a sophomore, Carter attended one of the Biology Department’s “flash talks” in which faculty presented short lectures about a wide range of topics. One of the presenters was Assistant Professor of Biology Alfred Simkin, who lectured about the evolution of genomes, or the genetic material of organisms.

Carter came to Elon with an interest in studying genetics and was immediately hooked.

Carter approached Simkin with the idea of working together to pursue the Lumen Prize, and the two began researching topics soon after. The search, however, presented several challenges. As Carter recalls, Simkin warned her finding a well-developed topic that hadn’t been researched before would be like “beating the big boss in a video game.”

“He was like, ‘finding your topic, you’re going to have to get beaten like 30 times, but then the 31st idea is going to be the idea that is the ticket, and it’s going to be so great, and you’re going to beat the big boss,’” Carter said.

Simkin immediately took note of Carter’s passion as she diligently worked to craft her topic.

“The thing that really struck me about Grace is that she kept coming back,” said Simkin, who has expertise in genome evolution and computational biology. “I would give her all of the reasons why something was totally infeasible, and I would expect her to be really dejected or disappointed by that. I felt kind of bad about saying these things, but she would always come back the next week with like five new ideas that were improved from the ideas before.”

After weeks of searching, Carter finally landed on a topic: the evolution of retroviruses. Retroviruses are viruses with the capability to insert DNA copies of their genetic information into the genome of host organisms. The most well-known retrovirus among humans is HIV. The virus has affected humans for roughly 60 years after it made the jump into the human genome from chimpanzees who have carried SIV, simian immunodeficiency virus, for tens of thousands of years.

Carter wanted to investigate the evolution of SIV in primates and the retrovirus’ ability to adapt and survive in those species for so many years without necessarily killing its hosts. She hopes learning more about SIV can one day help humans better understand and combat HIV.

“We’re using that to hopefully create some new knowledge regarding HIV that then people who develop the treatments can use to target HIV even better – to know how we can fight it off better. The biggest thing is learning about the virus – the more you know, the better you can fight it off. So, that’s kind of our goal is to contribute to that body of knowledge.”

Carter clearly showed her passion for the project and the worthiness of her research to the Lumen Prize selection committee, which in 2018 named her one of 15 Lumen Scholars in the class of 2020.

“It was very exciting,” she said. “It was definitely a moment of validation that we weren’t the only people who thought this was a good idea. So, it was an awesome feeling for sure.”

With the support of the Lumen Prize, Carter and Simkin began their work. Using programs designed to annotate new retroviruses, Carter scanned the entire chimpanzee genome to learn about the landscape of retroviruses in their DNA. The findings would help Carter compare SIV’s evolution to that of other dormant retroviruses to find out how the evolution of SIV differed and allowed it to survive for tens of thousands of years.

After scanning the chimpanzee genome with two different programs, Carter compared the outcomes to find areas where the results overlapped. Those overlaps would potentially reveal retroviruses not previously known.

Carter’s research returned 30,000 results. Nearly 5,000 of those hits were thought to be newly discovered and 370 of those were presented with more than 90 percent confidence.

“A lot of times in science, you’re going to find things and say, ‘oh my gosh, I discovered 30,000 new viruses!’ Well, probably not,” Carter said. “But the potential that one of those 30,000 is something really awesome is definitely there.”

To produce those findings, Carter relied upon one of the many skills she has developed during her Lumen Prize research. Before her junior year, Carter took a summer class to learn how to use the Python coding programs that would drive her research. After beginning her Lumen journey with no programming experience, Carter now considers herself a “handy” programmer. She even wrote the 300-line program that helped her find those 5,000 potentially new retroviruses.

“At first, coding can be a little difficult to master. In Grace’s case, after several months of diligent work, there was a definite moment one week where she was suddenly able to solve any problem I could come up with,” said Simkin of Carter, who later learned to use more advanced bioinformatics coding programs. “It’s like she cracked coding, and then after that, she was on fire. It was so rewarding as a mentor to see her fully swimming in the coding ocean. It was awesome.”

Carter plans to pursue a doctorate in genetics and says the Lumen Prize has given her invaluable experience in her field, offering two years of research on a topic that she developed. The biology major has also had the opportunity to present her work at conferences and was recently invited to present at Viruses 2020, a research conference in Barcelona, Spain, in February.

But for now, her work continues. Her next steps include taking a closer look at those nearly 5,000 retroviruses to confirm which of the findings are truly new discoveries. Carter hopes to one day publish her work and someday go on to make the individualized human genome more accessible to medical professionals who could possibly use her research to save lives.

“I want this work to help someone eventually,” she said.