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Honors Program

Swabs, Sewage and Strains

Sequencing the guts out of COVID-19

Instead of collecting houseplants or scrolling TikTok, senior Honors student Madelyn Grose spends her pandemic time at sewage plants and research labs. As a Bioinformatics major, Madelyn is interested in answering the questions surrounding SARS-CoV-2. This fascination led to the development of Madelyn’s thesis, “The Evolution Behind the COVID-19 Pandemic,” or in other words, sequencing the guts out of COVID-19. For the project, Madelyn is analyzing various COVID strains and how they uniquely affect people based on their genomes.

By nature of her interests, Madelyn spends most of her time in the buildings of south campus. Her lab research began in the Life Sciences and Benson Building: Madelyn dissected otoliths (fish ear bones) to see when the fish reproduced. Otoliths are similar to trees in that they have rings corresponding to their age. Madelyn’s team hoped to discover at what ages the fish reproduced, which involved mass spectrometry. They tested the elements in each of these rings, looking especially for elements associated with reproduction. The team did not have enough funding to finish the project, but the experience left Madelyn with a passion for evolutionary biology. This love led to a position as a teaching assistant for BIO 250: Evolutionary Medicine under Drs. Byron Adams and Jerry Johnson.

After completing this work, Madelyn moved onto the Engineering Building where she consulted on the 2020 Mars Rover Team. She created a way to sense biological patterns considering the limitations of being in space. Communicating these biological concepts to her engineering teammates proved to be complicated, but Madelyn persevered. Due to COVID, the team did not compete, but Madelyn enjoyed the interdisciplinary nature of the team and applying her skills in a way that was truly out-of-this-world.

While balancing her work with the engineers and the fish, Madelyn climbed the Honors ladder in the Maeser Building. Learning the Honors way was a difficult process for Madelyn as she retrained her brain to think in a certain new way. When asked how she was able to find her place in Honors, she said that her biggest piece of advice would be to "take everything in stride. Realize that there will be learning curves and prepare to ride them out to success.”

Her Honors thesis took her back to the Life Sciences Building where she began working in the lab with Dr. Mary Davis, Associate Professor of MMBio. After studying space and the ocean, Madelyn decided it was time to study what was right in front of her: SARS-CoV-2. There were positive COVID samples from hundreds of student swabs in the health center and she knew there would be valuable data within those samples. New research has shown that the virus can live in the gut and cause abdominal pain, intestinal strain, and diarrhea. Madelyn wanted to understand if these newer gut symptoms were the result of a new strain of SARS-CoV-2 or if personal genomes were reacting differently to the virus.

The local sewage plant was the first stop for her project. She rode in a golf cart to the collection site to learn more. She found it fascinating that sewage workers almost never get sick due to exposure of all sorts of microbes. This helps them to develop a strong immune system. Madelyn compares the viral strains in the sewage as the current group and uses previous student samples as the older group. Scientists typically use Arctic sequencing to label SARS-CoV-2 genomes, which includes breaking the virus genomes into 100 pieces. However, this process did not work with Madelyn’s plan because the sewage samples contained too many viruses. She found that breaking them into 100 pieces resulted in too many overlapping fragments but breaking them into 3 pieces ended up being too large. Finally, she discovered that breaking the genomes into 10 pieces resulted in the perfect size.

Now that her methodology is secure, Madelyn will sequence all of the genomes and begin comparing the strains. When commenting on the process so far, Madelyn remarked that she “lived and breathed scientific methodology papers and reference guides” to understand if the bad results in the sequencing process were from decaying RNA stands or bad samples. Instead of being discouraged by the failure, Madelyn was motivated to try harder until she found the right number of fragments.

This tendency to face failure with grit is a trait that will surely benefit Madelyn as she graduates and pursues higher education. Until then, Madelyn will be in the lab sorting out her Us and Gs from her As and Cs.

Madelyn is from right here in Provo, Utah, and studies Bioinformatics with a minor in Computer Science. When she isn’t demystifying COVID or studying fish ears, Madelyn enjoys running, cosplaying characters for Comic-Con, reading horror books, playing the Tahitian ukulele, and scuba diving whenever she can. After graduating in Summer 2022, she is planning on working on a PhD in bioinformatics, evolutionary biology, or marine biology.