2024 Undergraduate Research Showcase

Analyzing Base Pair Alignments for Pathogens in Patient Samples

Document Type

Student Presentation

Presentation Date


Faculty Sponsor

Dr. Stephanie Hudon


This past Spring, Dr. Stephanie Hudon and I analyzed pathogens in patient and wild animal samples using Next Generation Sequencing with the Illumina Respiratory Pathogen ID/AMR Enrichment Panel (RPIP). We found that Coronavirus OC43 was prevalent in many clinical samples in patients who had tested negative for COVID-19 and Influenza but were still exhibiting respiratory and other symptoms. I also found Coronavirus OC43 through surveillance of a ground squirrel. This may suggest the pathogen has a zoonotic origin. I analyzed the base pair alignment of each of our patients’ pathogen samples to the strains found in NCBI to determine if mutations had occurred. This research opens the door to furthering our understanding of how pathogens are transmitted between humans and animals. Additionally, many of the patients who tested negative for COVID-19 but had Coronavirus OC43 exhibited much harsher symptoms (such as throwing up) than patients usually exhibit with this pathogen. Our base pair alignment analyses could suggest that there may have been a mutation event that caused these more severe symptoms.

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