Honors Theses and Capstones

Date of Award

Winter 2021

Project Type

Senior Honors Thesis

College or School



Molecular, Cellular, and Biological Sciences

Program or Major

Biochemistry, Cellular and Molecular Biology

Degree Name

Bachelor of Science

First Advisor

Dr. W. Kelley Thomas


SARS-CoV-2, the etiological agent of the COVID-19 pandemic, has rapidly become a worldwide public health concern. Classified as a betacoronavirus, it is the third human coronavirus (HCoV) to emerge in the 21st century that causes severe disease, alongside SARS-CoV and MERS-CoV. The genome consists of open reading frames encoding accessory proteins and four structural proteins, including the spike protein which is a key determinant of host cell tropism. Mutations within the genome, particularly the spike gene, have been linked in-vitro to increased binding affinity to the human receptor angiotensin-converting enzyme 2 (hACE2), increased fitness in human hosts, and immune evasion. Here, both previously studied and novel mutations were correlated with an increase in case and death rates in California, U.S.A. Eleven mutations, occurring both within nonstructural proteins as well as the spike protein, were found to correlate with significantly increased deaths, while one mutation in the open reading frame 3a (ORF3a) gene correlated with both increased cases and death rates.