Publication Date

2023

Document Type

Thesis

Committee Members

Dawn P. Wooley, Ph.D. (Advisor); Christopher N. Wyatt, Ph.D. (Committee Member); Nancy J. Bigley, Ph.D. (Committee Member)

Degree Name

Master of Science (MS)

Abstract

This thesis tests the hypothesis that the spike protein of SARV-CoV-2 is under positive evolutionary selection. A consensus nucleotide sequence was generated for the most current SARS-CoV-2 variant, XBB1.5, by performing sequence alignments of recent isolates. The consensus nucleotide sequence was translated to obtain the amino acid sequence. The amino acid and nucleotide sequences were compared to the original Wuhan-hu-1 strain to identify mutations. Forty-three mutations were identified in the spike protein, and all but two changed the amino acid. The majority of mutations were found in the receptor binding domain of the spike protein, which is the region of the protein that interacts with the ACE-2 receptor on cells to allow viral entry. A novel mathematical formula was created to calculate random genetic drift. Using this formula, the percentage of mutations that changed the amino acid sequence due to random genetic drift was calculated for the Wuhan-hu-1 reference sequence and compared with the observed percentage for the Omicron XBB1.5 variant. There was a statistically significant difference between the observed number of mutations that changed the amino acid and the number expected from random genetic drift for the receptor binding domain and spike protein as a whole. It is concluded that the spike protein of SARS-CoV-2 is under positive evolutionary selection. This mathematical formula can be used to track future variants of SARS-CoV-2 and to analyze other emerging viruses and ongoing pandemic threats, such as highly pathogenic avian influenza A virus strains.

Page Count

134

Department or Program

Department of Neuroscience, Cell Biology and Physiology

Year Degree Awarded

2023


Included in

Anatomy Commons

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