Publication Date

2022

Document Type

Dissertation/Thesis

First Advisor

Hou, Minmei

Degree Name

M.S. (Master of Science)

Legacy Department

Department of Computer Science

Abstract

The COVID-19 pandemic caused by the SARS-Cov-2 virus has affected the lives of everyone around the world. There has been a rapid appearance of new variants. As the variants affected the efficacy of vaccines, it is important to study the mutations of the variants. A pipeline of tools, SARS-CoV-2 Analyzer, was created to study the mutations in the most mutated S-gene of SARS-Cov-2. Two batches of data were used in this study: all samples available at The National Center for Biotechnology Information (NCBI) were downloaded in September 2021 (before the emergence of the first omicron variant) and December 2021 (after the emergence of the first omicron variant) respectively. After redundancy elimination, sequences were aligned to the original virus genome. Substitutions and deletions were detected from the alignment results.

Based on all samples, we found that most nucleotide positions in the S-gene have mutated in at least one sample; however only very few of these mutations have preserved in dominant strains. It was also found that the S-gene has three main hotspot regions separated by two relatively conserved regions. One type of mutation, deletion, is found to be mostly limited to the first hotspot within a region of 200 bases. Beside the discovery of these patterns, a visualization tool, Subunit Analyzer, was developed to visualize which nucleotide positions in a range of amino acid positions have had substitutions or deletions based on various input parameters. This tool will continue to be useful in future research on this subject.

Extent

119 pages

Language

eng

Publisher

Northern Illinois University

Rights Statement

In Copyright

Rights Statement 2

NIU theses are protected by copyright. They may be viewed from Huskie Commons for any purpose, but reproduction or distribution in any format is prohibited without the written permission of the authors.

Media Type

Text

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