THE MOLECULAR BIOLOGY OF SARS-COV-2 AND ITS EVOLUTION WITHIN THE PRINCETON COMMUNITY

Abstract

SARS-CoV-2, a novel and highly pathogenic coronavirus, has caused unprecedented

global disruption following its introduction into the human population. From the first individual’s falling ill with COVID-19 (the disease resulting from SARS-CoV-2 infection) in December 2019, the pandemic has claimed millions of lives and caused nations around the world to implement drastic public health measures. College campuses across the United States have executed numerous strategies aimed towards reducing the spread of COVID-19 through mask-wearing, social distancing, asymptomatic testing, and contact tracing. Beginning in the 2021 spring semester, Princeton University invited all students to campus and initiated an asymptomatic testing protocol using PCR-based detection of human saliva samples. RNA extracted from PCR-positive human saliva samples was sequenced for surveillance purposes. Using this sequence data, I monitor the evolution of SARS-CoV-2 and emergence of variants over time at Princeton University. Further, in the SARS-CoV-2 Variant Detection project section of this thesis, I optimize a CRISPR-based detection assay for a cluster of eight B.1.1.7 lineage variants possessing a 48-nucleotide deletion in the 3’- UTR of the SARS-CoV-2 genome, eight ancestral B.1.1.7 lineage variants, and validate these assays on Princeton University de-identified extracted SARS-CoV-2 RNA from human saliva samples. Thus, in this senior thesis, I: 1) monitor and characterize the emergence and spread of SARS-CoV-2 variants at Princeton University, 2) provide evidence of the SARS-CoV-2 transmission chain at Princeton University between January 25, 2021 and March 1, 2022, and 3) report my work to develop, optimize, and validate a CRISPR-based detection assay for two B.1.1.7 lineage variants.