Date of Award

Spring 5-6-2023

Document Type

Honors Thesis


Arts and Sciences

First Advisor

Victor Huber, Ph.D.

Second Advisor

Lisa McFadden, Ph.D.

Third Advisor

Andrea Herrera, Ph.D.


SARS-CoV-2, wastewater-based epidemiology (WBE), variant, spike (S) gene, reverse transcription quantitative polymerase chain reaction (RT-qPCR)

Subject Categories

Biological Factors | Community Health and Preventive Medicine | Epidemiology


The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from the subgenus Sarbecovirus, has presented numerous public health challenges for communities across the globe. As demonstrated by the Delta variant (B.1.617.2) and the recent Omicron variants, the virus can mutate and pose new risks for communities, such as reinfection, increased transmissibility, and variable mortality. As such, accurately monitoring the spread of specific variants has become a priority for public health agencies. However, clinical testing faces various limitations, and the increased use of at-home test kits inhibits surveillance. Wastewater-based epidemiology (WBE) can monitor infection rates of entire communities and holds the potential to track variants by detecting SARS-CoV-2 mutations in wastewater. The objective of this research endeavor was to detect SARS-CoV-2 mutations in viral RNA extracted from wastewater samples collected in Vermillion, South Dakota. Utilizing the Promega SARS-CoV-2 Variant Panel-8 Target kit (CS3174B02), several key mutations in the spike (S) gene were targeted utilizing probe-based RT-qPCR, allowing for the detection of specific variants. This thesis explores the evolution and application of wastewater-based epidemiology, details the protocol utilized for variant detection, assesses the efficiency and sensitivity of the Promega kit, and reports original data from samples collected in Vermillion, South Dakota, on February 1, 2022.



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