Date of Award

9-2025

Degree Name

MS in Biological Sciences

Department/Program

Biological Sciences

College

College of Science and Mathematics

Advisor

Pat Fidopiastis

Advisor Department

Biological Sciences

Advisor College

College of Science and Mathematics

Abstract

Problem

The SARS-CoV-2 (COVID-19) pandemic revealed both the systemic vulnerabilities of our healthcare system as well as the importance of timely, localized data for informing public health responses. Traditional testing approaches were essential but often failed to capture the full extent of viral spread, especially in those with mild or asymptomatic conditions that relied on at home testing. This underreporting hindered effective allocation of resources and made developing effective intervention strategies difficult. We also realized the potential for wastewater surveillance to be applied to tracking antimicrobial resistance gene markers. Taken together, this approach should have important implications for improving public health.

Methods

Wastewater-based epidemiology has emerged as a promising tool to monitor community infection trends without relying on individual testing compliance. This study explored the use of wastewater surveillance to retrospectively track the prevalence and genetic variants of SARS-CoV-2 in San Luis Obispo, a region characterized by its dynamic college-town population. By analyzing nucleic acids in wastewater through qRT-PCR and next generation sequencing, this research was looking to show that these methods can accurately monitor public health threats that are circulating in college towns.

Results

The quantification of wastewater in this study revealed six major spikes of SARS-CoV-2 RNA that corresponded closely with the coming and going of students on breaks, as well as the emergence of the Omicron variant surge. Three samples were sequenced and, although there was high quality data, no COVID-19 sequence data was detected. This suggests that there are limitations of the RPIP kit in capturing viral RNA from wastewater under certain conditions. However, genetic markers of many pathogenic bacteria that pose serious threats to public health were successfully sequenced. In addition, genetic markers of antimicrobial resistance (AMR) that help these pathogens withstand our most relied upon medications were also successfully identified in the sequencing data.

Conclusion

This study confirmed the value of wastewater surveillance for tracking outbreak patterns and AMR gene prevalence in dynamic, high risk-communities. Overall, quantification effectively reflected outbreak trends and sequencing highlighted microbial diversity and persistent antibiotic resistance. These findings support the integration of wastewater surveillance into public health infrastructure and stress the need for optimized molecular tools to enhance detection of public health threats in environmental samples.

Download

Share

COinS