Date of Award

Fall 2022

Degree Type


Degree Name

Master of Science (MS)


Bioinformatics & Computational Biology


Polyomaviruses are the smallest closed-circular supercoiled double-stranded viruses found in the human microbiota. The polyomavirus JC (JCPyV) is most commonly found within the urinary tract, and prior studies estimate that 20-80% of older adults carry JCPyV. In very rare cases, JCPyV leaves the kidneys, causing progressive multifocal leukoencephalopathy. However, the role of JCPyV within the urinary tract remains an open question. In a prior study conducted by our group, the bladder microbiota of females with and without overactive bladder symptoms (OAB) were sequenced. Interestingly, JCPyV was only detected in females with OAB; none of the control (“asymptomatic”) microbiota contained JCPyV. However, the sample size for this study was small (n=30). This thesis is a multidisciplinary approach to explore the presence and prevalence of polyomaviruses in the urinary microbiome (urobiome). In a bioinformatic investigation of JCPyV and BKPyV, a closely related polyomavirus to JCPyV, 165 publicly available urinary virome and urinary metagenome data sets were mined for these two polyomaviruses. Sequence diversity between JCPyV and BKPyV genomes was explored to design a new primer pair to uniquely identify JCPyV in urobiome samples. Using these ultra-specific JCPyV primers, 190 urine samples, including 99 from females with OAB, 33 from females with UTI, and 58 from females without lower urinary tract symptoms, were screened for JCPyV to assess the prevalence of the virus as well as to assess the association of JCPyV with symptom status, age, and race/ethnicity. Additionally, the urobiome of JCPyV+ individuals was sequenced in an effort to identify associations between JCPyV and bacterial taxa. We found no associations between JCPyV presence or abundance and any of the factors when tested individually. However, some associations were found when some of the factors were considered together in predicting JCPyV prevalence. Additionally, both our bioinformatic and molecular survey suggests that JCPyV is less prevalent in the female population than previously thought.

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.