Major
Bioinformatics
Anticipated Graduation Year
2021
Access Type
Open Access
Abstract
The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are thought to be common viruses in the human urinary tract, and prior studies estimate JCPyV infects between 20-80% of older adults and BKPyV infects between 65-90% of individuals by age 10. These estimates largely stem from PCR-based tests. Recent shotgun metagenomes of the urinary microbiota have similarly reported the presence of these two polyomaviruses based on sequence homology searches. However, JCPyV and BKPyV encode for the same six genes and share 75% nucleotide sequence identity across their genomes. This prompted our in-depth investigation into the detection of and distinguishing between these two closely realted viruses within microbiome data. This study examines publicly available whole-genome sequencing reads from urinary microbiome and urinary virome studies (n=165) to ascertain the abundance and prevalence of these two polyomaviruses.
Faculty Mentors & Instructors
Dr. Catherine Putonti, Professor, Department of Biology
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.
Detecting Polyomaviruses in the Urinary Microbiome
The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are thought to be common viruses in the human urinary tract, and prior studies estimate JCPyV infects between 20-80% of older adults and BKPyV infects between 65-90% of individuals by age 10. These estimates largely stem from PCR-based tests. Recent shotgun metagenomes of the urinary microbiota have similarly reported the presence of these two polyomaviruses based on sequence homology searches. However, JCPyV and BKPyV encode for the same six genes and share 75% nucleotide sequence identity across their genomes. This prompted our in-depth investigation into the detection of and distinguishing between these two closely realted viruses within microbiome data. This study examines publicly available whole-genome sequencing reads from urinary microbiome and urinary virome studies (n=165) to ascertain the abundance and prevalence of these two polyomaviruses.