The JC polyomavirus (JCPyV) is most commonly found within the urinary tract, and prior studies estimate that this virus persists within the kidneys of 20-60% of older adults [1]. To date, only two shotgun metagenomic sequencing studies have been conducted of the urinary viral community (urinary virome or urovirome) of individuals with UTI symptoms (N=54) [2,3]. Both studies reported the presence of JCPyV in the urovirome of these individuals, but JCPyV has not been previously associated with UTI symptoms. This prompted our investigation into the prevalence of JCPyV in women with UTI-like symptoms.

Urine samples from 53 women with UTI-like symptoms and 30 women without UTI symptoms were collected as part of previous IRB-approved studies. DNA was extracted from the urine samples using a phenol-chloroform protocol, and JCPyV was detected by PCR using the following primers: JCPyV-1f (5’-CAG GAA AGT CTT TAG GGT C-3’) and JCPyV-1r (5’-CCC TGT TTA ATG TGC ATG-3’). 

In parallel, raw reads from the two aforementioned UTI urovirome studies were retrieved from NCBI’s SRA database and the iMicrobe database. These data sets include 54 uroviromes from individuals with UTI-like symptoms and 10 uroviromes from individuals without UTI-like symptoms. The presence of JCPyV within these samples was determined by mapping the raw sequencing reads to the JCPyV RefSeq genome (Accession no. NC_001699.1) using Bowtie2 in Geneious Prime.

The PCR assay detected JCPyV in 4 (7.5%) of the 53 urine samples from women with UTI-like symptoms. Likewise, bioinformatic analysis of the urovirome datasets detected sequencing reads mapping to the JCPyV genome in 9 (16%) of the 54 urovirome samples from individuals with UTI-like symptoms; all 9 were from the same study [2] and all came from women. In contrast, neither the PCR assay nor analysis of the urovirome datasets detected JCPyV in samples from individuals without symptoms (N=30 and N=10, respectively). 

We could reconstruct the JCPyV genome from one of the samples from a woman with UTI-like symptoms, Figure 1, indicative of a high abundance of the polyomavirus within the urine sample.

Our study suggests that the incidence of JCPyV in the urine of women with UTI-like symptoms is greater than in the urine of women without symptoms. This has been confirmed via both PCR using JCPyV-specific primers and shotgun metagenomic sequencing of urinary samples.

Further PCR-based testing and urovirome sequencing of women without UTI-like symptoms is needed to ascertain if JCPyV shed in the urine is a biomarker of infection. This is a critical first step in ascertaining if JCPyV contributes to UTI-like symptoms and/or is a consequence of infection.

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Santiago-Rodriguez TM et al. 2015. The human urine virome in association with urinary tract infections. Front Microbiol 6:14.