Discriminating between JCPyV and BKPyV in Urinary Virome Data Sets.

Area of Science:

• Virology
• Human Microbiome
• Genomics

Background:

• Polyomaviruses, including JC virus (JCPyV) and BK virus (BKPyV), are widespread in the human body.
• Both JCPyV and BKPyV are frequently detected in the human urinary tract.
• These viruses share significant genomic similarity (75% nucleotide identity) and encode identical genes, complicating their differentiation.

Purpose of the Study:

• To compare the prevalence of JCPyV and BKPyV in the human urinary tract.
• To re-evaluate existing urinary virome data for accurate JCPyV and BKPyV identification.
• To establish reliable methods for distinguishing between closely related polyomaviruses.

Main Methods:

• Retrieved and analyzed publicly available shotgun metagenomic sequencing data from 165 urinary microbiome and virome studies.
• Specifically mined data for JCPyV and BKPyV sequences.
• Employed uniform genome coverage analysis to confirm viral identification and differentiate between closely related species.

Main Results:

• While approximately one-third of analyzed datasets showed hits to JCPyV, detailed investigation revealed most were misidentified BKPyV.
• Accurate differentiation confirmed BKPyV as the predominant polyomavirus in the analyzed urinary virome samples.
• The refined identification method ensures high confidence in taxonomic assignments for closely related viruses.

Conclusions:

• Many previous reports of JCPyV in the urinary tract likely represent BKPyV due to sequence similarity.
• Precise methods are crucial for accurate epidemiological studies of polyomaviruses.
• This study underscores the importance of rigorous bioinformatic approaches for distinguishing between highly homologous viral genomes.