Multiplex qPCR assay for ultra sensitive detection of JCV DNA with simultaneous identification of genotypes that discriminates non-virulent from virulent variants

J Clin Virol. 2013 Jul;57(3):243-8. doi: 10.1016/j.jcv.2013.03.009. Epub 2013 Apr 23.


Background: JC virus (JCV) is the etiologic agent for progressive multifocal leukoencephalopathy (PML), a demyelinating disease occurring in the brain of patients with underlying immune compromised states. All viable JCV genomes contain a conserved region in the T protein coding nucleotide sequence that when detected by PCR in CSF is a confirmatory diagnostic marker for PML along with clinical and neuroradiological evidence. The non-coding regulatory region (NCRR) is hypervariable, as evidenced by nucleotide sequence of the non-virulent variant, which is predominantly excreted in urine, versus that of virulent variants found in brain and CSF of PML patients. All variants can be found in blood.

Objective: A single assay that quantifies and identifies JCV DNA in clinical samples and discriminates between variants has significant value to physicians and patients at risk for PML.

Study design: Separate primer pairs were tested together to quantitatively detect conserved viral DNA nucleotide sequence in patient samples, while simultaneously detecting the NCRR specific for the non-virulent variant.

Results: In testing using control plasmids and patients' CSF, blood, and urine, PML patients predictably demonstrated the non-virulent, archetype NCRR in urine, but virulent NCRR variants in CSF and blood.

Conclusion: The JCV qPCR multiplex assay targets two regions in JCV genomes to simultaneously identify and measure viral DNA, as well as distinguish between variants associated with PML and those that are not. The multiplex results could signal risk for PML if patients are viremic with JCV variants closely associated with PML pathogenesis.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Intramural

MeSH terms

  • DNA, Viral / genetics
  • DNA, Viral / isolation & purification
  • Genotype
  • Humans
  • JC Virus / classification*
  • JC Virus / genetics
  • JC Virus / isolation & purification*
  • JC Virus / pathogenicity
  • Leukoencephalopathy, Progressive Multifocal / diagnosis*
  • Leukoencephalopathy, Progressive Multifocal / virology
  • Molecular Diagnostic Techniques / methods*
  • Multiplex Polymerase Chain Reaction / methods*
  • Real-Time Polymerase Chain Reaction / methods*
  • Virology / methods*
  • Virulence


  • DNA, Viral