JC Virus Type 1 Has Multiple Subtypes: Three New Complete Genomes

J Gen Virol. 1998 Apr;79 ( Pt 4):801-5. doi: 10.1099/0022-1317-79-4-801.


The complete genomes of three new Type 1 strains of JC virus (JCV) from urine have been analysed. These were subtype 1A, subtype 1B and Type 4 as assigned from a short typing fragment in the VP1 gene. They differ from Mad1 (subtype 1A) by less than 1.0% of the DNA sequence. Based on its complete genome, the JCV Type 4 strain falls into a Type 1 subgroup. Type 4, with several Type 3-like sites in the short typing fragment, is a possible recombinant strain. The consensus of Type 1 DNA sequences is distinguished within the coding region from both Type 2 (strain GS/B) and five Type 3 (African and African American) strains at 64 sites. Most mutations are silent, but at 21 positions amino acid changes occur. Our findings define the subtypes of JCV Type 1 and support the validity of genotyping within the short VP1 fragment.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Consensus Sequence
  • DNA, Viral / genetics
  • Genome, Viral*
  • Humans
  • JC Virus / classification*
  • JC Virus / genetics*
  • JC Virus / isolation & purification
  • Male
  • Middle Aged
  • Molecular Sequence Data
  • Papillomavirus Infections / virology
  • Phylogeny
  • Polymerase Chain Reaction
  • Tumor Virus Infections / virology
  • Urine / virology


  • DNA, Viral

Associated data

  • GENBANK/AF015526
  • GENBANK/AF015527
  • GENBANK/AF015528