The complete genomes of three new Type 1 strains of JC virus (JCV) fro
m 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 diff
er 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 sub
group. Type 4, with several Type 3-like sites in the short typing frag
ment, is a possible recombinant strain. The consensus of Type 1 DNA se
quences is distinguished within the coding region from both Type 2 (st
rain GS/B) and five Type 3 (African and African American) strains at 6
4 sites. Most mutations are silent, but at 21 positions amino acid cha
nges occur. Our findings define the subtypes of JCV Type 1 and support
the validity of genotyping within the short VP1 fragment.