Figure 1

Alignment of the nucleotide sequence corresponding to the VP2(VP3) C-terminus region. Nucleotide alignment of reference sequences for Simian Agent 12 (NC_007611.1; nucleotides 1347-1589), Simian virus 40 (NC_001669.1; nucleotides 1378-1620), JCV (NC_001699.1; nucleotides 1342-1560), and BKV (NC_001538.1; nucleotides 1437-1679) is shown. The positions of nucleotide polymorphisms among 487 JCV isolates relative to the reference sequence are shown below the JCV reference sequence. The guanine at position 150 (bold) is replaced by cytosine in six out of 487 JCV isolates. The locations of polymorphisms among 271 BKV isolates are shown below the BKV reference sequence and the number of BKV isolates with that particular set of polymorphism(s) is given in brackets. The positions of the primers (underlined) and probe (boxed) are indicated on the BKV reference sequence. There are no observed polymorphisms at the Polyoma_4.2(f) forward primer in either BKV or JCV sequences available at this time. There are no known polymorphisms at the relative position of the BKV_MGB probe (boxed) among either the BKV isolates or JCV isolates. There are three nucleotide differences between JCV and BKV at the probe binding site. There are three nucleotide differences between SV40 and BKV at the BKV_5.1(r) reverse primer binding site.