Figure 3. Alignment of John Cunningham polyomavirus non-coding control region (JCPyV NCCR) isolates from different clinical specimens of patients with bladder cancer the archetypal NCCR sequence. The NCCR sequence of the archetypal JCPyV strain CY, as proposed by Yogo et al. (32) is shown at the top of the figure and the consensus sequences of the NCCR showing variations isolated from malignant (high- and low-grade) bladder tissues (CPT and NPT, respectively) and urine specimens, with related genotype, are shown below. The four nucleotide changes (G95C, G108A, A133C and G217A), identified by comparing with CY isolate, are indicated by bold highlighted letters. The JCPyV NCCR isolated from specimens of the other patients always showed an archetypal CY-like structural organization and the nucleotide substitution G217A in those patients with a JCPyV European genotype (data not shown). The six boxes commonly used to divide the archetypal NCCR (6) are indicated under the NCCR sequences, while proven and putative binding sites for transcriptional factors are illustrated above the CY NCCR sequence. U: Urine; HGBC: high-grade urothelial bladder carcinoma; LGBC: low-grade urothelial bladder carcinoma.