BK virus replication is regulated by the noncoding control region (NCCR); major NCCR rearrangements could modify the strength of viral replication, having a role in the development of polyomavirus-associated nephropathy (PAN). Urine (n = 34), blood (n = 32), and renal biopsy samples (n = 13) from 5 transplant recipients with PAN underwent nested polymerase chain reaction to search for the NCCR region. Sequence analysis was performed on all NCCR fragments obtained. Decoy cells were evaluated semiquantitatively in urine and PAN staged in renal biopsy specimens; the results were related to the presence and type of NCCR sequence variations. Major NCCR rearrangements were found in urine (9/75 [12%]), blood (7/30 [23%]), and renal biopsy (4/15 [27%]) samples in 3 cases; 2 cases had only unrearranged strains. Neither the detection and number of decoy cells nor the PAN stage were related to the specific type of NCCR sequence rearrangements. NCCR rearrangements do not seem essential for the development of PAN
