Identification of a new control region in the genome of the DDP strain of BK virus isolated from PBMC

The various strains of human polyomavirus BK (BKV) show a marked heterogene ity in the noncoding control region (NCCR), which includes the origin of re plication and the regulatory region for early and tate transcription. A new BKV strain (DDP, U91605) was identified by direct detection and sequencing of PCR products of BKV-NCCR DNA obtained from PBMC samples of HIV-positive or -negative subjects. The DDP strain NCCR sequence showed an organisation not described previously in vivo with the maximum homology with the archet ypal strain (WW) (M34048), as compared with those collected in GenBank. Str ucturally, P-68, Q(39), and S-68 boxes were perfectly conserved, whereas th e R-63 box was completely deleted. This deletion involves the loss of seque nces able to bind cellular factors essential for the DNA transcription, suc h as NF1 binding sites, normally present twice in the R box and the modific ation of SP1. It is possible that these rearrangements represent a cause of the loss of the VP1 region observed in 9/22 PBMC samples and never observe d in urine isolates, which are similar to the WW strain. J. Med. Virol. 58: 413-419, 1999. (C) 1999 Wiley-Liss, Inc.