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

Department of Cellular and Developmental Biology, University "La Sapienza", Rome, Italy.
Journal of Medical Virology (Impact Factor: 2.22). 09/1999; 58(4):413-9. DOI: 10.1002/(SICI)1096-9071(199908)58:43.0.CO;2-W
Source: PubMed

ABSTRACT The various strains of human polyomavirus BK (BKV) show a marked heterogeneity in the non-coding control region (NCCR), which includes the origin of replication and the regulatory region for early and late 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 archetypal strain (WW) (M34048), as compared with those collected in GenBank. Structurally, P68, Q39, and S68 boxes were perfectly conserved, whereas the R63 box was completely deleted. This deletion involves the loss of sequences able to bind cellular factors essential for the DNA transcription, such as NF1 binding sites, normally present twice in the R box and the modification 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 observed in urine isolates, which are similar to the WW strain.

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    ABSTRACT: Background: Hemorrhagic cystitis (HC) in allogeneic bone marrow transplanted (BMT) patients isassociated with BK virus (BKV) reactivation manifested as BK viruria. However, since 77–90% of alladult BMT patients excrete BKV, viral reactivation alone cannot be responsible for HC. Recently, asignificant overrepresentation of C→G mutations in the Sp1 binding site in the non-coding controlregion (NCCR) of BKV was shown to be present in HC patients and absent in non-HC patients. Weaimed to investigate if this mutation resulted in excessive BKV excretion in HC patients. Study design:A Real-Time PCR was developed and used to quantify BKV in urine samples from 21 patients withHC, with and without the mutations, as well as from patients without HC.Material and method: A Real-Time PCR was developed and used to quantify BKV in urinesamples from 21 patients with HC, with and without the mutations, as well as from patients withoutHC.Results: Quantification of BKV was successful in 18 of 21 urine patients (six with and six withoutC→G mutations) and six patients without HC. A mean of 3.0×106 BKV copies/μl was detected inurine samples of HC patients with C→G mutations, compared to a mean of 1.5×106 BKV copies/μl inHC patients without C→G mutations and a mean of 1.0×106 BKV copies/μl in patients without HC.The obtained differences were however not statistically significant, due to one individual non-HCpatient with an extremely high BKV copy number. Nevertheless, while 50% of the samples in the HCgroups expressed 1×106 copies/μl or more, only one of the samples in the non-HC group contained avirus quantity higher than 5×105 copies.Conclusions: Although we could not confirm that the C→G mutations in the Sp1 site of BKV wereresponsible for an increased viral load in patients with HC, our data suggest that levels of BKV above104 copies/μl may indicate a risk for HC .
    Koomesh 01/2008;
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    ABSTRACT: Haemorrhagic cystitis (HC) in allogeneic bone marrow transplanted (BMT) patients is associated with reactivation of BK virus (BKV) manifested as BK viruria. However, it has been suggested that BKV reactivation alone is not responsible for HC, since BKV can be detected in the urine of 50-90% of all adult BMT patients. In the present study, we analysed if BK viruses with specific mutations in the non-coding control region (NCCR) or in the region encoding the major capsid protein (VP1) were more frequently associated to the appearance of HC in BMT patients. The NCCR and the region encoding VP1 of BKV excreted in the urine from 25 BMT patients, 16 with and nine without HC, were sequenced by an ABI Prism Big Dye terminator cycle sequencing ready reaction kit. A statistically significant (P=0.019) overrepresentation of C to G mutations within the NCCR Sp1 binding site was observed in 7/16 (43%) patients with HC (six cases at position 249 (P=0.035) and one case at position 251), as compared with 0/9 (0%) of the patients without HC. Major differences were not observed in the VP1 sequences of patients with and without HC. BKV WW and WWT-variants as well as BKV subtype I were most commonly encountered in both groups of patients. In conclusion, C to G point mutations, within the BKV NCCR Sp1 binding site, were significantly more common in patients with HC, suggesting that these mutations may be indicative for the clinical diagnosis of HC and could influence the virulence of the virus.
    Journal of Clinical Virology 05/2001; 21(1):1-7. · 3.47 Impact Factor
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    ABSTRACT: BK and JC polyomaviruses (BKV and JCV) are widespread in humans and are thought to persist and reactivate under immune alterations. In addition to the kidney, lymphoid cells have been proposed as a site of latency. However, while this was shown to occur in immunocompromised patients, discordant data were published for healthy humans. To help to solve this issue, an extensive study (231 healthy subjects) was carried out on peripheral blood mononuclear cells (PBMC) from blood donors of two towns and from operators of a blood transfusion centre. To discriminate between past and recent infection, nested PCRs for BKV and JCV non-coding control region (NCCR) and VP1 DNA sequences were carried out. Twenty-two per cent of subjects had BKV NCCR, but only 7% also had BKV VP1, as detected by PCR assays of similar sensitivities; the latter positivity was found to decrease with age. In both towns, the BKV WW archetypal DDP strain, subtype I, was found. Only 0.9% of subjects contained JCV DNA, for both NCCR and VP1. Blood operators presented a statistically significant increased prevalence of BKV NCCR (3. 0-fold) and BKV VP1 (9.4-fold) sequences with respect to blood donors of comparable ages, suggesting the possibility of occupational risk of BKV (re)infection or reactivation. Since the possibility of amplifying BKV VP1 sequences from PBMC of healthy humans is lost with age, this suggests that PBMC are not a site of polyomavirus persistence in healthy individuals and that detection of BKV VP1 DNA in PBMC is probably indicative of recent infection or reactivation.
    Journal of General Virology 09/2000; 81(Pt 8):1967-73. · 3.53 Impact Factor