Viral regulatory region sequence variations in kidney tissue obtained from patients with BK virus nephropathy

Unique BK virus non-coding control region (NCCR) variants in hematopoietic stem cell transplant recipients with and without hemorrhagic cystitis

Hematopoietic stem cell transplant recipients frequently develop BK virus (BKV)-associated hemorrhagic cystitis, which coincides with BK viruria. However, the precise role of BKV in the etiology of hemorrhagic cystitis in hematopoietic stem cell transplant recipients remains unclear, since approximately 50% of all such adult transplant recipients excrete BKV, yet do not develop this clinical condition. In the present study, BKV were analyzed to determine if mutations in the non-coding control region (NCCR), and specific BKV sub-types defined by sequence analysis of major capsid protein VP1, were associated with development of hemorrhagic cystitis in hematopoietic stem cell transplant recipients. The regions encoding VP1 and NCCRs of BKV in urine samples collected from 15 hematopoietic stem cell transplant recipients with hemorrhagic cystitis and 20 without this illness were amplified and sequenced. Sequence variations in the NCCRs of BKV were identified in urine samples from those with and without hemorrhagic cystitis. Furthermore, five unique sequence variations within transcription factor binding sites in the canonical NCCR, O-P-Q-R-S, were identified, representing new BKV variants from a population of cloned quasi-species obtained from patients with and without hemorrhagic cystitis. Thirty-five BKV VP1 sequences were analyzed by phylogenetic analysis but no specific BKV sub-type was associated with hemorrhagic cystitis. Five previously unrecognized naturally occurring variants of the BKV are described which involve amplifications, deletions, and rearrangements of the archetypal BKV NCCRs in individuals with and without hemorrhagic cystitis. Architectural rearrangements in the NCCRs of BKV did not appear to be a prerequisite for development of hemorrhagic cystitis in hematopoietic stem cell transplant recipients.

BK virus nephritis after renal transplantation

BK viremia and nephritis are increasing problems in renal transplant recipients. The exact cause of the increasing prevalence of this condition remains poorly understood. Increasing prevalence has been correlated with newer immunosuppressive agents and the decline in acute rejection rates in recent years. The clinical manifestation varies from the asymptomatic state of viremia and nephritis to clinical renal dysfunction. The diagnosis of this infection is based on the combination of the presence of urinary decoy cells, virus in the urine/blood, and typical renal histological findings of interstitial nephritis. Routine post-transplant screening for BK viremia and viruria prior to the occurrence of nephritis and the reduction in immunosuppressive therapy for subjects with viremia appear to be attractive approaches. The treatment of BKV nephritis (BKVN) consists of reduction in immunosuppressive therapy and antiviral therapy with cidofovir or leflunomide or a combination of both. Approximately 30-60% of subjects with BKVN experienced irreversible graft failure. However, in recent years, the combinations of early detection, prompt diagnosis, and appropriate reduction in immunosuppressive therapy have been associated with better outcome. The pathogenesis of BK virus infection in renal transplant recipients needs to be explored. The source of BKV infection (donor as opposed to recipient), the role of host humoral, and cellular immunity to BKV, and the role of alloimmune activation in renal graft to the occurrence of nephritis are discussed in this review.

Stability of the BK polyomavirus genome in renal-transplant patients without nephropathy

To clarify the stability of the BK polyomavirus (BKPyV) genome in renal transplant (RT) recipients, three to five complete BKPyV genomes from each of six RT recipients with surviving renal allografts were molecularly cloned. The complete sequences of these clones were determined and compared in each patient. No nucleotide difference was detected among clones in two patients, and a few nucleotide variations were found among those in four patients. In each of these patients a parental sequence (usually the major sequence), from which variant sequences (usually minor sequences) with nucleotide substitutions would have been generated, were identified. A comparison between the parental and variant sequences in each patient identified a single nucleotide substitution in each variant sequence. From these findings, it was concluded that the genome of BKPyV is stable in RT recipients without nephropathy, with only minor nucleotide substitutions in the coding region.

Genetic variability in BK Virus regulatory regions in urine and kidney biopsies from renal-transplant patients

The human Polyomavirus BK (BKV) contains a hypervariable non-coding control region (NCCR), which regulates DNA replication and RNA transcription. The aim of this study was to characterize BKV NCCR-variants in kidney biopsies and urine samples from renal-transplant patients and to see whether there is any association between NCCR variability and BKV-nephropathy. Kidney biopsies and urine samples were examined from 11 patients with elevated serum creatinine and >5,000 genomic BKV copies per ml of urine. BKV-nephropathy was diagnosed in seven patients. Using PCR, BKV NCCR was amplified from urine from all BKV-nephropathy patients. The dominant NCCR corresponded to the archetype (WWT). In addition, a total of 14 non-archetype NCCR-variants were detected. Thirteen of these NCCR-variants were found in urine from one single BKV-nephropathy patient also suffering from hepatitis C. The NCCR of BKV was amplified from kidney biopsies of six BKV-nephropathy patients. Three patients demonstrated WWT NCCR, while three other patients harbored rearranged NCCR variants. The WWT NCCR was also detected in urine from control patients, except for one patient who harbored two non-archetypal NCCR variants. However, these variants were not resulting from complex rearrangements but instead had a linear NCCR anatomy with deletion(s) in the P-block. No BKV DNA was detected in biopsies from control patients. The results indicate that rearranged BKV NCCR is associated with BKV-nephropathy.

Specific and quantitative detection of human polyomaviruses BKV, JCV, and SV40 by real time PCR

BACKGROUND

The polyomaviruses that infect humans, BK virus (BKV), JC virus (JCV), and simian virus 40 (SV40), typically establish subclinical persistent infections. However, reactivation of these viruses in immunocompromised hosts is associated with renal nephropathy and hemorrhagic cystitis (HC) caused by BKV and with progressive multifocal leukoencephalopathy (PML) caused by JCV. Additionally, SV40 is associated with several types of human cancers including primary brain and bone cancers, mesotheliomas, and non-Hodgkin's lymphoma. Advancements in detection of these viruses may contribute to improved diagnosis and treatment of affected patients.

OBJECTIVE

To develop sensitive and specific real time quantitative polymerase chain reaction (RQ-PCR) assays for the detection of T-antigen DNA sequences of the human polyomaviruses BKV, JCV, and SV40 using the ABI Prism 7000 Sequence Detection System.

STUDY DESIGN

Assays for absolute quantification of the viral T-ag sequences were designed and the sensitivity and specificity were evaluated. A quantitative assay to measure the single copy human RNAse P gene was also developed and evaluated in order to normalize viral gene copy numbers to cell numbers.

RESULTS

Quantification of the target genes is sensitive and specific over a 7 log dynamic range. Ten copies each of the viral and cellular genes are reproducibly and accurately detected. The sensitivity of detection of the RQ-PCR assays is increased 10- to 100-fold compared to conventional PCR and agarose gel protocols. The primers and probes used to detect the viral genes are specific for each virus and there is no cross reactivity within the dynamic range of the standard dilutions. The sensitivity of detection for these assays is not reduced in human cellular extracts; however, different DNA extraction protocols may affect quantification.

CONCLUSION

These assays provide a technique for rapid and specific quantification of polyomavirus genomes per cell in human samples.

Polymerase Chain Reaction Detection of BK Virus and Monitoring of BK Nephropathy in Renal Transplant Recipients at the University Hospital La Fe

INTRODUCTION

Reactivation of BK infection occurs in immunocompromised hosts causing tubulointerstitial nephropathy (BKVN). Approximately 5% of kidney transplant recipients (KTR) develop BKVN, special half of whom lose their grafts. However, BKVN morphologic diagnosis on a renal biopsy is complicated, because the cytopathic changes can sometimes mimic rejection. Thus, BKV DNA-polymerase chain reaction (PCR) assay on serum, urine, and renal tissue is useful for early detection and monitoring of BKV.

MATERIALS AND METHODS

We performed routine monthly urine cytologies looking for decoy cells as a marker of virus replication. Then, we performed a qualitative PCR on urine and serum in all recipients (independently of positive or negative cytology). We amplified 3 BK viral genome regions, LT (early transcription region) and VP1 (late transcription region) seeking a more accurate virus detection, and the TCR (control transcription region) region to perform a polymorphism sequence analysis to identify the BK genomic variant. Finally, the BKVN diagnosis was confirmed using renal biopsy.

RESULTS

At present, 132 patients have been monitored. Thirteen of 40 (33%) were PCR-urine-positive cases (5 LT+/VP1- and 8 LT+/VP1+), and 10 of 132 (7.5%) were PCR-serum-positive cases (7 LT+/VP1- and 3 LT+/VP1+). When we compared PCR-urine and cytology results, 11 of 40 (27.5%) patients showed a positive cytology, 6 of whom were PCR- urine-positive (1 LT+/VP1- and 5 LT+/VP1+); whereas, 29 patients showed a negative cytology, 7 of whom were PCR-urine-positive(3 LT+/VP1- and 4 LT+/VP1+). Thus, comparison of PCR- urine and cytology results revealed false-positive and false-negative cases. Finally, TCR sequence analysis was performed in 9 patients to identify the BK genomic variants.

CONCLUSION

Testing for BKV DNA in urine and serum is a noninvasive early detection assay and monitoring tool.

LT, VP1 and TCR-BKV sequence analysis in a patient with post-transplant BKV nephropathy associated with EBV-related PTLD

A 10-year-old boy kidney transplant recipient (KTR) developed an abdominal post-transplant lymphoproliferative syndrome (PTLD) followed by BK virus nephropathy (BKVN). BK virus (BKV) and Epstein-Barr virus (EBV) were studied in renal and PTLD tissue by polymerase chain reaction (PCR) assay. Afterwards, the patient was monitored in relation to BKV in urine and serum; transcription control region (TCR)-BK polymorphism sequence analysis was also performed. In the PCR assay, both early large T antigen (LT) and late (VP1) transcriptional BKV coding regions were found in renal tissue, whereas EBV and only LT-BK were detected in PTLD abdominal tissue. On the other hand, TCR sequence analysis revealed the AS genomic BK variant.

The human polyomavirus BK: Potential role in cancer

In human cancer, a role has been suggested for the human polyomavirus BK, primarily associated with tubulointerstitial nephritis and ureteric stenosis in renal transplant recipients, and with hemorrhagic cystitis in bone marrow transplant (BMT) recipients. After the initial infection, primarily unapparent and without clinical signs, the virus disseminates and establishes a persistent infection in the urinary tract and lymphocytes. There is correlative evidence regarding potential role of polyomavirus BK in cancer. In fact, the BK virus (BKV) DNA (complete genome and/or subgenomic fragments containing the early region) is able to transform embryonic fibroblasts and cells cultured from kidney and brain of hamster, mouse, rat, rabbit, and monkey. Nevertheless, transformation of human cells by BKV is inefficient and often abortive. Evidence supporting a possible role for BKV in human cancer has accumulated slowly in recent years, after the advent of polymerase chain reaction (PCR). BKV is known to commonly establish persistent infections in people and to be excreted in the urine by individuals who are asymptomatic, complicating the evaluation of its potential role in development of human cancer. Therefore, there is no certain proof that human polyomavirus BK directly causes the cancer in humans or acts as a cofactor in the pathogenesis of some types of human cancer.

A prospective longitudinal study of BK virus infection in 104 renal transplant recipients

BK virus (BKV) infection during the first year after renal transplantation was studied prospectively in 104 unselected consecutive patients. Viral DNA in urine (DNAuria) and plasma (DNAemia) samples was detected and quantified by real-time PCR. The noncoding control region (NCCR) of BKV isolates was sequenced. DNAuria and DNAemia occurred in 57% and 29% of patients, respectively. Three groups were defined, uninfected patients (group 1, n=45), patients with DNAuria (group 2, n=29) and patients with positive DNAemia (group 3, n=30). Active infection started within the first 3 months in 80% of patients. Cold ischemia duration over 24 h and the administration of tacrolimus were identified as significant risks factors for DNAuria, whereas it remains more frequently negative in patients receiving cyclosporine A. The risk for positive DNAemia was higher in patients with DNAuria (notably for viral load (VL)>4 log/mL) or treated with tacrolimus. No relationship was found with genetic variability in the NCCR sequence. Our data highlight the high frequency of active BKV infection after renal transplantation. Although high VL was detected in some patients, none developed a BKV nephropathy. A prospective follow-up of the whole population during the first year post renal transplantation is thus not useful to predict BKV disease.

Adjuvant low-dose cidofovir therapy for BK polyomavirus interstitial nephritis in renal transplant recipients

BK virus interstitial nephritis (BKVIN) is a serious complication after kidney grafting, necessitating drastic reduction of immunosuppressive therapy in order to enable viral clearance. Despite these measures, progressive graft dysfunction and graft loss occur in the majority of recipients. We diagnosed BKVIN in 21 recipients grafted between 1998 and 2004. Eight of 21 patients were treated with weekly, adjuvant low-dose cidofovir in addition to reduction of immunosuppressive therapy. BKVIN caused irreversible deterioration of graft function in all patients but renal function stabilized after antiviral treatment (creatinine clearance: 51.8-32 mL/min; p=0.001) and no graft loss occurred in cidofovir-treated recipients during 24.8 (8-41) months follow-up. Peak serum cidofovir concentrations were dose-dependent and attained approximately one-tenth of thein vitroEC50 for cidofovir against BK-virus, while pre-treatment with probenecid did not alter peak serum concentrations nor affected the incidence of nephrotoxicity. In fact, no cidofovir-related renal toxicity occurred; few patients had minor transient side effects (nausea, skin rash). In contrast, 9 of 13 patient who received no adjuvant cidofovir therapy lost their graft after median 8 (4-40) months. In this selected group of recipients with BKVIN, the use of adjuvant low-dose cidofovir therapy resulted in prolonged graft survival and stabilized graft function.

Polyomavirus-associated nephropathy in renal transplantation: interdisciplinary analyses and recommendations

Polyomavirus-associated nephropathy (PVAN) is an emerging cause of kidney transplant failure affecting 1-10% of patients. As uncertainty exists regarding risk factors, diagnosis, and intervention, an independent panel of experts reviewed the currently available evidence and prepared this report. Most cases of PVAN are elicited by BK virus (BKV) in the context of intense immunosuppression. No specific immunosuppressive drug is exclusively associated with PVAN, but most cases reported to date arise while the patient is on triple immunosuppressive combinations, often comprising tacrolimus and/or mycophenolate mofetil plus corticosteroids. Immunologic control of polyomavirus replication can be achieved by reducing, switching, and/or discontinuing components of the immunosuppressive regimen, but the individual's risk of rejection should be considered. The success rate of this intervention is increased with earlier diagnosis. Therefore, it is recommended that all renal transplant recipients should be screened for BKV replication in the urine: 1) every three months during the first two years posttransplant; 2) when allograft dysfunction is noted; and 3) when allograft biopsy is performed. A positive screening result should be confirmed in <4 weeks and assessed by quantitative assays (e.g. BKV DNA or RNA load in plasma or urine). Definitive diagnosis of PVAN requires allograft biopsy. If PVAN and concurrent acute rejection is diagnosed, antirejection treatment should be considered, coupled with subsequently reducing immunosuppression. The antiviral cidofovir is not approved for PVAN, but investigational use at low doses (0.25-0.33 mg/kg intravenously biweekly) without probenicid should be considered for refractory cases. Retransplantation after renal allograft loss to PVAN remains a treatment option for patients clearing polyomavirus replication.

Polyomavirus nephropathy: morphology, pathophysiology, and clinical management

PURPOSE OF REVIEW

Viral nephropathies, particularly those caused by polyomaviruses of the BK-virus strain, are serious complications following renal transplantation. The review will highlight the morphological, pathophysiological and clinical aspects of BK-virus nephropathy. New patient management strategies are discussed.

RECENT FINDINGS

Immunosuppression with tacrolimus and mycophenolate-mofetil promotes the activation of latent BK-virus in the urinary tract and increases the odds ratio for developing BK-virus nephropathy significantly. A productive infection with BK-viruses shows viral replication in tubular epithelial cells and acute tubular injury. BK-virus nephropathy can be further complicated by concurrent acute rejection episodes contributing to graft demise. Risk assessment after transplantation and patient management during ongoing viral nephropathy have undergone revision by the introduction of real time quantitative polymerase chain reaction techniques measuring BK-virus genome load fluctuations in the serum. Treatment strategies for BK-virus nephropathy include not only low-dose immunosuppression but also drugs with antiviral effects: cidofovir and leflunomide. Transient anti-rejection therapy, including anti-lymphocytic preparations, is a therapeutic option in cases of BK-virus nephropathy and concurrent acute rejection. Recent advances in patient management strategies have resulted in markedly improved graft survival. In cases of graft loss due to BK-virus nephropathy, re-transplantation should be considered.

SUMMARY

BK-virus nephropathy is a significant complication following renal transplantation. Recent advances have improved our understanding of the morphological changes, potential risk factors and patient management strategies would be optimized. The availability of quantitative viral load measurements now offers the opportunity for a more accurate and timely clinical intervention.

Polymorphism in the genome of non-passaged human polyomavirus BK: implications for cell tropism and the pathological role of the virus

Worldwide studies have demonstrated that the human polyomavirus BK resides ubiquitously in the human population. After primary infection, which occurs mainly during childhood, the virus seems to establish a life-long harmless infection in the host. However, impaired immune functions may lead to reactivation of BK virus. The recent findings that associate BK virus with an increasing number of clinical conditions, including renal, pulmonary, ophthalmologic, hepatic, neurological, and autoimmune diseases, has resuscitated the interest in this virus as a pathogenic agent. This review focuses on polymorphisms in the genomes of non-passaged BK virus isolates from nonneoplastic tissues, with special focus on the transcriptional control region, the regulatory proteins large T-antigen and agnoprotein, and the major capsid protein VP1. The possible implications of genome diversity with respect to cell tropism, pathogenicity, and therapeutic strategies are discussed.

Polyomavirus BK

Polyomavirus hominis 1, better known as BK virus (BKV), infects up to 90% of the general population. However, significant clinical manifestations are rare and limited to individuals with impaired immune functions. BKV has been associated with diverse entities such as haemorrhagic cystitis, ureteric stenosis, vasculopathy, pneumonitis, encephalitis, retinitis, and even multi-organ failure. In addition, BKV has been implicated in autoimmune disease and possibly cancer. Due to high prevalence and frequent reactivation, the role of BKV in some of these pathologies has been difficult to define. Development of BKV diseases is likely to require complementing determinants in the host, the target organ, and possibly the virus, that are subject to modulators such as immunosuppression. These complex aspects are highlighted in polyomavirus-associated nephropathy (PAN), an emerging disease in renal allograft recipients that may jeopardise the progress in renal transplantation accomplished in the past 10 years. Intervention is difficult due to the lack of specific antivirals and relies mostly on improving immune control. Diagnostic strategies using urine cytology and BKV load measurements in plasma have led to earlier diagnosis of PAN, which increased the success rate of intervention. Case series suggest that cidofovir might be effective, especially when combined with reduced immunosuppression.