BK Polyomavirus Subtype III in a Pediatric Renal Transplant Patient with Nephropathy

BK polyomavirus (BKV) is an emerging pathogen in immunocompromised individuals. BKV subtype III is rarely identified and has not previously been associated with disease. Here we provide the whole-genome sequence of a subtype III BKV from a pediatric kidney transplant patient with polyomavirus-associated nephropathy.     

Genomic mutations of viral protein 1 and BK virus nephropathy in kidney transplant recipients

Genomic variability in the viral protein 1 region of BK polyomavirus (BKV) may change the ability of the virus to replicate. The significance of such changes was studied in clinical samples taken from kidney transplant patients with and without BKV nephropathy. A 94 base‐pair fragment of viral protein 1 was amplified from 68 urine, 28 blood, and 12 renal biopsy samples from eight patients with BKV nephropathy, and from 100 urine samples, 17 blood and three renal biopsy samples from 41 of 218 controls. The DNA was sequenced and the amino acid changes were predicted by the Expert Protein Analysis System program (ExPASy, Swiss Institute of Bioinformatics, Geneva, Switzerland). Single base‐pair mutations were detected more frequently in the samples from the BKV nephropathy patients than in the controls, and this was the only statistically significant finding of the study (P < 0.05), thus suggesting a greater genetic instability in BKV nephropathy associated strains. The amino acid changes were distributed at random in both BKV nephropathy patients and controls. However, one aspartic acid‐to‐asparagine substitution at residue 75 was detected in all samples of the one patient with BKV‐associated nephropathy, who developed disease progression confirmed by histology, and not in any of the other patient or control samples. Whether this specific amino acid change plays a role in disease deserves further study. J. Med. Virol. 81:1385–1393, 2009. © 2009 Wiley‐Liss, Inc.     

Functional analysis of polyomavirus BK non‐coding control region quasispecies from kidney transplant recipients

Replication of the human polyomavirus BK (BKV) in renal tubular epithelial cells causes viruria and BKV‐nephropathy in kidney transplant recipients. Following prolonged high‐level BKV replication, rearrangement of the archetype non‐coding control region (NCCR) leads to a mixture of BKV variants. The aim of this study was to compare potential functional differences of 12 rearranged (rr)‐NCCR variants with the archetype (ww)‐NCCR (WWT) found in allograft biopsies or urine from three kidney transplant recipients including two with BKV‐nephropathy. Twelve different rr‐NCCRs and one archetype ww‐NCCR were inserted between the early and late protein coding region of BKV(Dunlop) to make recombinant BKV genomes for transfection into Vero cells. Immunoblotting, immunofluorescence staining, and quantitative PCR demonstrated that viral protein expression and extracellular BKV loads of 10 rr‐NCCR variants were similar or higher than observed for the ww‐NCCR BKV. Two rr‐NCCR variants (RH‐2 and RH‐19) were non‐functional. The functional rr‐NCCRs produced infectious progeny successfully infecting primary renal proximal tubular epithelial cells. The number of infected cells and extracellular BKV loads corresponded to the activity seen in Vero cells. Three rr‐NCCR variants (RH‐1, RH‐10, RH‐13) only gave rise to a few infected cells similar to ww‐NCCR, whereas seven variants had intermediate activity (RH‐5, RH‐6, RH‐8, RH‐9, RH‐11) or high replication activity (RH‐7 and RH‐18) with several hundred infected cells per well. The results indicate that both functional and non‐functional BKV rr‐NCCR variants arise during BKV replication in kidney transplant recipients and that most functional rr‐NCCR variants confer a higher replication capacity than archetype ww‐NCCR. J. Med. Virol. 81:1959–1967, 2009. © 2009 Wiley‐Liss, Inc.     

A rapid and efficient method BK polyomavirus genotyping by high-resolution melting analysis

A small percentage of renal patients become infected with the BK polyomavirus (BKV), a pathogenic virus that causes BKV-associated nephropathy (BKVN), after kidney transplantation. This study presents a simple, rapid, high-throughput method for BKV genotyping using high-resolution melt analysis (HRMA). Using this novel method, BKV genotypes were analyzed in 49 samples taken from BKV-positive renal transplantation patients for classification into 1 of 3 genotypes: GI-1 (subgroups Ia, Ib1, and Ic), GI-2 (subgroup Ib2), and GII-IV (subtypes II, III, and IV). HRMA was performed to compare each sample sequence to a reference sequence that contained a combination of 2 of the 3 genotype groups, and the findings validated by conventional DNA sequencing. Of the 49 samples, 20 samples were classified as GI-1, 18 as GI-2, and 11 as GII-IV, suggesting that the predominant BKV strain (77.6%) in these patients was subtype I (GI-1 and GI-2). The HRMA method presented here is a time-saving, reliable, and low-cost procedure that can be developed as a diagnostic tool in the detection of the specific BKV genotypes associated with BKVN.     

A comparative study of BK and JC virus infections in organ transplant recipients

JC virus (JCV) rarely causes kidney disease, whereas BK virus (BKV) is a known cause of viral nephropathy. Existing studies on prevalence of JCV in healthy and transplanted subjects have reported only qualitative detection of viral DNA. We used quantitative PCR (qPCR) to assess JC viral load in transplant recipients and non-immunosuppressed controls, and compared JCV loads to BKV loads. JC viruria was seen in 8/23 (34.7%) controls, 23/103 (22.3%) renal, and 10/44 (22.7%) liver transplant patients. No patient developed JC viremia. BK viruria was seen in 2/23 (8.7%) controls, 36/103 (34.9%) renal, and 7/44 (15.9%) liver transplant patients. BK viremia was seen only in the kidney (8/103 = 7.7%) patients. The mean BKV urinary load was higher in kidney compared to liver patients and controls (4.22E + 07 vs. 2.88E + 05 vs. 4.39E + 02 copies/ml), whereas JC viral load was similar for all three patient groups (1.55E + 06 vs. 2.66E + 06 vs. 2.13E + 06 copies/ml). JCV viral loads were surprisingly high in all patient categories studied, but did not result in viremia or viral nephropathy. Although both BKV and JCV are widely latent in patients accepted for transplantation, concurrent reactivation of both viruses was infrequent. BKV viremia was seen in kidney but not liver recipients. The mechanisms underlying these notable phenomena remain to be investigated.     

Rare subtypes of BK virus are viable and frequently detected in renal transplant recipients with BK virus-associated nephropathy

BK virus-associated nephropathy (BKVN) occurs in up to 5% of kidney transplants and is a significant cause of graft loss. Four major subtypes of BKV have been described, with the vast majority of individuals persistently infected with BKV Type I (> 80% of the population). Sequencing of BKV isolates subcloned from BKVN patients revealed a high percentage of variants in the urine (40%) in the VP1 subtyping region. In vitro analysis of several viral variants revealed that all variants recovered from the urine of BKVN patients produced infectious viral particles and were replication competent in cell culture while some of the variants induced cytopathic changes in infected cells when compared to the major BKV subtype, VP1 Type I. These results suggest that rare BKV VP1 variants are more frequently associated with disease and that some variants could be more cytopathic than others in renal transplant recipients.     

Recombined sequences between the non-coding control regions of JC and BK viruses found in the urine of a renal transplantation patient

Kidney cells are the common host for JC virus (JCV) and BK virus (BKV). Reactivation of JCV and/or BKV in patients after organ transplantation, such as renal transplantation, may cause hemorrhagic cystitis and polyomavirus-associated nephropathy. Furthermore, JCV and BKV may be shed in the urine after reactivation in the kidney. Rearranged as well as archetypal non-coding control regions (NCCRs) of JCV and BKV have been frequently identified in human samples. In this study, three JC/BK recombined NCCR sequences were identified in the urine of a patient who had undergone renal transplantation. They were designated as JC?CBK hybrids 1, 2, and 3. The three JC/BK recombinant NCCRs contain up-stream JCV as well as down-stream BKV sequences. Deletions of both JCV and BKV sequences were found in these recombined NCCRs. Recombination of DNA sequences between JCV and BKV may occur during co-infection due to the relatively high homology of the two viral genomes.     

Cross-reactive CTL recognizing two HLA-A*02-restricted epitopes within the BK virus and JC virus VP1 polypeptides are frequent in immunocompetent individuals

Two HLA-A*02-restricted epitopes have been identified within the VP1 polypeptide of a human polyomavirus, BK virus, which is associated with polyomavirus-associated nephropathy in kidney transplant patients. Immunization of transgenic mice with recombinant modified vaccinia Ankara expressing BKV VP1 (rMVA-BKV VP1) elicited functional CTL populations recognizing the sequences LLMWEAVTV (amino acids residues 108-116, BKV VP1p108) and AITEVECFL (residues 44-52, BKV VP1p44) and cross-reactive to the previously described JC virus VP1 homologs. Flow-based analyses of PBMC from a panel of thirty healthy HLA-A*02 human volunteers indicated that the majority of these subjects harbored functional CTL populations recognizing the BKV epitopes and cross-reactive with the JCV homologs. CTL recognizing the JCV VP1p100 and JCV VP1p36 epitopes have previously been associated with prolonged survival in progressive multifocal leukoencephalopathy patients. These findings suggest that infection with BKV or JCV could potentially induce cross-protective T-cell immunity against diseases associated with these viruses.     

Tubulointerstitial Nephritis Due to a Mutant Polyomavirus BK Virus Strain, BKV(Cin), Causing End-Stage Renal Disease

A renal biopsy from a 36-year-old man with AIDS showed a severe tubulointerstitial nephritis with intranuclear inclusions in epithelial cells. Electron microscopy revealed the characteristic findings of a polyomavirus (PyV) infection, and immunofluorescence indicated the presence of BK virus (BKV) antigen. Inoculation of rhesus monkey kidney cell cultures both with urine and with buffy coat blood cells resulted in a cytopathic response which was subsequently confirmed to be due to BKV. Further characterization of the viral DNA from the kidney by PCR amplification and Southern blot analysis with PyV and strain-specific primers and probes indicated that the virus was closely related to the BK(Dun) strain but different in its apparent sequence arrangement. Subsequent cycle sequencing showed a dinucleotide mutation of TG→AA which substitutes hydrophilic Gln for hydrophobic Leu in a sequence homologous to an origin DNA-binding domain of simian virus 40 T antigen. It is suggested that the mutation and a coding region rearrangement of this strain of BKV designated BKV(Cin) has the potential to alter viral DNA replication and enhance pathogenicity.     

Real-time polymerase chain reaction and laser capture microdissection for the diagnosis of BK virus infection in renal allografts

We used real-time polymerase chain reaction (PCR) technology to detect BK virus (BKV) in H and E-stained kidney biopsy sections, using laser capture microdissection. Renal allograft biopsy specimens from 4 patients with the histopathologic diagnosis of BKV-associated nephropathy (BKVAN; group 1) and 3 patients suspected to have BKVAN but without diagnostic histologic features (group 2) were retrieved. Diagnostic inclusion-bearing cells were microdissected by laser capture microscopy from group 1. Renal tubular epithelial cells were microdissected randomly in group 2. DNA was extracted and real-time amplification performed using primers targeting the large "T" and small "t" regions of the BKV and JC virus genomes. Tubular epithelial cells from a case without evidence of BKV infection were used as negative controls in a similar reaction. BKV presence was demonstrated only in epithelial cells containing typical viral inclusions. Group 2 and negative control samples were confirmed as negative for BKVAN. Real-time PCR technology can be used to detect BKV in H and E-stained, paraffin-embedded tissue sections. This technique detected BKV in tubular epithelial cells of renal allografts. To our knowledge, this is the first report of detecting BKV in laser capture microdissected renal biopsy specimens using real-time PCR.     

Detection and quantitation of BK virus DNA by real-time polymerase chain reaction in the LT-ag gene in adult renal transplant recipients

Determination of polyomavirus BK (BKV) load in urine and plasma has been advocated for monitoring adult renal transplant recipients suffering from BKV-related nephropathy. An "in-house" real-time quantitative PCR assay was developed using the BKV-1/BKV-3 primers set in the large tumor antigen (LT-ag) region to quantitate BK virus loads in plasma and urine in renal transplant patients. This assay was adapted to routine virology laboratory by evaluating two extraction procedures of nucleic acids from urine and plasma, one manual and the other using an automatic extractor, and by evaluating the Light Cycler versus Taqman apparatus. Both the manual and automatic extraction procedures and real-time PCR apparatus were equivalent. The Light Cycler and Taqman instruments allow similarly rapid, accurate, reproducible and specific quantitative detection of the three major BKV subtypes, with a detection limit of 10 BKV DNA copies/ml, and a range from 10(0) to 10(7) copies/ml. Of 855 renal transplant patients, 128 (15%) had BKV DNA in both plasma and urine samples with a mean viral load of 5.1 log/ml in plasma and 6.8 log/ml in urine and in 5 (4%) BKV-associated tubulo-interstitial nephropathy; 332 (39%) BKV DNA was found only in the urine, not in the plasma, without further development of nephropathy and 395 patients had no BKV in plasma and urine. These observations emphasize the usefulness of real-time PCR to assess the BKV load by routine testing, and confirm the need to combine both plasma and urine determinations of the BKV DNA load in order to identify renal transplant patient at high risk for BKV-associated nephropathy.     

Sequence variations of the VP1 gene of Polyomavirus hominis 1 among Bulgarians

Polyomavirus hominis 1 (BK virus, BKV) is an important pathogen in the field of transplantation medicine. BKV reactivation among renal‐transplant recipients could cause BK associated nephropathy, which has unfavorable prognosis and is a cause for graft rejection. It is not clear why only few transplanted patients develop BK associated nephropathy while most exhibit asymptomatic viruria. One of the possible reasons lies in the mutations of the VP1 gene, encoding the main structural protein, bearing important determinants for the recognition of specific cellular receptors. The change of amino acid sequence could result in altered pathogenicity of BKV. The amplified sequences of BK in this research were from urines of patients with various clinical conditions along with healthy individuals. Nevertheless the sequence analysis which was undertaken did not show correlation between the viral genotype and the clinical condition. It was demonstrated that the most common BKV genotype in Bulgaria is genotype I and that the strains common in Bulgaria (genotypes I and IV) have typical European origin. Most of the sequenced BKV DNA samples (8/10) were correlated with the highest degree of similarity (81%) to the subcluster Ib. A specific place among the samples is taken by Pr‐9, amplified from the urine of a pregnant woman that has a different evolutionary origins and might establish the beginning of a new distinct BKV strain. J. Med. Virol. 82:325–330, 2010. © 2009 Wiley‐Liss, Inc.     

BK polyomavirus diversity—Why viral variation matters

BK polyomavirus (BKPyV or BKV) is a non‐enveloped, circular double‐stranded DNA virus that may exceed 80% seroprevalence in adults. BKV infection typically occurs during childhood, and the majority of adults are latently infected. While BKV infection is rarely associated with clinical disease in most individuals, in immunosuppressed individuals, reactivation may cause kidney (BK‐associated nephropathy) or bladder (hemorrhagic cystitis and ureteral stenosis) injury. No antiviral therapies have been approved for the treatment of BKV infection. Reducing immunosuppression is the most effective therapy, although this is not feasible in many patients. Thus, a robust understanding of viral pathogenesis and viral diversity remains important for the development of future therapeutic strategies. Studies of BKV diversity are quite sparse compared to other common viral infections; thus, much of our understanding of BVK variability and evolution relies heavily analogous studies of other viruses such as HIV or viral hepatitis. We provide a comprehensive review of BKV diversity at the population and individual level with careful consideration of how viral variability may impact viral replication, pathogenesis, tropism, and protein function. We also discuss a number of outstanding questions related to BK virus diversity that should be explored rigorously in future studies.     

Transplacental transmission of human polyomavirus BK

The presence of BK virus (BKV) and JC virus (JCV) in autopsy materials (placenta, brain, and kidney) of aborted fetuses was investigated by PCR using two sets of primers, specific for the regulatory region (RR) and for the capsid protein VP1, respectively. The RR of BKV was detected in 12 samples of placenta and brain and in nine samples of kidney obtained from 15 fetuses. Out of the 12 positive cases, four placentas, one brain, and three kidney samples also showed the presence of BKV DNA in the VP1 region. Of 12 placentas from a control group with a normal pregnancy outcome, the RR of BKV was detected in six samples, four of which were also positive for the VP1 region. None of the samples from either group was positive for the RR of JCV. In two cases, the nucleotide sequence of the BK RR demonstrated that the viruses isolated from maternal and fetal tissues showed a high homology with one another and had a characteristic deletion of the R₆₃ box compared to the archetype strain. The results indicate that BKV may be transmitted vertically. J. Med. Virol. 56:372–376, 1998 . © 1998 Wiley-Liss, Inc.     

BKV and JCV large T antigen-specific CD8+ T cell response in HLA A*0201+ kidney transplant recipients with polyomavirus nephropathy and patients with progressive multifocal leukoencephalopathy.

BACKGROUND: BK virus (BKV), which causes polyomavirus-associated nephropathy (PVN) in kidney transplant recipients (KTx), has 75% homology with JC virus (JCV), the etiologic agent of progressive multifocal leukoencephalopathy (PML). The large T-antigen (T-ag) is the main regulatory protein of polyomaviruses that is expressed early in the viral cycle. OBJECTIVES: To characterize epitopes of BKV and JCV T-ag recognized by CD8+ T-cells and explore the role of these cells in containing polyomavirus infection. STUDY DESIGN: We tested peripheral blood mononuclear cells of HLA A*0201+ BKV- and JCV-seropositive individuals, including patients with active BKV or JCV infection and healthy control subjects in a cross-sectional study. RESULTS: CD8+ T-cells that recognized the nonamer BKV Tp579, which is identical to JCV Tp578, were detected by tetramer staining in 10/13 (77%) healthy individuals, 3/10 (30%) KTx/PVN, and 4/9 (44%) patients with PML and/or HIV-infection. Conversely, BKV Tp398- and Tp410-specific CD8+ T cells were detected in 3/13 (23%) and 1/13 (8%) healthy individuals only. CONCLUSION: These data suggest that, as it is the case for the VP1 protein, the same population of CD8+ T-cells may recognize epitopes located on the BKV and JCV T protein. The overall cellular immune response against polyomavirus T-ag, however, is lower than against the VP1 protein and is more frequently detected in healthy individuals than in patients with active BKV or JCV infection.     

Decoy cells and malignant cells coexisting in the urine from a transplant recipient with BK virus nephropathy and bladder adenocarcinoma

The search for decoy cells (DC) in urine is widely used as screening for BK virus (BKV) reactivation in transplant recipients. BKV cytopathic effect of DC must not be confused with high-grade urothelial carcinoma. This report presents a case of coexistence of DC and malignant cells in the urine from a transplant recipient with BKV-associated nephropathy (BKVN) and bladder adenocarcinoma. A 38-year-old female with type 1 diabetes mellitus and end-stage renal disease underwent a simultaneous pancreas and kidney transplant. Four years post-transplantation, BK virus studies were performed for renal dysfunction. Isolated DC and DC in casts were identified in urine. Also, the tests for BKV DNA were positive in serum and renal allograft biopsy. BKVN was treatment-resistant and the patient returned to hemodialysis. A kidney transplant nephrectomy was performed 2 years later. The next urine cytology showed, in addition to DC, other distinct cells with nuclear atypia highly suggestive of malignancy. Some cells showed both, malignant and DC features. A bladder adenocarcinoma was diagnosed on biopsy and BKV proteins were demonstrated on tumor cells, supporting a possible role for BKV in the oncogenic pathway in this clinical setting. The presence of DC in the urine from a transplant recipient is the hallmark of BKV activation, but it does not exclude the existence of carcinoma. Furthermore, the presence of highly atypical cells should raise, not eliminate, the possibility of neoplastic transformation of the bladder.