Evaluation of different urine protocols and DNA extraction methods for quantitative detection of BK viruria in kidney transplant patients

Rapid point-of-care detection of BK virus in urine by an HFman probe-based loop-mediated isothermal amplification assay and a finger-driven microfluidic chip

Background

BK virus (BKV)-associated nephropathy (BKVN) is one of the leading causes of renal dysfunction and graft loss in renal transplant recipients. Early monitoring of BKV in urine is crucial to minimize the deleterious effects caused by this virus on preservation of graft function.

Methods

We report a simple, rapid, sensitive loop-mediated isothermal amplification (LAMP) assay using an HFman probe for detecting BKV in urine. To evaluate the performance of the assay, a comparison of the HFman probe-based LAMP (HF-LAMP) assay with two qPCR assays was performed using urine samples from 132 HIV-1 infected individuals. We further evaluated the performance of HF-LAMP directly using the urine samples from these HIV-1 infected individuals and 30 kidney transplant recipients without DNA extraction. Furthermore, we combined the HF-LAMP assay with a portable finger-driven microfluidic chip for point-of-care testing (POCT).

Results

The assay has high specificity and sensitivity with a limit of detection (LOD) of 12 copies/reaction and can be completed within 30 min. When the DNA was extracted, the HF-LAMP assay showed an equivalent and potentially even higher sensitivity (93.5%) than the qPCR assays (74.2-87.1%) for 132 urine samples from HIV-1 infected individuals. The HF-LAMP assay can be applied in an extraction-free format and can be completed within 45 min using a simple heat block. Although some decreased performance was seen on urine samples from HIV-1 infected individuals, the sensitivity, specificity, and accuracy of the extraction-free BKV HF-LAMP assay were 95%, 100%, and 96.7% for 30 clinical urine samples from kidney transplant recipients, respectively.

Conclusion

The assay has high specificity and sensitivity. Combined with a portable finger-driven microfluidic chip for easy detection, this method shows great potential for POCT detection of BKV.

An efficient and cost-effective method for purification of small sized DNAs and RNAs from human urine

Urine holds great promise as a non-invasive sampling method for molecular diagnostics. The cell-free nucleic acids of urine however are small, labile, and difficult to purify. Here an efficient method for the purification of these nucleic acids is presented. An empirically derived protocol was devised by first identifying conditions that allowed recovery of a 100 base pair (bp) DNA, followed by optimization using a quantitative polymerase chain reaction (qPCR) assay. The resulting method efficiently purifies both small sized DNAs and RNAs from urine, which when combined with quantitative reverse transcription PCR (qRTPCR), demonstrably improves detection sensitivity. Fractionation experiments reveal that nucleic acids in urine exist both in the cell-free and cellular fraction, roughly in equal proportion. Consistent with previous studies, amplicons > 180bp show a marked loss in PCR sensitivity for cell-free nucleic acids. Finally, the lysis buffer developed here also doubles as an effective preservative, protecting against nucleic acid degradation for at least two weeks under simulated field conditions. With this method, volumes of up to 25ml of whole urine can be purified in a high-throughput and cost-effective manner. Coupled with its ability to purify both DNA and RNA, the described method may have broad applicability for improving the diagnostic utility of urine, particularly for the detection of low abundant targets.

Quantitative detection of BK virus in kidney transplant recipients: a prospective validation study

Introduction:

BK virus (BKV) infection in renal transplant patients may cause kidney allograft dysfunction and graft loss. Accurate determination of BKV viral load is critical to prevent BKV-associated nephropathy (BKVAN) but the cut-off that best predicts BKVAN remains controversial.

Objective:

To evaluate the performance of a commercial and an in-house qPCR test for quantitative detection of BK virus in kidney transplant recipients.

Methods:

This was a prospective study with kidney transplant recipients from two large university hospitals in Brazil. Patients were screened for BKV infection every 3 months in the first year post-transplant with a commercial and an in-house real time polymerase chain reaction (qPCR) test. BKVAN was confirmed based on histopathology. The area under the curve for plasma qPCR was determined from receiver operating characteristic analysis.

Results:

A total of 200 patients were enrolled. Fifty-eight percent were male, 19.5% had diabetes mellitus, and 82% had the kidney transplanted from a deceased donor. BKV viremia was detected in 32.5% and BKVAN was diagnosed in 8 patients (4%). BKVAN was associated with viremia of 4.1 log copies/mL, using a commercial kit. The cut-off for the in-house assay was 6.1 log copies/mL. The linearity between the commercial kit and the in-house assay was R²=0.83.

Conclusion:

Our study shows that marked variability occurs in BKV viral load when different qPCR methodologies are used. The in-house qPCR assay proved clinically useful, a cheaper option in comparison to commercial qPCR kits. There is an urgent need to make BKV standards available to the international community.

BK virus replication in renal transplant recipients: Analysis of potential risk factors may contribute in reactivation

BACKGROUND

Considering the increasing problem of BK virus infection during post renal transplant surveillance, it is necessary to distinguish the main risk factors leading to reactivation of latent BK virus. Up to now, some probable risk factors have been investigated in some studies, but the results have been confusing and contradictory.

OBJECTIVES

The goal of the present study was to determine the frequency and potential risk factors that may play a role in BK polyomavirus reactivation and nephropathy.

STUDY DESIGN

In this cross-sectional study, 110 patients, who underwent consecutive transplantation between 2010 and 2013, were enrolled without preliminary screening. Urine and blood samples were taken, and quantitative Real-time PCR assay was used to detect and measure the viral load. Demographic and clinical characteristics of the patients who had BK viremia and/or viruria were documented.

RESULTS

Among 110 cases of renal transplant recipients, BK viruria and viremia were found in 54 (49%) and 22 people (20%) respectively. The pre-transplant durations of dialysis among patients with BK viruia were found longer in comparison to BK negative patients. Treatment with Tacrolimus (p=0.03) was found to be a risk factor for development of BK viruria. In patients with viruria and viremia the median creatinine levels were 1.45mg/dl and 1.35mg/dl respectively, which were higher than those in the patients with negative results for BK viruria (p=0.002) and viremia (p=0.02). Also, treatment with Cyclosporine could significantly increase the incidence of BK virus shedding in both urine and blood among patients who received it (p=0.01). Significant relation between reactivation of BK virus and other factors such as age, sex, acute rejection and diabetes was not found.

CONCLUSION

Based on our findings, the main potential risk factors for shedding of BK virus into urine in renal transplant recipients were prolonged pre-transplant dialysis and Tacrolimus regimen. Cyclosporine regimens could be considered as risk factor for both BK viruria and viremia. A significant correlation between BK virus replication and elevated creatinine level was seen among our patients.

Quantification of BK Virus Standards by Quantitative Real-Time PCR and Droplet Digital PCR Is Confounded by Multiple Virus Populations in the WHO BKV International Standard

BACKGROUND

The WHO recently released a BK virus (BKV) international standard. This study evaluated the WHO international standard and commercially available BKV standards by quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR).

METHODS

WHO, Exact Diagnostics, Acrometrix, and Zeptometrix BKV standards were tested by qPCR and ddPCR. Two preparations of NIST BKV clones were also tested. Nucleic acid was extracted with the Roche MP96 and MPLC, followed by quantification in duplicate. To resolve discrepancies, we sequenced the WHO and NIST materials.

RESULTS

Manufacturers' expected copies/mL were close to WHO IU/mL: linear regression of qPCR data revealed 1.12 Exact copies/IU, 0.76 Acrometrix copies/IU, and 0.70 Zeptometrix copies/IU. For ddPCR, similar concentrations were measured when either the VP1 region or the T region was targeted, and concentrations were almost 2-fold higher when both regions were targeted simultaneously. ddPCR results for the VP1 and T regions were similar for all commercial standards, but targeting the T region of the WHO standard led to a 4-fold lower result than the VP1 region. Next-generation sequencing revealed no primer or probe mismatches. However, large differences in coverage across the WHO standard and junctional reads were observed, indicating subpopulations of the WHO standard with deletions in the T region.

CONCLUSIONS

BKV standards showed concordance among providers, but the WHO standard contains subpopulations of viruses with various deletions in the T region. PCR results will vary depending on which region of the WHO standard is targeted.

Correlation between the presence of degenerated inclusion-bearing cells in voided urine samples and the occurrence of polyomavirus infection

OBJECTIVE

The purpose of the present, prospective, cohort study was to monitor urine cytology samples from recipients of renal transplants to search for the occurrence of decoy cells and degenerated inclusion-bearing cells with an aim to correlate the existence of these cells with molecular detection of polyomavirus BK (BKV) DNA in urine.

MATERIAL AND METHODS

This study included patients who underwent renal transplantation. Patients had their urine tested quarterly, during the first year post-transplantation, for the presence of decoy cells and degenerated cells, as well as by quantitative determination of BKV load in the urine and plasma.

RESULTS

Three hundred and sixty-one examinations were performed on 101 patients within 12 months of attendance. Urine cytology results were: 198 (54.9%) negative and 60 (16.6%) positive for the presence of viral cytopathic effects depending on the presence of BKV infection, 72 (19.9%) positive for the manifestation of degenerated cells and 31 (8.6%) unsatisfactory for analysis. There was a subtle tendency towards the presence of degenerated inclusion-bearing cells in cases in which the virus was detected in voided urine. However, the presence of degenerated cells exhibited a tendency to BKV positivity in months 3, 6 and 9 and, exclusively in month 12, this trend was statistically significant.

CONCLUSIONS

There were not enough strong morphological and staining elements to state the origin of the degenerated cells or to describe the nature of the infection (viral or bacterial), given that these cells were undergoing an apoptotic process in post renal transplant patients.

Bright Field Microscopy to Detect Decoy Cells Due to BK Virus Infection in the Fresh and Unstained Urine Sediment in Kidney Allograft Recipients

BACKGROUND

BK virus (BKV) may reactivate in kidney allograft recipients ultimately leading to BKV nephropathy and graft loss. Decoy cells (DCs) are one of the early marks of BKV reactivation, and these can be detected in the urine sediment.

METHODS

A cohort of 102 kidney transplant patients was followed during months 3 and 6 after the transplant procedure. Urine samples were obtained to detect the presence of DC in the fresh and unstained urine sediment under bright field microscopy (BFM), in concomitance to the determination of the amount of BK viruria by qPCR.

RESULTS

Decoy cells were found in 14.7% of patients (15/102). There was a strong agreement (P < 0.001) between qualitative DC detection by two experienced analysts and by qPCR. The positive predictive value, negative predictive value, specificity, and accuracy of BFM were 80%, 75%, 97%, and 75%, respectively. Test sensitivity was 16%. The comparative method was the qPCR.

CONCLUSIONS

Despite its limited sensitivity, BFM of unstained urine sediment is an easily available, fast and cheap method to identify DCs in the population of kidney allograft recipients. The diagnostic performance of BFM on the hands of less experienced analysts deserves further investigation.

Cytomegalovirus is a potential risk factor for late-onset hemorrhagic cystitis following allogeneic hematopoietic stem cell transplantation

Late-onset hemorrhagic cystitis (LOHC) is a common complication following allogeneic hematopoietic stem cell transplantation (allo-HSCT) and is primarily associated with viral infection. We prospectively quantified cytomegalovirus (CMV), BK virus (BKV), and adenovirus in urine and plasma using Q-RT-PCR in 50 consecutive patients to define the relationship between virus and LOHC. Of the 50 patients, 21 developed LOHC at a median of 29 days (range 4-64 days), with a cumulative incidence of 42% (±7.1%). The cumulative incidence of LOHC on day 100 in patients with and without CMV viremia (prior to or at the onset of LOHC) were 56.3% (±8.9%) and 16.7% (±9.1%) (P = 0.018), respectively, and it was 59.3% (±9.8%) and 21.7% (±8.8%) in patients with and without CMV viruria (prior to or at the onset of LOHC) (P = 0.021), respectively. The cumulative incidence of LOHC was also higher in patients with a plasma BKV load increased ≥3 log10 or with a urine BKV load increased ≥4 log10 than those without the increase (P < 0.001). Only one patient with LOHC was tested positive for ADV. Both the univariate and multivariate analyses showed that CMV viremia (HR = 3.461, 95% CI: 1.005-11.922, P = 0.049) and a plasma BKV load that was increased ≥3 log10 (HR = 10.705, 95%CI: 2.469-46.420, P = 0.002) were independent risk factors for the development of LOHC. We conclude that both CMV viremia and an increase of plasma BKV are independent risk factors for LOHC. And the role of CMV viremia was firstly demonstrated.