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Journal of Clinical Microbiology, March 2004, p. 1176-1180, Vol. 42, No. 3
0095-1137/04/$08.00+0 DOI: 10.1128/JCM.42.3.1176-1180.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Departments of Pathology,1 Surgery, University of Pittsburgh School of Medicine,2 Department of Pediatrics, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania3
Received 21 July 2003/ Returned for modification 27 August 2003/ Accepted 2 November 2003
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DNA was extracted with the QIAamp Blood maxikit (catalog no. 51192; Qiagen) for urine or the QIAamp Blood minikit (catalog no. 51104; Qiagen) for plasma by using 5 ml of uncentrifuged urine or 200 µl of plasma. The final extraction volumes were 200 and 40 µl, respectively. The following oligonucleotide sequences, derived from the BKV (Dunlop strain; GenBank accession no. NC001538) capsid protein-1 (VP-1) gene, were synthesized (IT BioChem, Salt Lake City, Utah): forward primer, 5' GCA GCT CCC AAA AAG CCA AA 3'; reverse primer, 5' CTG GGT TTAGGA AGC ATT CTA 3'.
The sequences were checked for homology by a BLAST search performed on a website maintained by the National Center for Biotechnology Information and the National Library of Medicine (http://www.ncbi.nlm.nih.gov). Specificity for BKV DNA was confirmed by using a plasmid containing full-length BKV, JC virus, or simian virus 40 (SV40) genomic DNA (catalog no. 45025, 45027, or 45019, respectively; American Type Culture Collection [ATCC], Manassas, Va.).
Quantitative real-time PCR assays were performed using the Roche LightCycler. PCR amplifications were run in a reaction volume of 20 µl containing 2 µl of the DNA sample, Roche 10x SybrGreen FasStart mastermix, 2.5 mM magnesium chloride, and 500 nM (each) forward and reverse primers. Thermal cycling was initiated with a first denaturation step of 10 min at 95°C, followed by 40 cycles of 95°C for 10 s, 62°C for 10 s, 72°C for 5 s, and 78°C for 10 s, at the end of which fluorescence was read. Real-time PCR amplification data were analyzed with software provided by the manufacturer. Standard curves for the quantification of BKV were constructed using serial dilutions of a plasmid containing the entire linearized genome of the BKV Dun strain inserted into the BamHI restriction site of the pBR322 plasmid (ATCC 45025). The plasmid concentrations plotted ranged from 1 to 1011 genomic copies of BKV DNA per PCR. All patient samples were tested in duplicate, and the number of BKV copies was calculated from the standard curve. Data were expressed as copies of viral DNA per milliliter of urine or plasma, or per cell in the biopsy samples. Standard precautions designed to prevent contamination during PCR were followed. No-template control lanes and negative-control samples (DNA extracted from human peripheral blood lymphocytes) were included in each run.
Renal allograft biopsy specimens from these patients were subjected to routine formalin fixation and paraffin embedding. Viral DNA was demonstrated in the infected cells by using in situ hybridization with a commercially available probe (Enzo Diagnostics, Farmingdale, N.Y.). In 32 biopsy specimens, sufficient tissue was available to quantitate intrarenal concentrations of BKV DNA by real-time PCR, as previously published (9). Viral copy numbers were expressed on a per-cell basis after simultaneous amplification of the house keeping enzyme asparto-acylase. Pertinent clinical information was obtained by review of the medical records.
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FIG. 1. Characteristics of the BKV real-time PCR assay. (A) Agarose gel electrophoresis of PCR products generated by using BKV-specific primers and BKV or JC virus plasmid controls. Rightmost and leftmost lanes, DNA size markers; lane W, water blank; 2nd to 9th lanes, 10-fold serial dilutions of BKV plasmid DNA from 109 copies to 1 copy; 11th to 14th lanes, JC virus plasmid DNA from 10 to 107 copies. (B) Quantitative PCR assay of the same BKV standards with SybrGreen detection. (C) Linear range of the assay obtained by use of known serial dilutions of the BKV plasmid as a template. Shown is the BKV copy number calculated from the standard curve (BK measured) versus the known BKV copy equivalents put into the PCR as unknowns (BK expected). Each data point is an average from 3 to 10 separate experiments. At viral copy numbers of >109, the background template fluorescence becomes significant and linearity fails.
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(i) The negative-control group consisted of 76 urine and 76 plasma samples obtained from 51 patients with no evidence of BKVAN and negative PCR for viral DNA.
(ii) The asymptomatic BK viruria group consisted of 33 urine, 33 plasma, and 10 biopsy samples obtained from 15 patients (Table 1; Fig. 2). The median viral load in the urine was 6.02E+03 copies/ml (range, 0.00E+00 to 5.86E+09 copies/ml). No virus was generally detected in the plasma of these patients (median, zero). However, eight samples from five patients showed circulating BKV DNA levels ranging from 1.07E+03 to 2.90E+04 copies/ml, even though the allograft biopsies showed no viral nephropathy. One of these patients showed a rise in the serum creatinine level and was presumptively treated for viral nephropathy by reduction of immunosuppression. It is possible that the lack of demonstrable viral inclusions in the biopsy specimen was the result of sampling error. One patient who presented with asymptomatic viruria went on to develop biopsy-proven viral nephropathy. Quantitative PCRs on biopsy tissue generally showed no viral DNA or less than 1 copy per cell, except for a single sample which yielded 152 copies per cell. This was a consultation case for which no further follow-up is available.
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TABLE 1. Correlation of BKV loads in urine, plasma, and biopsy samples with clinical status
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FIG. 2. Distribution of BKV loads in renal transplant patient groups. Data are expressed as log viral copies per milliliter (for plasma and urine samples) or per 1,000 cells (for biopsy specimens). Data in the no BKVAN group (None) include samples from patients with asymptomatic viruria as well as from negative controls with no evidence of BKVAN. Dashed lines indicate the limit of detection in the various sample types. The open square represents a patient who subsequently developed BKVAN. Solid bars indicate the suggested viral load cutoffs useful for diagnosis of BKVAN. A cutoff of 1.00E+07 copies of BKV/ml in urine had a sensitivity of 100%, a specificity of 96%, a negative predictive value of 100%, and a positive predictive value of 67% for BKVAN. A cutoff of 5.00E+03 copies of BKV/ml in plasma had a sensitivity of 100%, a specificity of 93%, a negative predictive value of 100%, and a positive predictive value of 50% for BKVAN. A Mann-Whitney test indicated that viral loads in the active BKVAN group were significantly higher than those in the resolved BKVAN group (P < 0.001). There was no statistically significant difference between viral loads in the resolved BKVAN group and those in the asymptomatic viruria ("None") group.
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(iv) The resolved BKVAN group consisted of 32 plasma, 27 urine, and 9 biopsy samples from 10 patients who had a previous diagnosis of BKVAN. Thirteen samples had been obtained within 3 days of a biopsy confirming the absence of active viral nephropathy. The remaining samples were spaced farther out from the index biopsy, but a follow-up biopsy confirmed the absence of active nephropathy during the interval of observation. Hence, these samples were also assigned to the resolved BKVAN group. The urine samples in this group showed a median viral load of 2.24E+04 copies/ml (range, 0.00E+00 to 1.38E+08 copies/ml). There was usually no viremia in these patients (median plasma viral load, zero). However, four patients showed circulating viral DNA levels varying from 8.26E+03 to 1.58E+06 copies/ml. It appears that viral clearance from the blood lagged behind viral clearance from the allograft kidney in these individuals. Quantitative PCR performed on biopsy tissue in this group of patients demonstrated a median viral load of 1.24 copies per cell (range, 0.21 to 21.6 copies per cell). Thus, the absence of viral inclusions in light microscopic observations and negative in situ hybridization results for biopsy tissue do not necessarily equate with total viral clearance from the renal allograft, although the average viral load is extremely low.
Viral loads in different clinical categories were statistically analyzed by the Mann-Whitney test, since the data did not pass the normality test. Viral loads in plasma, urine, and biopsy samples were higher in the active BKVAN group than in the asymptomatic viruria group or the resolved BKVAN group (P < 0.01). There was no statistically significant difference between data in the asymptomatic viruria group and data in the resolved BKVAN group. Serial evaluation of multiple samples from the same patient usually showed proportionate changes in viral loads in urine and plasma. However, patients who went on to resolve viral nephropathy typically showed clearance of viremia, with reduced but persistent viruria. For a representative patient treated for BKVAN, BK viral load was above the proposed cutoff of 1E+07 copies/ml of urine and 5E+03 copies/ml of plasma at the time of diagnosis but dropped below those levels after treatment. (Fig. 3). The serum creatinine level did not always fall despite the clearance of viral DNA from biopsy and plasma samples. This likely represents irreversible allograft injury caused by virus-induced damage to the kidney parenchyma.
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FIG. 3. Serial changes in viral load observed for a patient with BKVAN. Time zero on the x axis corresponds to the time of biopsy diagnosis of viral nephropathy. Reduction in immunosuppression and four doses of cidofovir (indicated by multipliers) resulted in clearance of viremia (shaded squares) and a reduction in viruria (solid diamonds). Serum creatinine levels (open diamonds) fluctuated and did not drop significantly despite the reduction in viral load. This phenomenon results from the confounding influence of chronic allograft nephropathy.
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The occurrence of viremia in five samples in the resolved BKVAN group appeared to be a transient finding. Follow-up samples obtained 7 to 31 days later showed clearance of virus from plasma. Biopsy sampling error should also be kept in mind during the clinical evaluation of such patients, particularly if urine examination shows decoy cells with an abundant inflammatory response (2). Another point of interest is the persistence of low levels of viral DNA in biopsy specimens of patients with resolved nephropathy, even when there was cessation of viruria. It is not clear whether this corresponds to latent virus or persistent low-level viral replication.
It is impractical to perform repeated biopsies to monitor the clinical course of BKVAN. Hence, we were particularly interested in determining whether persistent nephropathy could be predicted by noninvasive monitoring of virus loads in urine samples. Unfortunately, we could not determine any absolute cutoff levels that could distinguish the resolved BKVAN group from the active BKVAN group. Nonetheless, 26 of 27 (96%) urine samples in the resolved BKVAN group carried a viral load of <1E+07 copies/ml. The only sample that exceeded this cutoff was obtained within 12 days of a biopsy showing active BKVAN. Conversely, 10 of 15 (66.7%) urine specimens with a viral load of
1E+07 were associated with active BKVAN.
Attempts to determine a viremia cutoff appropriate for separating out cases with active nephropathy demonstrate the need to accept a tradeoff between the competing clinical requirements for sensitivity and specificity. A cutoff of 5E+03 copies/ml diagnoses all cases of BKVAN (100% sensitivity) but yields a false-positive diagnosis for 5 of 33 (15.2%) samples associated with asymptomatic viruria and 5 of 33 (15.2%) samples associated with resolved BKVAN. A stricter cutoff of 1E+05 copies/ml correctly classifies only 7 of 10 (70%) samples with active BKVAN (70% sensitivity) but reduces the false-positive diagnoses to 2 of 33 (6.1%) in samples from patients with resolved nephropathy and to 0 of 33 (0%) in samples associated with asymptomatic viruria. It is worth noting that the sensitivity of quantitative PCR varies from laboratory to laboratory. Hence, every medical center will need to establish its own cutoff values for the purposes of clinical management. For example, Hirsch et al. found viral nephropathy to be associated with plasma viral loads of >7.7E+03 copies/ml. In three of five cases the viral load exceeded 1.0E+07 copies/ml (4). Another caveat in this study is that biopsies were not performed for all patients at the same time that samples classified as asymptomatic viruria were collected. Hence, the possibility of occult nephropathy cannot be entirely excluded. In fact, one patient initially labeled as having asymptomatic viruria did go on to develop biopsy-proven nephropathy. On the other hand, biopsies are prone to sampling error, and we elected to treat one viremic patient with rising serum creatinine levels, 2.86E+07 viral copies/ml in urine, 1.22E+04 viral copies/ml in plasma, and a negative biopsy result as having BKV nephropathy on clinical grounds.
Patients with asymptomatic viruria showed urinary viral loads below our proposed BKVAN cutoff of 1E+07 copies/ml in 29 of 33 (87.8%) samples. One patient with 1.49E+09 copies/ml in urine subsequently developed viral nephropathy, as was noted above. These data confirm a widely held belief that persistent excretion of high levels of BKV DNA is a risk factor for the development of BKVAN. Viremia was observed in eight samples from five patients. Four of 10 biopsy samples tested in the group with asymptomatic viruria showed detectable viral DNA, with concentrations ranging from 0.005 to 152 copies per cell.
In conclusion, serial measurement of viral loads in urine or plasma by quantitative PCR is a useful tool in monitoring the course of BKV infection. The results should be interpreted in conjunction with the clinical picture and biopsy findings.
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