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Journal of Clinical Microbiology, March 2004, p. 1142-1148, Vol. 42, No. 3
0095-1137/04/$08.00+0 DOI: 10.1128/JCM.42.3.1142-1148.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Fred Hutchinson Cancer Research Center and the University of Washington, Seattle, Washington 98109-1024
Received 13 March 2003/ Returned for modification 21 April 2003/ Accepted 3 October 2003
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CMV load detected in blood and in tissues is an important factor in predicting subsequent or ongoing CMV disease in transplant patients and individuals infected with human immunodeficiency virus (HIV) (2, 10, 22). Quantification of virus load may also be useful in preemptive treatment strategies in that certain threshold or increasing levels of viral load could be used to start antiviral therapy (2). CMV replicates rapidly in vivo and, among patients at high risk for fatal CMV disease (i.e., allogeneic hematopoietic stem cell transplant [HSCT] recipients), the time from first detection to overt disease may be less than 7 days (9). Thus, any quantitative test for CMV DNA needs to be highly sensitive with minimal variability and a short processing time (i.e., <24 h) to make it a useful tool in prevention strategies in high-risk patients. Many of the current techniques of virus quantification are either imprecise, have poor sensitivity, or require long processing times (2). The real-time PCR methodology with automated DNA extraction has the potential of improving these deficiencies (11, 13, 20, 23, 25).
Earlier studies suggested that plasma-based PCR assays result in delayed detection of CMV DNA due to the lower sensitivity of these assays compared to cell-based and whole-blood assays (2, 3, 6, 12, 19). Plasma does not require lengthy cell separation procedures and offers a much better opportunity to detect CMV viremia during periods of severe cytopenia when cell-based assays perform poorly. Moreover, the frequency of detecting CMV DNA in plasma in normal persons is low, making the specificity of plasma DNA testing high. Plasma viremia has been associated with overall mortality in stem cell transplant recipients (4) and HIV-infected individuals (22).
The purpose of the present study was to develop a highly sensitive and reproducible plasma-based PCR assay for CMV DNA using a high-throughput TaqMan system and the Qiagen Robot 3000 automated DNA extraction system. The goal was to develop a quantitative assay that is both a sensitive and a specific assay and that can be performed with minimal sample processing, independent of patients' peripheral neutrophil count, and with low assay variability. The assay was validated clinically by direct comparison with CMV detection by the pp65 antigenemia assay and conventional tube cultures.
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Assay variability studies and the comparison of manual versus automated extraction were performed with leftover clinical samples. The Institutional Review Boards at FHCRC and the University of Washington approved the studies.
CMV serologies. CMV serostatus was determined by enzyme-linked immunosorbent assay (Premier CMV IgG; Meridian Diagnostic, Cincinnati, Ohio).
Viral cultures. Viral cultures from blood, bronchoalveolar lavage, and tissue specimens were performed as previously described (16). Blood cultures were performed weekly from EDTA blood. Conventional cultures were maintained for at least 4 weeks, and positive results were confirmed with CMV-specific monoclonal antibodies (16).
pp65 antigenemia assay. CMV pp65 antigenemia testing was performed by using the CMV Brite kit (Biotest Diagnostic Corp., Denville, N.J.). Briefly, slides were tested in duplicate by using cytocentrifugation slides prepared with 1.5 x 105 PBL per slide, fixation with formaldehyde-NP-40, and immunofluorescence staining with the monoclonal antibodies C10 and C11 directed against pp65 (16). A positive result was defined as any positive cell in two slides. Quantitative results were expressed as the average number of positive cells per slide (5).
Detection of CMV DNA by quantitative TaqMan PCR. DNA extraction was performed on 200 µl of plasma or 5 x 104 to 5 x 105 dextran-separated PBL by using a QIAamp DNA blood kit (Qiagen, Inc., Valencia, Calif.). Then, 100 µl of Tris (10 mM, pH 8.0) was used to elute the DNA, and 10 µl of the DNA was used for each PCR. Three primer and probe sets were evaluated in plasma (Table 1). The first primer tested was designed from UL125, an intron of the commonly used primer site UL123, and close to a primer site used on a previously published semiquantitative assay (8). Due to low sensitivity with this primer, likely to be related to genomic diversity in clinical isolates, a primer from a conserved region of UL 126, another intron of UL123, was designed (Table 1) (17). To evaluate whether increased sensitivity and specificity could be achieved, a double-primer assay was designed consisting of two sets of primers and probes that were used simultaneously to amplify 68 bp of gB region (UL 55) and 84 bp of UL123 (exon 4) (Table 1). All of the probes used in the present study were labeled at the 5' end with 6-carboxyfluorescein (FAM) and at the 3' end with 6-carboxytetramethylrhodamine (TAMRA) (Synthegen, Houston, Tex.). The PCR conditions were 50°C for 2 min and 95°C for 2 min, followed by 45 cycles of 95°C for 20 s and 60°C for 1 min. Each 50 µl of PCR mixture contained a 400 nM concentration of primers, 5 µl of 10x buffer II (Perkin-Elmer Cetus), 10 mM MgCl2, 17.5 nM TaqStart antibody (Clontech), 1.25 U of AmpliTaq (Perkin-Elmer Cetus), 0.05 U of uracil-DNA-glycosylase, 8% glycerol, and 60 nM 6-carboxy-x-rhodamine. To ensure that negative results were not due to nonspecific inhibition of the PCR assay, each PCR also contained internal positive control EXO DNA (5,000 copies/reaction), primers, and probes (17). All negative CMV PCR results required detection of EXO DNA. One positive control with 5,000 copies of CMV DNA was coprocessed with specimens to ensure DNA recovery. To monitor for false-positive results, specimens were processed in parallel with aliquots of 1x phosphate-buffered saline. PCRs without DNA also were included in each PCR run. PCRs were run in duplicate, with results deemed positive if both reactions were positive; results that were positive-negative were deemed indeterminate and repeated. Quantitative PCR levels are shown as DNA copies per 106 copies of ß-globin and as copies per milliliter of plasma.
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TABLE 1. Primers and probes
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DNA recovery in vitro was determined by spiking CMV DNA into serial dilutions of Tris buffer.
Data analysis. Qualitative test results were compared by using two-by-two tables. For calculation of sensitivity, specificity, predictive values, and the rate of concordance between tests, only specimens in which all tests could be performed were considered. Discrepant results between PCR and pp65 antigenemia testing were analyzed by looking for evidence of CMV by different methods in the same sample (i.e., different primers for plasma and testing of the PBL from the same sample) and by analyzing whether there was prior or subsequent evidence of CMV infection in the same subject.
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Assay specificity for CMV. To determine the specificity of the PCR assay, 105 copies of herpes simplex virus type 1, human herpesvirus 6, human herpesvirus 8, varicella-zoster virus, Epstein-Barr virus, and human cells (HSB-2) were tested by PCR with the CMV UL55 and UL123 primers and probes. The standard curve consisted of 105, 104, 103, 102, and 10 copies of CMV (Towne strain), and three negative controls were included in the PCR run. All negative controls were negative, and all points were positive. The UL55/UL123-exon 4 primers and probes did not cross amplify the other human herpesviruses and did not cross-amplify the human genome.
Detection of different clinical strains. Ten clinical isolates obtained from different subjects were tested. DNA was extracted from 20 µl of CMV culture, and one-tenth of the DNA was tested by PCR with the UL55/UL123-exon 4 primer. Four negative controls, one positive control and one set of standards at 105, 104, 103, 102, and 10 copies were included in the experiment. All negative controls were negative. The positive control was positive. All 10 clinical CMV isolates were positive at levels ranging from 1.8 x 104 to 2.4 x 106 copies per reaction. Thus, this assay is able to detect randomly selected clinical strains of CMV.
Assay sensitivity in vitro. Assuming that one copy can be detected per reaction, the calculated lower level of sensitivity was 50 copies per ml with 200 µl of plasma and 25 copies with 400 µl of plasma. Spiking experiments performed in triplicate with serial dilutions of CMV DNA showed consistent detection of 100 copies per ml.
Study subjects and samples. Study subjects included stem cell transplant recipients (HSCT, n = 303) and CMV-seropositive transplant candidates or HIV-infected individuals (n = 21). Among HSCT recipients, 241 (79%) were allograft recipients and 62 (21%) were autograft recipients. The mean number of samples per patient was 6.1.
Qualitative PCR versus pp65 antigenemia and blood cultures. Two-by-two tables and sensitivity, specificity, and positive and negative predictive values for the three PCR assays versus antigenemia are shown in Tables 2 and 3. All three assays detected CMV in a larger proportion of samples than the antigenemia assay. The double-primer assay had the best performance characteristics compared to pp65 antigenemia in all four categories.
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TABLE 2. Quantitative real-time PCR versus pp65 antigenemiaa
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TABLE 3. Sensitivity, specificity, and predictive values of different primers for detection of CMV pp65 antigenemiaa
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Resolution of discrepancies. Discrepancies were analyzed on a per-sample level and on a per-subject level. On a per-sample level, samples with discrepant results were analyzed for the presence of CMV by the different diagnostic tests (antigenemia, DNA in PBL). Of the 122 samples that were positive by the double-primer assay but negative by antigenemia testing (Table 4), the median copy number was 1,150 copies per ml (range, 40 to 226,300). For 80 of these samples, PBL were available, and 50 of these samples (62.5%) were also found to be positive by PCR. Of 121 samples, 110 (90.9%) were determined to be positive in plasma by the UL123 primer (primer 2, Table 1). Overall, the presence of CMV in the 122 was confirmed in 121 by at least one other method.
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TABLE 4. Analysis of samples with discrepant results between the UL55/UL123 TaqMan assay and pp65 antigenemia on a study subject levela
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Results were also analyzed on a subject level by examining subjects for evidence of CMV at different time points by either PCR or antigenemia. As shown in Table 4, the majority of patients with discrepant samples with the double primer were at high risk for CMV reactivation or primary infection based on their serostatus and also had CMV detected at different time points during the longitudinal follow-up. This analysis highlighted the greater specificity of the double-primer assay, since none of the PCR-positive-antigenemia-negative results occurred in patients at low risk for CMV infection (D-/R-). By comparison, 20% of discrepant samples with primers 1 and 2 occurred in low-risk patients and could not confirmed by other methods or at other time points (data not shown).
Comparison of CMV quantitation. CMV quantitation by PCR was compared to quantitation by the pp65 antigenemia assay. There was a reasonable correlation among samples that were positive by both methods (R = 0.62, P < 0.0001). The coefficient of correlation was slightly lower among samples that were positive by either method (R = 0.57, P = 0.0001) (Fig. 1).
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FIG. 1. Correlation of CMV quantitation by CMV pp65 antigenemia and UL55/UL123 plasma PCR among samples determined to be positive by both methods (R = 0.62, P < 0.0001) (A) and among samples found to be positive by either method (R = 0.57, P = 0.0001) (B).
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FIG. 2. Time to first detection by double-primer PCR at different levels versus pp65 antigenemia in CMV-seropositive HSCT recipients.
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FIG. 3. PCR results in three patients with CMV disease who were missed by antigenemia surveillance. The dashed arrows indicate positive PCR results prior to the onset of the disease, and solid arrows represent positive tests after the onset. The numbers indicate copy numbers per milliliter of plasma.
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FIG. 4. Manual versus automated extraction in 70 samples (UL55/UL123 assay; R = 0.87, P < 0.001).
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Earlier studies suggested that detection of CMV in plasma is at best equivalent to detection of CMV by antigenemia and inferior to detection from PBL or whole blood (19). The present study demonstrates that quantitative detection of CMV DNA in plasma can be significantly more sensitive than detection by the antigenemia assay when optimized DNA extraction techniques, primers, and detection systems are used. Analysis of discrepant results indicated that almost all of the positive results with the UL55/UL123-exon 4 primer could be confirmed by other primers or methods or were obtained from patients who had evidence of CMV infection either after the test result or prior to the test result while on preemptive antiviral therapy. Thus, the PCR-positive-antigenemia-negative results seem to represent true positive results based on the increased sensitivity of the method. In a longitudinal analysis of CMV-seropositive HSCT recipients, the time to first detection was earlier and the proportion of patients who became positive was higher compared to the antigenemia assay (Fig. 2). The assay also became positive prior to the onset of CMV disease in two of three patients with CMV disease that were missed by antigenemia surveillance (Fig. 3). The higher sensitivity was also demonstrated in spiking experiments.
However, despite the overall higher sensitivity of the double-primer PCR assay, the assay was not positive in all specimens that were found to be positive by the antigenemia assay. Although our data suggest that some of these results may be false positive due to the higher degree of operator dependency with antigenemia testing, the concern might be raised that replacing the antigenemia assay with this new PCR assay may result in some cases of CMV disease since some of these cases of antigenemia may progress to CMV disease. In our study, we were unable to assess this question because preemptive therapy was administered to all patients with antigenemia. The theoretical risk of missing some cases of progressive antigenemia must be balanced against the two cases of CMV disease that the new PCR assay did detect (both patients were antigenemia negative) (Fig. 3). Ultimately, one cannot answer this question definitely with the present study due to the use of preemptive therapy. A randomized trial would be needed in which patients are randomized to be monitored by one of the two methods. Only such a trial can determine the overall risks and benefits of using what appears to be an overall more sensitive assay that misses some cases of antigenemia. This PCR assay is currently being used in a large randomized multicenter clinical trial based on its performance characteristics in the present study.
The present study suggests that the choice of primers is important. The high sensitivity may be due, in part, to the small size of the amplicon, as recently suggested (7). However, it is noteworthy that the increase in sensitivity resulted in clinically relevant information since most of the PCR-positive-antigenemia-negative samples resulted in earlier detection of CMV infection or more sensitive determination of clearance from blood in patients receiving preemptive therapy. Of the three primer sets evaluated in the present study, two single-primer assays proved to be unsuitable for clinical testing due to the failure to detect CMV in clinical samples with documented CMV by antigenemia or culture (Tables 2 and 3). The UL126 primer resulted in more positive samples; however, a large proportion of positive results occurred in patients who had no evidence of CMV by other methods or during follow-up. Indeed, most of the results that were found to be positive only by the UL126 assay were from seronegative HSCT recipients who had received a stem cell product from a seronegative donor and were treated with seronegative or leukocyte-reduced blood products. Thus, the significance of these results is uncertain. We therefore developed a double-primer assay, which seems better suited for clinical surveillance testing. The double-primer (UL55/UL123-exon 4) assay only rarely detected CMV DNA in seronegative patients with a seronegative donor and performed significantly better in samples with proven antigenemia or culture positivity. Overall, the assay was superior to pp65 antigenemia and viremia by culture with regard to sensitivity, specificity, and predictive values.
Although no direct comparison with other plasma-based PCR assays was performed, our data suggest that assay sensitivity is at least 0.5 log10 higher than other noncommercial and commercial assays, which have a lower limit of detection of
500 copies/ml (3, 12, 18). The clinical results are consistent with another recently published experience in which assay modifications resulted in significant increases in assay sensitivity of a commercial assay (15). In that study, the proportion of CMV detection in clinical samples was also doubled, with a reported assay sensitivity of 20 copies/ml (15).
The automated extraction technique we utilized simplified specimen processing and minimized operator variability. In our study, automated extraction not only provided fast and accurate quantitation of CMV but also appeared to increase sensitivity further. Assay variability was low and comparable to that reported for quantitative molecular assays for HIV and hepatitis C virus (1, 15, 24).
In conclusion, we developed a highly sensitive quantitative plasma PCR assay using primers in the UL55 and UL123-exon 4 region of CMV. This assay detected CMV more often than antigenemia in blood specimens submitted to the virology lab for virologic surveillance. The assay is particularly useful in situations in which antigenemia testing cannot be performed due to low cell counts or in which specimens need to be shipped or stored. In contrast to antigenemia testing, the assay is largely operator independent and provides highly reproducible quantitative results. When used with automated extraction, the assay allows large-scale testing of clinical samples with high sensitivity, low variability or quantitation, and a 1-day turnaround with minimal hands-on time. A comparative randomized clinical trial is needed to determine whether a preemptive therapy strategy based on this assay is superior to pp65 antigenemia-based strategies.
Grant support was provided by the National Institutes of Health (CA18029, CA15704, AI41754, HD40540, and AI01839-01).
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