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Journal of Clinical Microbiology, May 2007, p. 1426-1432, Vol. 45, No. 5
0095-1137/07/$08.00+0 doi:10.1128/JCM.01515-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
Simultaneous Quantification of Epstein-Barr Virus, Cytomegalovirus, and Human Herpesvirus 6 DNA in Samples from Transplant Recipients by Multiplex Real-Time PCR Assay
Kaoru Wada,1
Naomi Kubota,1
Yoshinori Ito,2
Hiroshi Yagasaki,2
Koji Kato,3
Tetsushi Yoshikawa,4
Yasuyuki Ono,5
Hisami Ando,5
Yasuhiro Fujimoto,6
Tetsuya Kiuchi,6
Seiji Kojima,2
Yukihiro Nishiyama,1 and
Hiroshi Kimura1*
Departments of Virology,1
Pediatrics,2
Pediatric Surgery,5
Transplant Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan,6
Department of Pediatrics, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan,3
Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan4
Received 22 July 2006/
Returned for modification 31 October 2006/
Accepted 12 March 2007

ABSTRACT
We developed a multiplex real-time PCR assay using 6-carboxyfluorescein,
6-carboxy-4',5'-dichloro-2',7'-dimethoxyfluorescein, and carbocyanine
5-labeled probes to simultaneously quantify Epstein-Barr virus
(EBV), cytomegalovirus (CMV), and human herpesvirus 6 (HHV-6)
DNA. When previously tested and stored DNA samples were examined,
results of the multiplex real-time PCR assay were as sensitive
and specific as those of a single real-time PCR assay. The multiplex
assay was used to quantify the EBV, CMV, and HHV-6 DNA in 46
transplant recipients. A total of 303 whole-blood and plasma
specimens were collected and analyzed. According to the results
of the multiplex assay, the detection rates for viral DNA in
whole blood and plasma were 23.8% and 5.9% for EBV, 11.2% and
5.3% for CMV, and 12.5% and 2.0% for HHV-6, respectively. All
forms of viral DNA were detected more frequently in whole blood
than in plasma. During the symptomatic period, EBV DNA was detected
in all whole-blood specimens but not in all plasma specimens.
Furthermore, the EBV DNA load in whole blood was higher during
the symptomatic period than during the asymptomatic period,
whereas the EBV DNA load in plasma was similar for both periods.
These results demonstrate that whole blood is more suitable
for the quantification of EBV DNA in transplant patients. However,
a cutoff value with clinical relevance still needs to be determined.

INTRODUCTION
Herpesviruses are ubiquitous in the human population and often
become reactivated in latently infected immunocompromised patients
(
4,
22). Herpesvirus reactivation frequently occurs after hematopoietic
stem cell or solid-organ transplantation and occasionally results
in symptomatic diseases (
2,
4,
28). Among human herpesviruses,
Epstein-Barr virus (EBV), cytomegalovirus (CMV), and human herpesvirus
6 (HHV-6) may cause life-threatening complications, such as
lymphoproliferative disorders (
3,
13,
27), interstitial pneumonia
(
7,
15), and encephalitis (
2,
12,
23,
25). Therefore, to ensure
the success of transplantation, it is essential to monitor for
these viruses and diagnose any virus-related diseases as early
as possible.
With the advent of real-time PCR technology, quantitative PCR assays are becoming widespread methodologies for diagnostic purposes (9, 11). We initially developed quantitative real-time PCR systems to detect EBV (5), CMV (18), and HHV-6 DNA (19). However, because each system was able to detect only one form of viral DNA, simultaneous virus monitoring was cost, time, and labor intensive. It was recently shown that quantification of more than one target per well is possible with the use of different fluorochromes (1, 14, 21, 24). One aim of the present study was to establish a system for the simultaneous quantification of EBV, CMV, and HHV-6 DNA by using a multiplex real-time PCR assay. Another goal was to identify specimens that would optimize virus monitoring. While peripheral blood cells, whole blood, and plasma are commonly used in quantitative real-time PCR, whole blood and plasma are more convenient to use and are suitable for clinical analysis. Since whole blood contains peripheral blood cells, we considered that whole blood could be used instead of peripheral blood cells. In the present study, we developed a multiplex real-time PCR assay to quantify EBV, CMV, and HHV-6 DNA. In addition, we sought to determine whether whole blood or plasma was more suitable for simultaneous virus monitoring in samples from transplant recipients.

MATERIALS AND METHODS
Patients and clinical specimens.
In total, 27 hematopoietic stem cell transplantation recipients
(16 men, 11 women) and 19 liver transplantation recipients (9
men, 10 women) were enrolled in the study. Beginning 1 week
after transplantation, EDTA blood samples were prospectively
obtained from subjects weekly until they were discharged. From
46 patients, 1 to 13 samples per patient (total 303, mean 6.6)
were collected from 1 to 15 weeks after transplantation (mean
7.8 weeks). From some patients, only a few samples could be
obtained because of their early death or follow-up loss. Informed
consent was obtained from all patients or guardians. The institutional
review board of Nagoya University Hospital approved the use
of specimens included in this study.
Among the hematopoietic stem cell transplantation recipients, 10 had acute leukemia, 6 had severe aplastic anemia, 4 had solid tumors, 2 had chronic leukemia, and 5 had other diseases. The patients underwent transplantation between November 2003 and October 2005 at Nagoya University Hospital or at Japanese Red Cross Nagoya First Hospital. The median age of the patients was 8.0 years (range, 1 to 22 years). Eight of 27 patients received antithymocyte globulin, which is known to be a risk factor for EBV-related lymphoproliferative disorders (3, 13).
The liver transplantation recipients received their organs from living donors at Nagoya University Hospital between February 2004 and December 2005. Of 19 patients, 8 had hepatic cirrhosis (hepatitis B virus, 3; hepatitis C virus, 2; other viruses, 3), 3 had biliary atresia, and 8 had other diseases. The median age of the patients was 48.0 years (range, 6 months to 62 years).
Symptomatic EBV infections were diagnosed from clinical findings (fever, enlarged lymph nodes, and hematochezia) and serological examinations. A lymph node biopsy provided histological confirmation that one patient with symptomatic EBV infection had posttransplant lymphoproliferative disorder. CMV hepatitis was diagnosed from the clinical findings and serological examination and confirmed by liver biopsy.
A total of 303 consecutive blood specimens were obtained from transplant recipients and divided into whole-blood or plasma samples, and the 303 paired samples were tested with the multiplex real-time PCR assay. Viral DNA was extracted from 200 µl of whole blood or 200 µl of plasma, using QIAamp DNA blood kits (QIAGEN, Hilden, Germany) and eluted in 100 µl of water.
Specificity and sensitivity studies were performed with 111 DNA samples that had been obtained from other transplantation recipients. These DNA samples had been extracted from either whole-blood or plasma samples and used to monitor viruses by either qualitative PCR or real-time PCR, and stored at 30°C.
The specificity was also confirmed with viral DNA from standard strains (KOS for herpes simplex virus type 1, 186 for herpes simplex virus type 2, Kawaguchi strain for varicella-zoster virus, B95-8 for EBV, AD169 for CMV, Sato strain for HHV-7, and a clinical isolate from a patient with exanthem subitum for HHV-6). Viral DNA was extracted from the supernatant of each virus culture and was used for the cross-reactivity study.
EDTA blood was taken from a patient who was seronegative for EBV, CMV, and HHV-6, and plasma was separated. A DNA extraction solution from either the whole blood or the plasma fraction was used for reconstruction studies.
Primers and probes.
The sequences of the primers and probes used for the multiplex real-time PCR assay are listed in Table 1. The primer and probe sets for the viruses have been described previously (5, 18, 19). Each probe was labeled with different fluorochromes, as follows: the EBV probe was labeled with 6-carboxyfluorescein and quenched with Black-Hole-Quencher 1a (BHQ1a); the CMV probe was labeled with 6-carboxy-4',5'-dichloro-2',7'-dimethoxyfluorescein and quenched with BHQ1a; the HHV-6 probe was labeled with carbocyanine 5 and quenched with BHQ3a. All primers (Fasmac, Kanagawa, Japan) and probes (Operon Biotechnologies, Huntsville, AL) were synthesized commercially.
Quantification of viral DNA by multiplex real-time PCR.
Multiplex and independent real-time PCR were performed with
a QuantiTect multiplex PCR kit (QIAGEN). The multiplex real-time
PCR assay was performed in a total reaction mixture (25 µl)
containing 5 µl of DNA extracts, 12.5 µl of 2
x QuantiTect
multiplex PCR master mix, each forward and reverse primer, and
each probe. To determine the optimal concentrations of the primers
and probes, we evaluated various concentrations of primer and
probe sets using the multiplex real-time PCR assay. The optimal
concentration of forward primer was 200 nM for EBV and 100 nM
for CMV and HHV-6. The optimal concentration of reverse primer
was 200 nM for EBV, 100 nM for CMV, and 200 nM for HHV-6. The
optimal concentration of each probe was 100 nM. The independent
real-time PCR was performed in the same way as the multiplex
real-time PCR assay except that only one primer/probe set was
included. Amplification and real-time fluorescence detection
were performed with a model Mx3000P real-time PCR system (Stratagene,
La Jolla, CA) using the following protocol: an initial denaturation
and polymerase activation step for 15 min at 95°C, followed
by 50 cycles of denaturation at 95°C for 15 s and 60°C
for 1 min. Real-time fluorescence measurements were taken, and
a threshold cycle value for each sample was calculated by determining
the point at which the fluorescence exceeded a threshold limit.
Each real-time PCR assay contained the dilution series of a
standard for the calibration curve, and all samples and the
standard were run in duplicate. The standards were plasmid controls
that contained the PCR products amplified by each primer set,
as described previously (
5,
18,
19). For the multiplex real-time
PCR, each plasmid control was mixed, diluted, and used to make
calibration curves. The number of viral DNA copies was calculated
from the standard curves and expressed as copies per 1 ml of
whole blood or plasma.
CMV antigenemia assay.
The CMV antigenemia assay was performed as previously described (18). The approximate antigenemia threshold was 1 positive cell per 5 x 104 leukocytes, as determined by guidelines from the Japanese Society for Hematopoietic Cell Transplantation. When the antigenemia assay was positive, patients were administered ganciclovir preemptively.
Statistical analysis.
StatView J 4.02 (Abacus Concepts Inc., Berkeley, CA) was used to perform the data analysis. A regression analysis compared the multiplex assay with the single assay. Fisher's exact test was used to compare the viral DNA detection rates, and Student's t test was used to compare the mean viral DNA log10 copy numbers. To determine the minimum detection level of each assay, 35 replicates each of one, two, and five copies of the plasmid standard were quantified. The 95% confidence interval (CI) was calculated from the t distribution using the following formula: 95% CI = the mean of the estimated copy number ± t x standard error, where t was estimated to be 2.042 from the Student's t table.

RESULTS
Specificity and sensitivity of the multiplex quantification using an Mx3000P real-time PCR system.
Serial dilutions of mixed viral standard plasmids were tested
with the multiplex assay, and three standard curves were constructed
from the cycle of threshold values. The assay was able to detect
each viral DNA form over a linear span between 5 and 5
x 10
6 copies per reaction mixture without interference (Fig.
1). The
standard curves generated from the multiplex real-time PCR were
almost equal to those generated from the single assay. Because
amplification efficiency may be influenced by the background
DNA of the clinical specimen, we evaluated the performance of
the multiplex assay using standard plasmids diluted in water
or in water containing EBV-, CMV-, and HHV-6-negative human
genomic DNA. The standard curves generated from the standard
plasmids in background DNA were almost equal to those generated
from the standard plasmids in water, indicating that amplification
efficiency was not influenced by the background DNA (data not
shown). We also performed reconstruction studies to confirm
the absence of the inhibitor from whole-blood or plasma samples.
DNA-extraction solution from either whole blood or plasma was
added to serially diluted plasmid controls. The DNA solutions
from both whole blood and plasma did not inhibit the amplification
efficiency, indicating the absence of inhibitors in these samples.
To confirm the specificity of the multiplex assay, viral DNA
from standard strains was tested. None of the primer/probe sets
reacted with the other viral DNA, indicating that no cross-reactivity
occurred. Furthermore, the quantitative linearity, which was
made using a standard plasmid, was not influenced by the presence
of two other kinds of viral DNA.
The minimum detection level established with this multiplex
assay was 2 copies per reaction for EBV (95% CI, 1.16 to 3.89),
2 copies for CMV (95% CI, 1.01 to 2.95), and 2 copies for HHV-6
(95% CI, 0.49 to 2.64). By contrast, the minimum detection level
with the single assay was 2 copies for EBV (95% CI, 1.39 to
3.96), 2 copies for CMV (95% CI, 1.01 to 2.71), and 5 copies
for HHV-6 (95% CI, 4.35 to 7.58). The multiplex assay had an
overall dynamic range of 200 to 5
x 10
8 copies/ml of specimen.
DNA samples (111), which had been tested and stored previously, were evaluated with the multiplex and the single assays. Compared to the results of the single assay, the sensitivity and specificity values of the multiplex assay were 96.0 and 100% for EBV, 94.7 and 95.7% for CMV, and 89.2 and 94.6% for HHV-6, respectively (Table 2). Some discordant results, however, were obtained between the multiplex and single assays. The viral loads of all of these discordant samples were low and around the detection limits. The viral DNA copy numbers were compared using all samples determined to be positive according to both assays. Strong correlations were detected between the viral DNA copy numbers determined by the multiplex assays and those by single assays (Fig. 2). The slopes of the correlation curves ranged from 0.957 to 1.133, indicating that no significant shifts occurred in the actual quantitative values, using the multiplex assay.
Detection of EBV, CMV, and HHV-6 DNA in whole-blood and plasma specimens from transplant recipients.
Using the multiplex real-time PCR assay, we serially measured
the EBV, CMV, and HHV-6 DNA levels in whole-blood and plasma
specimens from 46 transplant recipients. In total, 303 paired
samples (6.6 paired samples per patient) were tested. Positives
were defined as any positive samples for a given patient. Because
we had different numbers of samples from each patient, it was
possible that the variety of sample numbers per patient would
introduce some bias in the results. Using the whole-blood specimens,
at least one form of viral DNA was detected in 36 of 46 recipients
(78.3%), plural viral DNA forms were detected in 13 recipients
(28.3%), and all three viral DNA forms were detected in 3 recipients
(6.5%). Using the plasma specimens, at least one viral DNA form
was detected in 18 of 46 recipients (39.1%), and plural viral
DNA forms were detected in 5 recipients (10.9%).
Four patients who underwent hematopoietic stem cell transplantation developed symptomatic EBV infections and were preconditioned with antithymocyte globulin. The patients had prolonged fever, lymphadenopathy, diarrhea, or hematochezia, which could not be explained by other causes. One patient who underwent liver transplantation developed CMV hepatitis despite preemptive ganciclovir therapy. None of the patients developed HHV-6-related diseases. Each form of viral DNA was detected in both the whole-blood and plasma specimens of these five symptomatic patients, and the peaks of the viral DNA loads were concordant with the symptoms observed.
Of the 303 whole-blood samples tested, 112 were positive for at least one viral DNA form, and 29 were positive for plural viral DNA forms. Conversely, 37 of 303 plasma samples were positive for at least one viral DNA form, and only 3 samples were positive for plural viral DNA forms (Table 3). The detection rates of viral DNA in whole blood and plasma were 23.8% and 5.9% for EBV, 11.2% and 5.3% for CMV, and 12.5% and 2.0% for HHV-6, respectively. The three viral DNA forms of interest were detected more frequently in whole blood than in plasma. EBV DNA loads ranged from 220 to 8.6 x 106 copies/ml in whole blood and from 250 to 7.5 x 104 copies/ml in plasma. CMV DNA loads ranged from 220 to 3.8 x 105 copies/ml in whole blood and from 200 to 8.5 x 104 copies/ml in plasma. HHV-6 DNA loads ranged from 240 to 1.3 x 105 copies/ml in whole blood and from 290 to 1.1 x 104 copies/ml in plasma. The viral DNA copy numbers were compared using samples determined to be positive in both whole blood and plasma (Fig. 3). Weak correlations were seen between the viral loads in whole blood and those in plasma.
Comparison of EBV DNA loads between whole blood and plasma.
We divided the 303 samples into two groups based on EBV infection-related
symptoms, symptomatic and asymptomatic. In the symptomatic group,
EBV DNA was detected in all nine whole-blood samples with high
viral loads but not in two plasma samples (Fig.
4). Among the
whole-blood samples, the viral loads of the symptomatic group
were significantly higher than those of the asymptomatic group.
However, among the plasma samples, the viral loads were similar
between the two groups (Fig.
4).
Comparison of antigenemia and multiplex real-time PCR assays.
The antigenemia assay was applied to 235 of 303 blood specimens
that had been evaluated with the multiplex assay. CMV antigen
was detected in 13 of 235 blood samples (5.5%). With the multiplex
assay, CMV DNA was detected in 32 of 235 whole-blood specimens
(13.6%;
P = 0.002 versus antigenemia) and 14 of 235 plasma specimens
(6.0%;
P = 0.5 versus antigenemia). When the antigenemia assay
was defined as the standard, the specificity of CMV DNA detection
was higher for the plasma specimens than for the whole-blood
specimens (Table
4). On the other hand, the sensitivity seemed
to be higher for the whole-blood specimens, although statistical
significance was not achieved, probably due to the small sample
size.
The 235 specimens were classified into four categories by the
antigenemia values (negative, 0; low, 1 to 10; intermediate,
11 to 100; high, >100), and CMV DNA loads were compared (Table
5). Although the sample numbers for each group were small, it
appeared that CMV DNA loads increased in proportion to increases
in the antigenemia values. Correlations between antigenemia
values and CMV DNA loads were then analyzed using the positive
samples. Antigenemia values were significantly correlated with
CMV DNA loads, both in whole blood (
n = 12;
r = 0.776;
P = 0.002)
and in plasma (
n = 9;
r = 0.861;
P = 0.002).
Monitoring of EBV, CMV, and HHV-6 DNA loads in a transplant recipient.
Figure
5 shows changes in the viral DNA loads in a representative
case. The patient was a 4-year-old girl with severe aplastic
anemia who underwent bone marrow transplantation. Two weeks
after transplantation, CMV DNA was detected in her whole-blood
and plasma samples (Fig.
5). Shortly after the detection of
CMV DNA, the patient's blood tested positive for the CMV antigen.
Although the patient had no symptoms associated with CMV infection,
ganciclovir was administered preemptively. Her CMV DNA load
decreased in accordance with the ganciclovir therapy. During
treatment, a high level of EBV DNA was detected in her blood.
In the fifth week after transplantation, she developed a fever
and hematochezia. Since EBV DNA had been detected at a high
level in her whole blood and plasma and other pathogens and
causes that may have explained her symptoms were excluded, an
EBV-related lymphoproliferative disorder was suspected. Immunosuppression
was tapered, but that was not effective. Therefore, the monoclonal
anti-CD20 antibody rituximab was administered. Immediately after
rituximab administration, her EBV DNA load decreased in conjunction
with her clinical symptoms. During the period of viral monitoring,
HHV-6 DNA was undetectable in her whole blood and plasma.

DISCUSSION
Real-time PCR is a powerful tool for quantifying gene targets
using fluorogenic probes and real-time laser scanning. Although
multiplex real-time PCR is theoretically possible using probes
with spectrally different fluorophores, the overlap of fluorophores
prevents accurate quantification and limits amplification to
two genes per tube (
21). Only two targets could be quantified
reliably in a single tube. However, recent advances in the development
of real-time PCR platforms and master mix have made it possible
to quantify more than three different genes in a single tube
(
21).
To our knowledge, this is the first study using the multiplex real-time PCR assay in the quantification of EBV, CMV, and HHV-6 DNA. Our results showed that the multiplex assay was as sensitive and specific as the single real-time PCR assay. The viral DNA loads determined by the multiplex real-time PCR assay were consistent with those described previously using other assays (6-8, 12, 26). Monospecific PCR assays require separate amplification of each target and are therefore more cost, time, and labor intensive than multiplex assays. The multiplex real-time PCR assay offers a major advantage in the field of clinical virology as it permits simultaneous amplification of several viruses in a single reaction mixture (1, 14, 21). The multiplex real-time PCR assay is particularly useful in the management of posttransplant patients, in whom frequent viral monitoring is required. The multiplex assay facilitates cost-effective diagnosis and may contribute to a decrease in the use of antiviral agents and in viral complications and hospitalizations.
One aim of the present study was to determine whether whole blood or plasma was more suitable for simultaneous virus monitoring in transplant recipients. EBV latently infects B lymphocytes. In EBV-associated lymphoproliferative disorders, EBV-infected B lymphocytes are usually found in the blood (27). Therefore, peripheral blood mononuclear cells are the best specimens to use in quantifying the EBV DNA load in transplant patients. However, whole blood, which contains mononuclear cells and is convenient to use, has been suggested as an acceptable alternative (17, 26). CMV latently infects a variety of leukocytes but predominantly cells in the monocyte/macrophage lineage. CMV quantification can be performed with acellular fractions of the blood, such as plasma and serum (7, 20, 29); however, in transplant recipients, the quantity of viral DNA is greater in leukocytes than in plasma (6, 10). HHV-6, which is closely related to CMV, infects mainly CD4+ T lymphocytes and is predominantly found in latently infected monocytes/macrophages (28). Since considerable amounts of the HHV-6 genome persist in monocytes/macrophages, detection of HHV-6 DNA in whole blood may reflect both latent and active viral infection. Therefore, it has been suggested that the HHV-6 viral load in plasma is an effective indicator of active infection (16, 28).
In the present study, we compared whole-blood and plasma specimens in the simultaneous detection of EBV, CMV, and HHV-6 DNA. The detection rate for each viral DNA form was higher in the whole-blood specimens than in the plasma specimens. During the symptomatic periods, EBV DNA was found in all whole-blood specimens obtained but not in all plasma specimens. EBV DNA loads in whole blood were higher during the symptomatic period than during the asymptomatic period, whereas EBV DNA loads in plasma were similar during both periods. These results support the use of whole-blood specimens for multiplex real-time PCR assays in transplant patients, although we have insufficient data to conclude that whole blood is preferable for assaying CMV and HHV-6 loads. On the other hand, EBV, CMV, and HHV-6 latently infect blood corpuscles, and asymptomatic reactivation may occur in transplant patients. Therefore, it is necessary to determine a cutoff value that reflects clinical relevance. In this study, we could not determine the cutoff value because of the sample size and heterogeneity of the transplantations. Since the number of peripheral blood cells varies, especially after stem cell transplantation, this may influence the viral load in whole blood. A large prospective study to determine the clinical cutoff value for each virus and each transplantation type is currently under way.
In summary, we developed a multiplex real-time PCR assay for the simultaneous detection of EBV, CMV, and HHV-6 DNA. The results of the multiplex assay were as sensitive and specific as those of the single real-time PCR assay. Compared to plasma, whole blood was more suitable for quantifying EBV DNA in transplant patients. The savings in cost, time, and labor associated with multiplex real-time PCR validate its use in the management of transplant recipients.

ACKNOWLEDGMENTS
We thank the following individuals for their contributions to
this study: Yukiko Watanebe, Kenichiro Kaneko, Youhei Yamauchi
(Nagoya University Graduate School of Medicine), and Hideki
Muramatsu (Japanese Red Cross Nagoya First Hospital).
This study was supported by grants from the Ministry of Education, Culture, Sport, Science and Technology of Japan (17209037).

FOOTNOTES
* Corresponding author. Mailing address: Department of Virology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 466-8550, Japan. Phone: 81-52-744-2207. Fax: 81-52-744-2452. E-mail:
hkimura{at}med.nagoya-u.ac.jp 
Published ahead of print on 21 March 2007. 

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Journal of Clinical Microbiology, May 2007, p. 1426-1432, Vol. 45, No. 5
0095-1137/07/$08.00+0 doi:10.1128/JCM.01515-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
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