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Journal of Clinical Microbiology, June 2003, p. 2408-2416, Vol. 41, No. 6
0095-1137/03/$08.00+0 DOI: 10.1128/JCM.41.6.2408-2416.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Development of Group- and Serotype-Specific One-Step SYBR Green I-Based Real-Time Reverse Transcription-PCR Assay for Dengue Virus
Pei-Yun Shu, Shu-Fen Chang, Yu-Chung Kuo, Yi-Yun Yueh, Li-Jung Chien, Chien-Lin Sue, Ting-Hsiang Lin, and Jyh-Hsiung Huang*
From Division of Research Development and Laboratory Diagnosis, Center for Disease Control, Department of Health, Taipei, Taiwan, Republic of China
Received 12 November 2002/
Returned for modification 6 January 2003/
Accepted 18 March 2003

ABSTRACT
A quantitative one-step SYBR Green I-based reverse transcription
(RT)-PCR system was developed for the detection and differentiation
of four different dengue virus serotypes in acute-phase serum
samples. A set of group- and serotype-specific primer pairs
was designed against conserved sequences in the core region
and evaluated for clinical diagnosis. A linear relationship
was obtained between the amount of input RNA and cycle threshold
(Ct) value over a range of 10 to 10
7 PFU per ml of cell culture-derived
dengue viruses. The detection limit of the group-specific primer
pair was between 4.1 and 43.5 PFU/ml for four dengue serotypes.
The detection limit of each of the serotype-specific primer
pairs was calculated to be 10 PFU/ml for dengue virus serotype
1 (DEN-1), 4.6 PFU/ml for DEN-2, 4.1 PFU/ml for DEN-3, and 5
PFU/ml for DEN-4. Comparisons between the one-step SYBR Green-based
RT-PCR assay and the conventional cell culture method in the
clinical diagnosis of dengue virus infection from acute-phase
serum samples of confirmed dengue patients were performed. The
results showed that 83 and 67% of 193 acute-phase serum samples
tested were positive by the one-step SYBR Green-based RT-PCR
method and cell culture method, respectively. Further analysis
showed that the one-step SYBR Green-based RT-PCR method could
detect twice as many acute-phase serum samples with positive
dengue-specific immunoglobulin M (IgM) and/or IgG antibodies
than cell culture method. Our results demonstrate the potential
clinical application of the one-step SYBR Green I-based RT-PCR
assay for the detection and differentiation of dengue virus
RNA.

INTRODUCTION
Dengue virus is a mosquito-borne flavivirus and the most prevalent
arbovirus in tropical and subtropical regions of Asia, Africa,
and Central and South America (
7).
Dengue virus belongs to the
family
Flaviviridae. It produces a spectrum of illness ranging
from inapparent infection to moderate febrile illness to severe
and fatal hemorrhagic disease (
2,
18). There are four distinct
serotypesdesignated DEN-1, DEN-2, DEN-3, and DEN-4which
can be distinguished by serological and molecular methods. The
flavivirus genome is approximately 11 kb in length, and the
complete genome sequence is known for isolates of all four dengue
virus serotypes. The genome is composed of three structural
protein genes, encoding the nucleocapsid or core protein (C),
a membrane-associated protein (M), an envelope protein (E),
and seven nonstructural (NS) protein genes (
4). The order of
proteins encoded is 5'-C-prM(M)-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5-3'.
The two basic methods used by most laboratories for the diagnosis of dengue virus infection are detection of virus or antidengue antibodies. For convalescent-phase sera, serological diagnosis of antibodies based on capture immunoglobulin M (IgM) and IgG enzyme-linked immunosorbent assay (ELISA) has become the new standard for the detection and differentiation of primary and secondary dengue virus infection (21). However, antibody detection has less impact on patient management and control measures exercised by medical and public health personnel. Therefore, there is a great demand for the rapid detection of dengue virus infection in the acute phase of illness in order to provide timely clinical treatment and etiologic investigation and disease control.
For virus detection, virus isolation by cell culture remains the "gold standard" although it has the disadvantage in that longer than 7 days is usually required to complete the test. Recently, two different methods had been demonstrated to be useful in the detection of dengue virus. These include genomic sequence detection by RT-PCR and dengue virus antigen detection by ELISA (1, 21). Several laboratories have published various RT-PCR protocols for dengue virus identification (8, 9, 10, 14, 17, 19, 20). Among these, the two-step nested RT-PCR protocols originally reported by Lanciotti et al. and later modified to single-step multiplex RT-PCR for the detection and typing of dengue virus by Harris et al. are well known (9, 14). These assays used dengue core-to-premembrane gene regions as its target sequence for dengue virus detection. It had the advantage of detecting and differentiating four dengue serotypes by analyzing the unique sizes of amplicons in the agarose gel. More recently, several investigators have reported fully automatic real-time PCR assays for the detection of dengue virus in acute-phase serum samples (3, 5, 11, 15). The real-time PCR assay has many advantages over conventional RT-PCR methods, including rapidity, quantitative measurement, lower contamination rate, higher sensitivity, higher specificity, and easy standardization. Thus, nucleic acid-based assays or real-time quantitative assay might eventually replace virus isolation and conventional RT-PCR as the new gold standard for the rapid diagnosis of virus infection in the acute-phase serum samples.
In an attempt to develop a simple, reliable, and universal RT-PCR protocol to systemically detect and differentiate various arbovirus, we have recently developed a real-time quantitative RT-PCR system based on SYBR Green I DNA dye-binding fluorophore. The rationale is to develop a diagnostic system with an automated platform using real-time PCR equipment and a universal RT-PCR protocol that allows multiple primer sets designed and tested without the need to change the RT-PCR conditions. Theoretically, this approach will increase the successful rate in generating a panel of optimal primer pairs. In addition, all the primer pairs can be run simultaneously in a single unit of a real-time RT-PCR instrument. Indeed, G. Kuno had originally proposed this concept using conventional RT-PCR in the detection of arbovirus (13). In the present study, we report the development of a group- and serotype-specific one-step SYBR Green I-based real-time RT-PCR assay by Mx4000 for the screening and typing of dengue virus RNA. The results demonstrated that the one-step SYBR Green I-based real-time RT-PCR assay is more sensitive than the standard cell culture method.

MATERIALS AND METHODS
Design of oligonucleotide primers for SYBR Green-based quantitative RT-PCR.
The following dengue virus nucleotide sequences were retrieved
from GenBank (accession numbers shown in parentheses): DEN-1
West Pac (
U88535), DEN-1
16007 (
AF180817), DEN-1 S275/90 (
M87512),
DEN-2 New Guinea C (
AF038403), DEN-2
16681 (
U87411), DEN-2 JAM
(
M20558), DEN-2 FJ-10 (
AF276619), DEN-3 H87 (
M93130), DEN-3
MALAY94-3 (
AB010990), DEN-3 80-2 (
AF317645), DEN-3
CH53489 (
AF008555),
DEN-4 H241 (
M14931), and DEN-4 China Guangzhou B5 strain (
AF289029).
Nucleotide sequences were aligned to identify conserved regions
using DNA Star software (Perkin-Elmer, Norwalk, Conn.). Potential
target regions were selected and primers were synthesized and
evaluated for quantitative RT-PCR. The final sequences of the
group- and serotype-specific primer pairs are shown in Table
1.
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TABLE 1. Degenerated primer sequences for the dengue group- and serotype-specific one-step SYBR Green-based RT-PCR assay
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Preparation of RNA from dengue viruses and control flaviviruses.
Viral RNAs were prepared for four dengue virus serotypes, including
4 prototype strains (DEN-1, Hawaii; DEN-2, New Guinea C; DEN-3,
H87 [Philippines]; and DEN-4, H241 [Philippines]) and 12 local
isolates from imported or indigenous dengue patients during
1987 to 2000 as listed in Table
2. Viruses were propagated in
Vero cells and viral titers were determined by plaque forming
assay (
6). Viral RNAs (70 µl) were extracted from 140
µl of cell culture supernatants or serum samples using
the QIAamp viral RNA mini kit (Qiagen, Hilden, Germany) according
to the manufacturer's instructions and stored at -70°C.
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TABLE 2. Detection and differentiation of various flaviviruses using dengue group- and serotype-specific primer pairsa
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One-step SYBR Green I-based quantitative RT-PCR.
One-step SYBR Green I-based RT-PCR amplification was performed
in the Mx4000 quantitative PCR system (Stratagene). After optimization
of each of the primer pairs, samples were assayed in a 50-µl
reaction mixture containing 10 µl of sample RNA and optimal
concentration of each of the primers by using the Brilliant
single-step quantitative RT-PCR core reagent kit (Stratagene)
with MgCl
2 at a 3 mM final concentration, dimethyl sulfoxide
at a 3% final concentration, and 0.5 µl of SYBR Green
stock solution (Stratagene SYBR Green QPCR core reagent kit)
diluted 1:333 in dimethyl sulfoxide. The thermal profile for
one-step SYBR Green-based RT-PCRs consisted of a 30-min RT step
at 45°C and 10 min of
Taq polymerase activation at 95°C,
followed by 45 cycles of PCR at 95°C for 20 s (denaturation),
55°C for 30 s (annealing), and 72°C for 30 s (extension).
Melting curve analysis.
Following amplification, a melting curve analysis was performed to verify the correct product by its specific melting temperature (Tm). Melting curve analysis consisted of a denaturation step at 95°C for 1 min, lowered to 55°C for 30 s, and followed by 40 cycles of incubation in which the temperature is increased to 95°C at a rate of 1°C/30 s/cycle with continuous reading of fluorescence. Results were analyzed with the melting curve analysis software of the Mx4000. For SYBR Green-based RT-PCR amplification, amplification plots and Tm values were routinely analyzed to verify the specificities of the amplicons.
Human serum samples.
The serum samples used in this study were collected from patients with confirmed cases of dengue reported to the Department of Health, Centers for Disease Control and Prevention, during the period between 1998 and 2002. A confirmed case of dengue virus infection was defined as febrile illnesses associated with the isolation of dengue virus, positive RT-PCR result, or
4-fold increase of dengue-specific IgM or IgG antibody in paired serum samples. It should be emphasized that all of the 193 acute-phase serum samples analyzed in this study were selected from patients with cases of dengue confirmed by either positive dengue virus isolation or positive serological test (
4-fold increase of dengue-specific IgM or IgG antibody in paired serum samples) without taking into account RT-PCR results. Sera collected during the period between days 1 and 7 after the onset of symptoms are referred to as acute-phase samples.
Virus isolation by cell culture.
The isolation of dengue virus was performed using the mosquito cell line Aedes albopictus, clone C6/36. For each acute-phase serum, 4 µl of serum sample was diluted in 200 µl of cultured medium (RPMI, Gibco/BRL, Life Technologies) (containing 1% FCS) and added to a 96-well microtiter plate, 50 µl/well in quadruplicate. Then, 105 cells/100 µl/well of C6/36 were added into the microtiter plate and incubated at 37°C for 7 days. Cells were harvested and viruses were identified with dengue virus group-specific, serotype-specific monoclonal antibodies and fluorescein isothiocyanate-conjugated goat anti-mouse antibody.
Capture IgM and IgG ELISA.
A modified capture IgM and IgG ELISA was developed to measured the IgM and IgG antibodies of patients infected with dengue virus as previously described by Innis et al. (12). Each microtiter well was coated with affinity-purified goat anti-human IgM (µ-specific) or IgG (
-specific) antibodies (5 µg/ml, 100 µl/well), followed by incubation with 100 µl of 1:100 diluted serum. Subsequent incubations were performed with 100 µl of cocktail containing 1:3 diluted pooled virus antigens from culture supernatants of DEN-1-, DEN-2-, DEN-3-, or DEN-4-infected Vero cells and MAb D56.3 (1 µg/ml), followed by incubation with 1:1,000 diluted alkaline phosphatase-conjugated goat anti-mouse IgG (
-specific). Then, substrate p-nitrophenyl-phosphate was added, and the optical density taken at the dual wavelengths of 405 and 630 nm. A positive sample was defined as having a test absorbance/negative control ratio of
2.0, and a negative sample was defined as having a ratio of <2.0.

RESULTS AND DISCUSSION
Design of primer pairs with group- and serotype-specificities.
One of the advantages of SYBR Green-based real-time RT-PCR is
that it is relatively easy to design and test primer pairs suitable
for RT-PCR analysis. Primers were selected based on highly conserved
regions of dengue virus genome. After nucleotide sequence alignment
using DNA Star software (Perkin-Elmer), potential target regions
were identified in the regions of core, NS3, NS5, and 3' noncoding
genes. More than 30 primer pairs were synthesized and screened
for initial evaluation. Among these primers tested, a set of
group- and serotype-specific primer pairs in the core gene region
was found to be most sensitive. The primers were designed to
take into account of mismatches among strains and to avoid primer-dimer
formations. The final sequences and the genomic locations of
these primers are shown in Table
1. The condition of thermal
profile for one-step SYBR Green-based RT-PCRs and the optimal
concentrations of primer pairs were then optimized to increase
the sensitivity and specificity. The optimal concentrations
for each of the primer pairs were titrated and found to be 50
and 50 nM for the DN-F and DN-R pair (group specific), 50 and
50 nM for the DN-F and D1-R pair (DEN-1 specific), 50 and 50
nM for the DN-F and D2-R pair (DEN-2 specific), 50 and 25 nM
for the DN-F and D3-R pair (DEN-3 specific), and 50 and 50 nM
for the DN-F and D4-R pair (DEN-4 specific), respectively. The
Tm values of primer-dimers were found to be below 75°C,
whereas the
Tm values of each of these amplicons from the group-
and serotype-specific primer pairs were in the range of 79 to
83°C depending on the various strains tested. No primer-dimers
were detected as demonstrated by melting curve analysis if optimal
primer concentrations were followed.
Sensitivity of SYBR Green I-based one-step RT-PCR.
To ascertain the detection limits of the one-step SYBR Green-based RT-PCR method using group- and serotype-specific primer pairs in dengue diagnosis, we tested 10-fold serial dilutions of seed viruses that had been quantitated by plaque forming assay. Figure 1 and Fig. 2 showed the standard curves of four dengue prototype viruses using group- and serotype-specific primer pairs, respectively. The detection limit of each group-specific primer pair was between 4.1 and 43.5 PFU/ml for various dengue serotypes. The detection limits of the serotype-specific primer pairs were calculated to be 10 PFU/ml for DEN-1, 4.6 PFU/ml for DEN-2, 4.1 PFU/ml for DEN-3, and 5 PFU/ml for DEN-4.
Specificity of SYBR Green I-based one-step RT-PCR.
To verify that the dengue group- and serotype-specific primer
pairs can be used to detect and differentiate the majority strains
of four dengue virus serotypes, we had selected and tested 16
dengue virus strains from our virus bank. These included 4 prototype
strains collected from the American Type Culture Collection
and 12 local isolates from patients with imported or indigenous
dengue during 1987 to 2000. Most of the strains had been sequenced
at the core and envelope gene regions and could be assigned
to distinct genotypes. Among these, D4 8700544 was an unique
isolate which could neither be grouped into the DEN-4 genotype
I nor II based on the sequences in the core and envelope regions
(data not shown). Table
2 showed the results of SYBR Green I-based
one-step RT-PCR analysis. It was demonstrated that these group-
and serotype-specific primer pairs were highly specific in the
detection and differentiation of various dengue virus strains.
None of these primer sets, however, amplified West Nile virus
(Eg101 strain), yellow fever virus (17D vaccine strain), and
Japanese encephalitis virus (JaGAr strain). This is in contrast
to a panel of primer pairs with broad specificity to flavivirus
or restricted specificity to West Nile virus, yellow fever virus
or Japanese encephalitis virus, which had been shown to successfully
detect and differentiate each of these corresponding viruses
(data not shown). Figure
3 shows the results of agarose gels
demonstrating that this group- and serotype-specific primer
pairs are highly specific in the detection and differentiation
of various strains since the amplicons generated have the correct
size with expected sequences (data not shown). The 171 bp that
appear in Fig.
3 were the expected products for all four dengue
serotypes using group-specific primer pair (DN-F/DN-R), whereas
the 193-, 204-, 204-, and 132-bp amplicons were the expected
products for each of the DEN-1, DEN-2, DEN-3, and DEN-4 serotype,
respectively, using type-specific primer pairs. The 375-bp amplicon
appeared in Fig.
3A was found to be a longer product sharing
the same sequences with 171-bp amplicon at its 5' end with additional
DEN-1 sequences following it.
Evaluation of SYBR Green I-based one-step RT-PCR for the detection of dengue virus RNA in the acute-phase serum samples.
To evaluate the SYBR Green I-based one-step RT-PCR in the clinical
diagnosis of dengue virus RNA, we analyzed 193 acute-phase serum
samples collected from confirmed dengue patients during the
period between 1998 and 2002. These acute-phase serum samples
selected for analysis were collected from confirmed dengue patients
with either positive dengue virus isolation or positive serological
test without taking into account of RT-PCR result. The results
are shown in Table
3 and revealed that 83 versus 67% out of
193 acute-phase serum samples tested were positive for one-step
SYBR Green-based RT-PCR method and cell culture method, respectively.
The positive rates for each of four dengue serotypes were found
to be 63% for DEN-1, 67% for DEN-2, 77% for DEN-3, and 60% for
DEN-4 using the virus isolation method, versus 75% for DEN-1,
82% for DEN-2, 92% for DEN-3, and 100% for DEN-4 using the one-step
SYBR Green-based RT-PCR. Further analysis showed that the sera
that were dengue virus negative by virus isolation and dengue
virus positive by the SYBR Green-based RT-PCR assay had relatively
fewer amplicons than those samples that were positive by both
virus isolation positive and the SYBR Green-based RT-PCR assay
(Fig.
4).
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TABLE 3. Comparison of results obtained by one-step SYBR Green-based RT-PCR assay and cell culture method for detection of dengue virus in acute-phase seraa
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Comparison of sensitivities of the one-step SYBR Green-based RT-PCR method with cell culture assays in the detection of dengue virus in the acute-phase sera with dengue-specific IgM and/or IgG antibodies.
To further address the detection limit of the one-step SYBR
Green-based RT-PCR, we had reclassified the above 193 serum
samples with the criterion of presence or absence of dengue-specific
IgM and/or IgG antibodies. The results are listed in Table
4.
Compared with the cell culture method, the one-step SYBR Green-based
RT-PCR method could detect twice as many acute-phase serum samples
with positive dengue-specific IgM and/or IgG antibodies as the
cell culture method. Two factors may account for the lack of
sensitivity of the cell culture method: (i) a greater volume
of serum samples is available (4 µl for cell culture versus
20 µl for real-time RT-PCR was added for each reaction,
respectively) (Fig.
4) and (ii) real-time RT-PCR is less influenced
by neutralizing IgM and/or IgG antibodies than cell culture
method (Table
4). This result is very encouraging and suggests
that one-step SYBR Green-based RT-PCR could replace the conventional
cell culture method as the new gold standard in future clinical
diagnosis of dengue virus infection.
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TABLE 4. Comparison of results obtained by one-step SYBR Green-based RT-PCR assay and cell culture method for antibody detection in acute-phase seraa
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The application of PCR in molecular diagnosis has gradually
replaced traditional cell culture method as the gold standard
for virus detection. The real-time PCR assays have many advantages
comparing to conventional PCR including simplicity, rapidity,
sensitivity, and low contamination. There are currently five
main chemistries used for the detection of PCR product during
real-time PCR (
16). Among these, the most widely used format
is the 5'

3' nuclease oligoprobe (TaqMan assay) although this
is most likely due to its commercial maturity. The TaqMan real-time
PCR is highly specific due to the sequence-specific hybridization
of the probe. Theoretically, it has the potential to develop
multiplex up to four fluorophores in a single tube. This has
led to a great expectation to analyze multiple pathogens and
serotypes in clinical diagnosis. Ideally, a four-color multiplex
protocol could be developed to detect and differentiate the
four dengue serotypes using TaqMan one-step real-time RT-PCR.
This goal, however, had not been realized at the present time.
Although the SYBR Green-based real-time PCR assays is less specific than the TaqMan real-time RT-PCR, it has the advantages of simplicity in primer design and universal RT-PCR protocols suitable for multiple target sequences. We have found that the optimization of primer concentration is critical in preventing primer-dimers and nonspecific amplification of other unrelated gene products. Indeed, nonspecific products such as primer-dimers and nonspecific amplification of other unrelated gene products could be occasionally detected at higher primer concentrations. However, these nonspecific products could be prevented if optimal concentrations were followed using the real-time RT-PCR protocol reported in this study. To assure the specificity of amplicons produced from SYBR Green I-based real-time RT-PCR in daily routine screening, both flavivirus-specific (FL-F, GCC ATA TGG TAC ATG TGG; FL-R, TGT CCC ATC CTG CGG TAT CAT [200 to 100 nM]) and dengue-specific primer pairs were used for each of the serum samples tested. Those serum samples positive for initial screening will then be tested for serotype by each of the four serotype-specific primer pairs. Excellent correlation was found among these six primer pairs over a thousand of serum samples tested so far. To further confirm the positive results of the SYBR Green-based RT-PCR method in clinical diagnosis, various confirmatory tests could be used. These include (i) virus isolation, (ii) TaqMan RT-PCR assay, and (iii) capture IgM and IgG ELISA to detect increased IgM and/or IgG antibodies using paired serum samples. We considered capture IgM and IgG ELISA the most suitable method for a confirmatory testing for the use of the SYBR Green-based RT-PCR method in clinical diagnosis due to its simplicity and reliability. In addition, most dengue virus laboratories routinely perform this test for their suspected dengue patients.
In an attempt to develop a universal diagnostic real-time RT-PCT protocol for arbovirus, we have taken an alternative approach using a SYBR Green I-based detection system. Kuno (13) was the first to propose a two-stage procedure for the systemic diagnosis of arbovirus using old conventional RT-PCR. In the first stage, broadly group-reactive primers are used to narrow the range of possible etiologic agents; in the second stage, virus-specific primers are employed for identification. It was emphasized that multiple group-reactive primers is essential to ensure the successful screening of a clinical sample against a multiple number of potential etiologic agents. Through careful design and testing, we have successfully developed a one-step RT-PCR system that can be used to detect and differentiate several flaviviruses, including dengue virus, Japanese encephalitis virus, Yellow fever virus, and West Nile virus (data not shown).
In the present study, we reported the development of group- and serotype-specific one-step SYBR Green I-based real-time RT-PCR assay for the screening and typing of dengue virus RNA. Analysis of clinical acute-phase serum samples demonstrated that the one-step SYBR Green-based RT-PCR method could detect twice as many acute-phase serum samples with positive dengue-specific IgM and/or IgG antibodies than cell culture method. The greatest advantage of this system is that one can actually detect and differentiate multiple viruses in a single run using the universal RT-PCR protocol with a panel of group- and type-specific primer sets. Our results suggest that one-step SYBR Green I-based RT-PCR system using the universal RT-PCR protocol should have great potential in the clinical diagnosis and epidemiological surveillance of viral diseases.

ACKNOWLEDGMENTS
We thank Yun-Yih Chang, Hsiu-Ling Pan, and Chih-Heng Chen for
their expert technical assistance.
This work was in part supported by grant NSC 89-2318-B-043B-001-M51 from the National Science Council and grant DOH90-DC-2015 from the Center for Disease Control, Department of Health, Taipei, Taiwan, Republic of China.

FOOTNOTES
* Corresponding author. Mailing address: Division of Research Development and Laboratory Diagnosis, Center for Disease Control, Department of Health, 161, Kun-Yang St., Taipei, Taiwan, Republic of China. Phone: 886-2-26531374. Fax: 886-2-27883992. E-mail:
jhhuang{at}cdc.gov.tw.


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Journal of Clinical Microbiology, June 2003, p. 2408-2416, Vol. 41, No. 6
0095-1137/03/$08.00+0 DOI: 10.1128/JCM.41.6.2408-2416.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
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