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Journal of Clinical Microbiology, September 2005, p. 4551-4557, Vol. 43, No. 9
0095-1137/05/$08.00+0 doi:10.1128/JCM.43.9.4551-4557.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen, Universitätsklinik der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
Received 1 February 2005/ Returned for modification 11 April 2005/ Accepted 18 June 2005
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An endogenous IC is a template that occurs naturally within the specimen being analyzed. In gene expression analysis and virus screenings, housekeeping genes are often used as ICs and references for transcript quantification (7, 16), but they have to be proven for each experiment and target. Exogenous ICs are added before nucleic acid isolation (extraction control) or amplification (amplification control), where coamplification is performed within the same reaction. Ideally, these ICs hybridize to the same primers, have identical amplification efficiencies, and contain discriminating features, such as length or sequence variations, targeted by hybridization probes. However, these competitive ICs can lower the amplification efficiency, which results in a lower detection limit (8). Therefore, noncompetitive IC templates are used, where the target and IC are amplified with different primer sets. The disadvantage is that amplification of the IC may not accurately reflect amplification of the target.
Currently, most diagnostic assays in which viral RNA is detected or quantified rely on RNA standards (19). Some assays use RNA standards synthesized by in vitro transcription, which are very susceptible to degradation by RNases. Therefore, the armored RNA technology produces RNase-resistant RNA controls and standards by assembling specific RNA sequences and viral coat proteins to pseudoviral particles (6, 15). This IC RNA contains the same primer binding sites as the target RNA but has a different probe region (3, 6).
For viral nucleic acid amplification tests (NAT), the detection of model viruses has been described. In these approaches, clinical specimens were spiked with a known amount of an animal virus (4, 13, 23) to monitor the efficiency of extraction, reverse transcription, and amplification. The advantage of such model viruses is the stability of RNA and the control of decapsulation of the viral RNA during the extraction procedure. The production of these animal pathogenic viruses may raise issues of safety, and virus cultivation needs substantial technical skill. Therefore, it should be demanded that the preparation of the control viruses be performed under standard laboratory conditions. Regarding this requirement, it is simple to establish the cultivation of Escherichia coli bacteriophages, such as Q-beta or MS2, in every laboratory. The F+-specific coliphage MS2 has been widely used as a surrogate for human enteric viruses in many studies on virus transport, disinfection, and fate (1, 5, 17, 20, 21). Here we present an MS2 NAT for different real-time RT-PCR approaches, which was used to monitor RT-PCRs for the detection of human RNA viruses.
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The PFU were determined by plating assays. The MS2 RNA was quantified (copies per ml) with a genomic MS2 RNA purchased from Roche Diagnostics (Mannheim, Germany). RNA quantitation was carried out with a sensitive fluorescence-based solution assay for RNA, using RiboGreen RNA quantitation reagent (Molecular Probes, Leiden, The Netherlands) as described by the manufacturer. The MS2 stock solution contained at least 6 x 1010 PFU per ml and was quantified to 6 x 1012 copies per ml. As an internal control of RT-PCR, MS2 phage dilutions were spiked into plasma pools.
Nucleic acid isolation. RNA was extracted from 140 µl plasma with a QIAamp viral RNA kit (QIAGEN, Hilden, Germany) according to the manufacturer's protocol. The RNA was eluted with 60 µl AVE buffer (QIAGEN). For blood donor screening NAT, RNA was prepared from EDTA plasma of volunteer blood donors spiked with MS2 phage by using a QIAamp UltraSens virus kit (QIAGEN). For this purpose, the working lysis solution was prepared with 5.6 µl carrier RNA, 50 µl MS2 phage lysate containing 6 x 104 PFU per ml (final concentration of 3,000 PFU MS2 per ml of plasma), and 800 µl AC buffer (QIAGEN). Total nucleic acid from up to 1 ml of plasma was eluted in 60 µl AVE buffer, of which 15 µl was applied to the RT-PCR. Each extraction run included a negative control plasma and two low-copy positive run controls for the corresponding RT-PCR assay.
Primer and probe design. The oligonucleotides were designed by utilizing OLIGO 5.0 primer analysis software (National Biosciences, Plymouth, Minn.), Primer Express software (Applied Biosystems, Darmstadt, Germany), and LightCycler Probe Design Software, v. 1.0 (Roche Diagnostics, Germany). The degree of nucleotide sequence homology was checked by using the BLAST algorithm (www.ncbi.nlm.nih.gov/BLAST), which searches the EMBL, GenBank, and DDBJ databases.
Real-time RT-PCR using hybridization probes. A Superscript II one-step RT-PCR with Platinum Taq kit (Invitrogen, Karlsruhe, Germany) was used as the basis for the reaction mixture in the LightCycler (LC) RT-PCR assay. A volume of 20 µl was used in each reaction capillary. An aliquot of 5 µl of the RNA was added to 15 µl of the reaction mixture containing 1x Reaction Mix (Invitrogen), 4.5 mM MgSO4 (Invitrogen), 500 ng per µl nonacetylated bovine serum albumin (BSA) (Sigma-Aldrich, Taufkirchen, Germany), 600 nM of forward primer KY-78s (5'-CAA GCA CCC TAT CAG GCA GT), 600 nM of reverse primer KY-80s (5'-AGC GTC TAG CCA TGG CGT), 250 nM of donor probe HCV-3FL (GCA GCC TCC AGG ACC CCC C-FAM [6-carboxyfluorescein]), 250 nM of acceptor probe HCV-5LC (5'-LC Red 640 [LightCycler-Red 705-phosphoramidite]-CCC GGG AGA GCC ATA GTG GTC TG-Ph [3'-phosphate]) (18), 300 nM of each MS2 primer (MS2-2717F and MS2-3031R), 50 nM of each MS2 probe (MS2-FL and MS2-LC) (Table 1), and 0.6 µl RT-Platinum Taq mix (Invitrogen). In addition to the positive run control, each test run included one no-target control containing 15 µl of the reaction mixture and 5 µl PCR-grade water. The reaction capillaries were capped, centrifuged, and placed into the carousel of the LightCycler instrument (Roche Diagnostics).
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TABLE 1. Primers and probes used for RT-PCR
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Real-time RT-PCR using scorpion primers. The specific fluorescence resonance energy transfer scorpion primer for MS2 is shown in Fig. 1. The oligonucleotide consists of a probe region with a 5'-ROX (carboxy-X-rhodamine) dye, an internal fluorescein (FAM), a PCR blocker (HEG [hexaethylene glycol]), and a 3'-PCR primer sequence. The scorpion was quenched by the second primer reverse complementary to the probe region of the scorpion. The primer QSc-MS2-3R was labeled with the dark quencher methyl red twice, once at its 3' end and once internally. Each reaction mixture contained 1x Reaction Mix (Invitrogen), 4.5 mM MgSO4, 500 ng per µl nonacetylated BSA (Sigma-Aldrich), 300 nM of scorpion primer Sc-MS2-3R, 900 nM of quencher primer QSc-MS2-3R, 300 nM of forward primer MS2-TM3-F (Table 1), and 0.6 µl per 20 µl RT-Platinum Taq mix (Invitrogen). The PCRs were carried out on the LightCycler instrument. The cycling conditions were as follows: reverse transcription at 50°C for 10 min, denaturation at 95°C for 2 min, 40 cycles at 95°C for 0 s, annealing at 50°C for 3 s, monitoring at 60°C for 4 s (channel F2), and elongation at 72°C for 5 s. A single fluorescence measurement was made in each cycle during the monitoring step.
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FIG. 1. Duplex scorpion structure. The elements of the MS2 duplex scorpion showing the probe sequence (box), primer (arrow), PCR blocker, and fluorophores FAM and ROX (A). Excitation of the ROX dye is mediated by the emission of FAM (fluorescence resonance energy transfer scorpion). The quencher oligonucleotide is reverse complementary to the probe sequence and labeled internally and at the 3' end with the dark quencher methyl red (MR) (B). After amplification, the scorpion primer is incorporated into the amplicon, while the cDNA strand is terminated by the PCR blocker that prevents separation of the scorpion quencher primer complex (C). During the next cycle, the probe region of the scorpion hybridizes intramolecularly to the newly synthesized target sequence (D).
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The Rotorgene RT-PCR assay reactions were performed in a volume of 50 µl including 15 µl nucleic acid extract. The reaction mixture was done as described above, but without BSA, and the MS2 probe was labeled with the reporter dye JOE (6-carboxy-4',5'-dichloro-2',7'-dimethoxyfluorescein). Cycling conditions were 50°C for 10 min and 95°C for 2 min, followed by 45 cycles at 95°C for 10 s and 60°C for 45 s. Amplification, detection, and data analysis were performed with the Rotorgene 3000 cycler system (Corbett Research, Sydney, Australia). This HCV/MS2 RT-PCR assay was validated and compared with the RealArt HCV RG RT-PCR reagents on the Rotorgene 3000 (Artus GmbH, Hamburg, Germany). This assay is validated for HCV RNA screening of blood donations according to the criteria released by the Paul Ehrlich Institute, the federal licensing agency of Germany, for routine NAT.
Stability of the MS2 phage. Purified MS2 phage with 1.7 x 105 PFU per ml (1.7 x 107 copies per ml) SM buffer was aliquoted in single-time-point samples of 0.2 ml. Samples were stored at the assigned temperatures until they were assayed. In this study, three different storage temperatures (20, 4, and 22°C) were examined and samples were assayed in quadruplicate at every time point from day 1 to day 7. RNA extraction of 140-µl samples was performed with a QIAamp viral RNA kit (QIAGEN). RNA samples were stored at 80°C. All of the samples were assayed in duplicate with real-time RT-PCR in a single run on the Rotorgene platform.
Probit analysis on experimental data. Probit analysis to determine the lower detection limit of NAT assays was performed using SPSS 10.0 software (SPSS GmbH Software, Munich, Germany).
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FIG. 2. MS2 RT-PCRs with different probe formats. RT-PCR was performed on the LightCycler 2.0 with TaqMan (A), duplex scorpion (B), or hybridization (C) probes, respectively. MS2 RNA (Roche Diagnostics) was spiked into the RT-PCRs in a range of 21 to 2.1 x 107 copies per reaction. Samples were assayed in quadruplicate at every concentration, and amplification efficiencies were determined by the slopes of standard curves. CT values were determined by the second derivative maximum method.
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The comparison of the three probe formats with MS2 RNA demonstrated very good reaction efficiencies in a range of 1.868 to 1.951 (Fig. 2), which is near the optimal PCR efficiency. The MS2 RT-PCR assays were suited for internal control when using a second target (e.g., HCV RNA) in duplex PCR (data not shown).
Sensitivity of the MS2 RT-PCR assay. To determine the analytical sensitivity of the MS2 assay, we used human plasma spiked with different MS2 titers from 1.5 x 103 to 1.5 x 105 copies per ml plasma, corresponding to 21 to 2,097 copies of MS2 per RT-PCR. Eight plasma pools of each concentration were processed through all steps of nucleic acid isolation and RT-PCR. The 95% detection limit was calculated by probit analysis to 44.9 copies per PCR (range, 38.4 to 73.4) when using the MS2 TaqMan assay on the Rotorgene 3000.
Stabilities of the MS2 phage. We investigated the stabilities of the MS2 phage preparations stored at 20°C, 4°C, and room temperature for 7 days. The MS2 phage aliquots were used for RNA isolation and assayed for MS2 RNA with RT-PCR. Starting from 1.9 x 105 PFU per ml, the copy number was determined to 1.9 x 104 copies per RT-PCR. The CT values were compared to the starting values (Table 2). Probes stored at the three different temperatures showed no significant loss in copy number over the time period analyzed. Long-time storage (over 6 months) of MS2 phage in SM buffer at 20°C showed no decline of copy number compared to the original input (data not shown).
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TABLE 2. Stabilities of MS2 phage at different incubation temperaturesa
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FIG. 3. Determination of MS2 IC concentrations (conc.) in HCV RT-PCRs. Four sets of RT-PCR samples were prepared, each with an identical dilution series of HCV (0 to 105 IU/ml). Each set of HCV sample was spiked with a different amount of MS2 phage: (A) 3 x 104 PFU/ml; (B) 3 x 102 PFU/ml; (C) 3 x 101 PFU/ml; and (D) 0 PFU/ml. RNA was prepared from 1 ml EDTA plasma by using a QIAamp UltraSens virus kit (QIAGEN). RT-PCR was performed on the Rotorgene 3000 platform with the MS2-TM3 RT-PCR system and HCV primer and probes as described previously (12). Norm. Fluoro., normalized fluorescence; NC, negative control (H2O).
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TABLE 3. Precision testing of the HCV/MS2 RT-PCRa
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Precision testing. The results of the experiments for the screening of blood donation pools for HCV RNA were used to calculate the intra-assay variation and the total variation of the assay. Inter- and intra-assay variations were calculated for CT values. The assay was used in parallel with our established blood donor screening PCR to screen pools of plasma in a 2-week test period. The reproducibility of the method was demonstrated by intra-assay analysis (Table 3). The CVof CT was <2.6% for all 114 plasma pools tested. The interassay variability was calculated from 11 independent RT-PCR runs with CVs ranging from 1.33 to 2.33% and a mean CT of 22.54 ± 0.63 (Table 3).
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The use of nucleic acid-based assays for the diagnosis and monitoring of viral RNA is widespread. Most of these assays depend on the use of synthetic RNAs such as in vitro transcripts or armored RNA as the positive control, internal control, or external standards (3, 6, 14, 15). For that, the control RNA has to be placed in long-term storage without degradation or loss of copy numbers. Naked RNA molecules are often affected by hydrolysis due to an insufficient storage environment or minor contamination with RNase. Therefore, the development of armored RNA technology overcomes the problem of instability of control RNA, as demonstrated previously (6, 15). The disadvantage of these pseudoviral particles is that they are difficult to synthesize and represent only a minor part of the viral genome. For highly conserved targets, such as the 5' untranslated region of the HCV genome, the construction of a "universal" armored RNA control is significant. Viruses with divergent subtypes, like human immunodeficiency virus, are problematic because commercial and in-house NATs use different targets and primers.
As an alternative, the use of intact viruses for external standards in absolute quantification assays or positive control is preferred (4, 13, 23), but the risk of infection for laboratory workers has to be considered when human or animal pathogenic viruses are used. Our approach avoids these disadvantages by using E. coli phage MS2 as a target for the IC. A resistance to RNase degradation, even at high storage temperatures, was demonstrated. The precision of the MS2 RT-PCR was high. We observed no failure of the internal control in the 2-week test period, and the coamplification of MS2 RNA did not prohibit day-to-day application of the assay. The analytical sensitivity of the MS2 NAT was determined by probit regression analysis with different input titers of MS2 phage. The MS2 RNA was sufficiently stable for routine use and did not decrease the detection limit of the multiplex RT-PCRs in which it was used.
For routine clinical applications, the laboratory can maximize the test sensitivity by using an IC to monitor amplification in every specimen. We used the MS2 RT-PCR assays to monitor amplification by spiking MS2 RNA into the RT-PCR master mixture and also MS2 phage for controlling the nucleic acid extraction and all subsequent steps of the procedure. The control phage was simple to produce in high yields, and standardization was possible by plating assays to determine PFU. The MS2 genome sequence was absent from the human specimens, cell cultures, and veterinary samples. Therefore, this approach should be used for different diagnostic NATs, as demonstrated in several RT-PCR assays.
In conclusion, the use of MS2 phage to control clinical diagnostic NAT was demonstrated. The present study supplies evidence that noncompetitive ICs are suitable for many different assays and combine most of the features that are required for valid ICs.
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