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Journal of Clinical Microbiology, August 2007, p. 2570-2574, Vol. 45, No. 8
0095-1137/07/$08.00+0 doi:10.1128/JCM.00647-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Roche Diagnostics GmbH, Penzberg, Germany
Received 23 March 2007/ Returned for modification 4 May 2007/ Accepted 24 May 2007
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In a similar approach, a chimeric viral sequence was cloned into a lambda bacteriophage to generate nuclease-resistant double-stranded DNA (12). The intention was to use it as an IC in real-time PCR screening for herpesvirus and hepatitis B virus. This new construct is superior to unprotected plasmid DNA IC in its storage and handling properties and also enables lysis efficiency to be monitored during sample preparation. However, there are concerns that this lambda phage-based control is unstable in human plasma and still infective to bacteria. Since marked stability in human plasma is a critical prerequisite in any PC, lambda phage control technology requires further improvement before it can fully exploit the potential of nuclease-resistant DNA (13).
In contrast to herpesvirus and HBV, parvovirus B19 (B19V) is a small nonenveloped virus with a single-stranded instead of double-stranded DNA genome. Infection with the virus usually occurs during childhood via the respiratory route causing mild fifth disease (erythema infectiosum). B19V primoinfection in adults may be more severe, with arthropathy or transient aplastic crisis. Fetal infection following placental transfer may cause hydrops fetalis or intrauterine death (reviewed in reference 17). High prevalence means that B19V is often present in, and transmissible via, blood and blood products (2, 5, 6, 10, 16). PCR assays for this pathogen have therefore been implemented in routine blood screening and quality control of blood product manufacturing (1, 3).
From a technical point of view, the single-stranded DNA character of the B19V genome has implications for the design of full process controls. PCs and ICs of nucleic acid purification and amplification efficiency need to behave identically to the target if they are to flag process failures. Critical determinants of nucleic acid behavior during sample preparation are size, secondary structure, and charge (7). In addition, especially during the early cycles of real-time PCR, primer and probe hybridization site accessibility is a key to amplification and detection efficiency. Such accessibility is greatly determined by the secondary structure of the target nucleic acid. A double-stranded DNA control clearly cannot mimic single-stranded DNA properties such as charge and secondary structure. We therefore conceived a new control concept combining single-stranded DNA with the physical and biochemical stability of armored RNA. We report the development of a nuclease-resistant single-stranded DNA (nrssDNA) derived from a deletion mutant of the filamentous phage fd-tet, fKN16 (8).
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fKN16 culture grown in 2xYT medium (Roth, Karlsruhe, Germany) supplemented with 20 µg of tetracycline (Roche Applied Science)/ml. fKN16 plasmid was linearized with HindIII, dephosphorylated using shrimp alkaline phosphatase (Roche Applied Science), and purified by using a High Pure PCR template purification kit (Roche Applied Science) for subsequent ligation (T4 DNA ligase; Roche Applied Science) with the HindIII-cut B19V insert. The ligation reaction was transformed into chemically competent E. coli K802 and plated onto LB agar supplemented with 20 µg of tetracycline/ml. Plasmids were prepared from colony PCR-positive clones, and the sequence was verified by sequence analysis as described above. One plasmid was designated fKN16-B19V-PC and retransformed into K802 to generate the nrssDNA-B19V-PC expression strain. Plasmid fKN16-B19V-QS was generated by a similar process, except that the target probe binding sequence was changed by standard molecular biology techniques to allow hybridization to the B19V-QS probe sequence (see below). fKN16-B19V-QS was accordingly retransformed into K802 to generate the nrssDNA-B19V-QS expression strain. B19V-related sequence inserts of both plasmids are shown in Table 1. |
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TABLE 1. B19V related sequence insert of nrssDNA-B19V-PC and nrssDNA-B19V-QS
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The final nrssDNA concentration was calculated by using the equation: virions/ml = (A269 – A320) x 6E16/number of bases per virion (www.biosci.missouri.edu/smithgp/PhageDisplayWebsite/AbsorptionSpectrum.doc) (Absorption spectroscopy and quantitation of filamentous phage; accessed December 2005).
B19V real-time PCR assay was performed as follows. Generic nucleic acid purification from the sample was automated on the COBAS AmpliPrep instrument as previously described (11), with slight modifications. For amplification, a primer set similar to that for the cloning procedures was used, omitting the HindIII cleavage sites, i.e., the forward primer (5'-GAAACCCCGCGCTCTAGTAC-3') and the reverse primer (5'-CCCAACTAACAGTTCACGAA-3'). The target probe was 5'-(FAM)TCCCCGGGACCAGTTCAGGAGAATCATTTGTCGGAAG(BHQ2)-3' and the QS probe was 5'-(HEX)TGGACTCAGTCCTCTGGTCATCTCACCTTCT(BHQ2)-3' to distinguish between B19V target and B19V QS. The TaqMan Generic RNA amplification kit (Roche Molecular Systems, Branchburg, NJ) was used as the master mix supplemented with 7% (vol/vol) dimethyl sulfoxide and 2.75 mM manganese acetate (final concentration). For amplification and detection on the COBAS TaqMan analyzer (Roche Instrument Center, Rotkreuz, Switzerland), a recently described PCR profile (15) was used.
DNase I resistance assay. A total of 10 µl of nrssDNA-B19V-QS solution (1E12 copies/ml; i.e., 1 x 1012) was supplemented with DNase I (2 U, 10 µl of 10x DNase incubation; Roche Applied Science) and incubated for 10 min at 37°C. After enzyme inactivation for 10 min at 70°C, the samples were diluted 1:10,000 in ICQS diluent and subjected to real-time PCR analysis as described above, omitting the sample preparation step. ssDNA extracted from the nrssDNA-B19V-QS was used as a control.
Infectivity assay. For this assay, 1.5 ml of an E. coli XL1-Blue MRF' kanamycin (Stratagene, La Jolla, CA) overnight culture (10 ml of imMedia kanamycin liquid [Invitrogen]) was supplemented with either 10 µl of nrssDNA-B19V-PC or 10 µl of nrssDNA-B19V-QS stock solution (1E12 copies/ml each) and incubated at 37°C for 2 h of 130-rpm agitation to permit potential infection. To screen for infected cells, a 20-µl portion of each sample was plated on LB-tetracycline or LB-kanamycin, followed by incubation at room temperature for 68 h.
Stability assay. For analysis of concentrated stock stability, nrssDNA-B19V-PC was diluted to a final concentration of 1E11 copies/ml in storage buffer (25 mM Tris, 50 mM NaCl, 0.09% [wt/vol] NaN3; pH 7.5), and 100-µl aliquots in 1.5-ml screw cap reaction tubes incubated at 4, 37, or 45°C. The nrssDNA-B19V-PC stock was then diluted 1:1,000,000 in EDTA plasma and subjected to real-time PCR analysis. To analyze nrssDNA stability diluted in buffer, nrssDNA-B19V-QS was diluted 1:10,000 in ICQS diluent [10 mM Tris, 0.1 mM EDTA, 0.05% (wt/vol) NaN3, 20 µg of poly(rA)/ml (pH 8.1)], and 10-ml aliquots in 25-ml screw-cap bottles were incubated at 4, 37, or 45°C. Testing was done straight without further dilution. nrssDNA-B19V-PC was diluted 1:2,000,000 in normalized human plasma (NHP; Seracare, Milford, MA), divided into aliquots at 1.2 ml in 1.5-ml screw-cap reaction tubes, and stored at 4, 37, or 45°C while awaiting real-time PCR analysis. Based on the Arrhenius equation, this temperature stress model assumed that the stability at 37°C for "x" weeks equals the stability at 2 to 8°C for 8x weeks and that stability at 45°C for "y" weeks equals the stability at 2 to 8°C for 16y weeks.
Electron microscopy. A drop of appropriately diluted sample was placed on a 400-mesh carbon-coated copper grid, freshly hydrophilized by glow discharge. After incubation for 2 min, the drop was quickly removed with a Pasteur pipette, and the grid was air dried before being stained with 2% uranium acetate and 0.01% glucose, washed with a drop of water, and air dried again. Micrographs were taken with an EM 912 electron microscope (Zeiss, Oberkochen, Germany) equipped with an integrated OMEGA energy filter operated at 100 kV in zero-loss mode.
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Growth and purification of nrssDNA. The original fKN16 sequence was derived from the American Type Culture Collection and used to clone nrssDNA-B19V-PC and nrssDNA-B19V-QS as described above (Table 1). During production and purification of nrssDNA, serial process samples were taken for analysis. After the nrssDNA expression strains were grown for approximately 15 h, the yield plateaued, as demonstrated by real-time PCR analysis (data not shown). To standardize further studies, harvesting was set at 18 h after inoculation. To confirm that the expression strains secreted nrssDNA into the supernatant, electron micrographs were taken of resolubilized PEG/NaCl precipitates of both, i.e., the nrssDNA-B19V-PC and nrssDNA-B19V-QS expression strain supernatants, along with that of the original fKN16 strain as a reference (Fig. 1). The images clearly demonstrate the filamentous shape of nrssDNA. Nor did the morphology of the genetically modified nrssDNA-B19V-PC and nrssDNA-B19V-QS appear to differ from the original fKN16. The nrssDNA purification method was then optimized as described above. After CsCl gradient ultracentrifugation, nrssDNA purity in the upper, middle, and lower bands and the previous resolubilized PEG/NaCl precipitate was determined by spectrophotometry (Fig. 2). Except for the lower band, all samples were reactive for the presence of B19V target DNA (data not shown). However, compared to the other samples, the scan showed slight shifting of the upper band peak to the far end, i.e., 269 nm, the reported absorption maximum of filamentous phages (see Materials and Methods). It can therefore be assumed that after CsCl gradient ultracentrifugation the upper band largely consists of enriched nrssDNA, whereas the middle band is probably a mixture of nrssDNA and ssDNA. Enzyme-linked immunosorbent assay for E. coli proteins demonstrated that the enriched nrssDNA was largely depleted of expression strains proteins (data not shown). The yield was 1E14 to 5E14 copies of nrssDNA/liter expression culture, using the Smith lab equation cited above. In summary, the optimized growth and purification method we have described here is a robust procedure for manufacturing high-yield highly enriched nrssDNA.
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FIG. 1. Electron micrographs of nrssDNA. fKN16 (A), nrssDNA-B19V-QS (B), and nrssDNA-B19V-PC (C) were expressed as described in the text, and supernatants were precipitated with polyethylene glycol-NaCl. Pellets were resuspended in low-salt buffer and prepared for electron microscopy.
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FIG. 2. Spectrophotometry of nrssDNA samples taken at different purification steps. Line 2, resolubilized nrssDNA PEG-NaCl precipitate. Lines 1, 3, and 4 represent the upper, middle, and lower bands, respectively, that resulted from CsCl gradient ultracentrifugation. Rhombi, absorption maxima.
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nrssDNA is resistant to DNase I treatment. Full-process nucleic acid testing (NAT) controls are designed to monitor the efficiency of nucleic acid purification, amplification, and detection. If control recovery is outside the defined acceptance criteria the reaction or run is invalid. Controls must be able to tolerate a variety of stressors if they are to yield robust results. In the case of controls mixed with biological fluids such as plasma, resistance to ubiquitous nucleases is critical. To test the assumption of nuclease resistance, nrssDNA-B19V-QS was incubated in the presence or absence of DNase I. The control experiment demonstrated naked ssDNA extracted from nrssDNA to be sensitive against DNase I treatment, as shown by the threshold cycle (CT) shift of approximately 17 in the absence or presence of DNase I (data not shown). Assuming a PCR efficiency of near 100%, ssDNA copies decreased by 5 logs, indicating a digest efficiency exceeding 99.99%. In contrast, nrssDNA-B19V-QS showed the same CT values regardless of whether the sample was pretreated with DNase I or not. This led us to conclude that nrssDNA is made nuclease resistant by its protective protein coat. Although the assay only used DNase I, it is compelling to assume that the protein coat serves as a protective barrier against all nucleic acid modifying enzymes that may be present in biological fluids.
nrssDNA is highly stable. In the routine NAT laboratory, streamlined workflow is essential for standardization, simplification, and operating-cost containment. Ready-to-use PCs are usually manufactured in batches, divided into aliquots, and stored until use. In the preceding experiment, we showed that nrssDNA resists treatment by nucleases due to its protective protein coat. However, proteinases may also be present in human plasma, leading us to stress the possibility that enzymatic hydrolysis of the nrssDNA protein coat during storage could leave the ssDNA open to degradation by nucleases. In order to gain insight into nrssDNA storage stability, we subjected nrssDNA-B19V-PC and nrssDNA-B19V-QS to thermal stress and tested nucleic acid recovery (Table 2): nrssDNA-B19V-PC diluted in NHP gave very stable CT values after storage for at least 4 weeks at 37 and 45°C, equivalent to stabilities at 2 to 8°C of 32 and 64 weeks based on the Arrhenius equation. When incubated concentrated at 1E11 copies/ml in TBS, the CT value increased by approximately 1 after 1 week regardless of whether the samples were stored at low or high temperature. The same observation was made with nrssDNA-B19V-QS in ICQS diluent. However, after 1 week all CT values plateaued, demonstrating that the nrssDNA remains stable with no further decrease in signal recovery. There are at least two explanations for this transient response. First, misassembled or fragmented nrssDNA could be less nuclease resistant, leading to initial ssDNA degradation. Arguments against this hypothesis are that the buffer diluents were nuclease free and that the degradation kinetics were the same at low and high temperatures (Table 2). Second, some of the nrssDNA may have clotted and sedimented or adhered to the storage bottle wall, thus reducing the availability of free nrssDNA. Adhesion is a particularly tempting explanation because it is consistent with the negligible effect observed with dilution in a high-protein-containing solution, e.g., human plasma, when the bottle wall is presumably already saturated with serum protein. In summary, these accelerated stability studies demonstrate marked nrssDNA stability in human plasma and buffered systems for at least 32 weeks at 2 to 8°C.
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TABLE 2. Stability of nrssDNA-B19V-QS and nrssDNA-B19V-PCa
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TABLE 3. Quantification of nrssDNA-B19V-PC dilution series in normalized human plasma by using an in-house B19V real-time PCR assay
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In summary, we have developed novel control constructs for use in NAT assays for pathogens with a single-stranded DNA genome, e.g., parvovirus B19. These controls are superior to current methodologies such as the use of lambda phage or plasmid-derived controls since they closely resemble the properties of the viral genome and are highly resistant to nuclease-mediated degradation. In addition, nrssDNA controls comprise a pronounced stability and are noninfectious to humans as well as to bacteria. Depending on the cloned probe binding sequence, nrssDNA may be used as a PC or IC to aid in the detection or diagnosis of parvovirus B19 infection.
Published ahead of print on 6 June 2007. ![]()
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