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Journal of Clinical Microbiology, December 2008, p. 3997-4003, Vol. 46, No. 12
0095-1137/08/$08.00+0 doi:10.1128/JCM.00563-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands,1 Laboratory of Medical Microbiology, OLVG, Amsterdam, The Netherlands,2 Laboratory of the Municipal Health Service, GGD Amsterdam, Amsterdam, The Netherlands3
Received 25 March 2008/ Returned for modification 17 May 2008/ Accepted 7 October 2008
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Disseminating AV infections can be diagnosed by the culture of AV from specimens obtained from multiple body sites, but this method is time-consuming and not very sensitive (2, 12, 16). The detection of AV DNA in serum or plasma by PCR has been shown to predict disseminated AV infection very reliably (7, 19). In recent years, several sensitive AV PCR assays have been developed (1, 5, 11, 14, 19, 20, 24). However, these PCR assays do not detect all known human AV types, they are nested PCRs, or they are not all internally controlled. The aim of our study was to develop an internally controlled real-time PCR assay detecting all known human AV types.
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Clinical samples. One hundred fifty-one clinical samples from 96 patients suspected of having AV infection were tested in the AV PCR. This selection comprised 86 fecal samples (10 AV culture negative and AV antigen positive, 36 AV culture positive with an unknown AV antigen status, and 40 AV culture negative and AV antigen negative), 62 respiratory samples (23 AV culture positive and 39 AV culture negative), 2 skin swabs (1 AV culture positive and 1 AV culture negative), and 1 cerebrospinal fluid (CSF) specimen (AV culture negative).
For specificity testing, we used 41 EDTA plasma samples (2 PCR positive for BK virus, 6 PCR positive for cytomegalovirus [CMV], and 33 PCR positive for Epstein-Barr virus [EBV]), 4 urine samples PCR positive for BK virus, 13 fecal samples (10 PCR positive for CMV and 3 PCR positive for EBV), and 8 bronchoalveolar lavage (BAL) samples (5 PCR positive for CMV and 3 PCR positive for EBV).
Viral culture. Clinical samples were cultured on human lung adenocarcinoma A549 cells, human diploid fibroblasts, tertiary monkey kidney cells, and Vero cells. The viral cultures were examined twice weekly for the appearance of an (AV-specific) cytopathological effect. The identification of the isolates was performed according to the cytopathological effect in unstained cultures or the staining seen after incubation with a specific monoclonal antibody (Dako, Glostrup, Denmark). In addition to virus culture, AV antigen detection (using an assay kit from Dako, Glostrup, Denmark) was performed with fecal samples in order to detect AV types which are difficult to culture (e.g., AV types 40 and 41). Viral titers of serotypes were determined by 50% tissue culture infective dose (TCID50) analysis according to the Reed-Muench method (21).
Primers and probe. Primers from the hexon region of the AV were chosen. Forty-nine complete genomes representing all subgroups, as well as around 1,550 hexon genes of different serotypes and isolates, were analyzed in the Vector NTI Advance program (Invitrogen). The most conserved region of 103 bp was chosen as a target. In order to amplify all known types, the following degenerate primers were constructed: a forward primer, 5'-CAGGACGCCTCGGRGTAYCTSAG-3', and a reverse primer, 5'-GGAGCCACVGTGGGRTT-3' (where R is A or G, S is C or G, V is A, C, or G, and Y is C or T). The following 24-nucleotide consensus probe sequence was chosen: 5'-CCGGGTCTGGTGCAGTTTGCCCGC-3'. Both the forward (n = 8) and reverse (n = 6) primers had maximum redundancy.
Alignments of sequences. All known complete genome sequences of AV were aligned using Vector NTI and ClustalW.
Construction of the AV-containing plasmid. AV DNA was purified from 200 µl of AV type 2 (AV2) stock (1 in 1,000 dilution) in lysis buffer as described in "DNA purification" below. Amplification was performed with the following nondegenerate target primers: forward, 5'-CAGGACGCCTCGGAGTACCTGAG-3', and reverse, 5'-GGAGCCACCGTGGGGTT-3'. The 103-bp amplicon was cloned into a PCRII-TOPO plasmid according to the instructions of the manufacturer (Invitrogen). Verification of the AV-containing plasmid was performed by sequencing. The concentration of AV DNA from the AV-containing plasmid was determined by evaluating the optical density at 260 nm, and serial dilutions of AV DNA were used to determine the sensitivity of the AV PCR.
Construction of the IC-containing plasmid. We designed two oligonucleotides (linkers) for the construction of internal control (IC) DNA, which were synthesized by Applied Biosystems: adeno hexon linker 1 (5'-CAGGACGCCTCGGAGTACCTGAGCCGATGTGTCCGCCGTGGTCCCCTGGACCGAGACGTACTT-3') and adeno hexon linker 2 (5'-GGAGCCACCGTGGGGTTTCTAAACTTGTTATTCAGGCTGAAGTACGTCTCGGTCCAGGGGACCACGG-3'). These two linkers, which together represent the same 103-bp hexon region as that present in the in vitro AV DNA control, overlapped over a stretch of 28 nucleotides (underlined) and contained the same primer binding sites as the in vitro AV DNA control (doubly underlined) but with a shuffled probe region (bold). The IC probe region allows discrimination between AV and IC DNA amplicons during amplification and detection. The IC DNA control was constructed by the hybridization and elongation of 1 ng of linker 1 and 1 ng of linker 2 in a mixture of 2.5 U of AmpliTaq gold, 5 µg of bovine serum albumin, 1x PCR II buffer, deoxynucleoside triphosphates at a concentration of 200 µM each, and 3 mM MgCl2. The mixture was incubated for 10 min at 95°C, 5 min at 55°C, and 10 min at 72°C. The resulting hybrid was subsequently amplified with the nondegenerate target primers and cloned into a PCRII-TOPO plasmid according to the instructions of the manufacturer (Invitrogen). Verification of the IC-containing plasmid was performed by sequencing. The concentration of DNA was determined by evaluating the optical density at 260 nm.
DNA purification. The 51 prototypes were isolated alternately with negative controls by using the MagNA Pure (MP) system (Roche Diagnostics, Penzberg, Germany) as follows: 5 µl of each prototype together with 104 IC DNA copies was mixed with 350 µl of MP lysis buffer. For isolation from the clinical samples, we used 200 µl of throat fluid, sputum, or plasma and 350 µl of MP lysis buffer or 50 µl of fecal material and 500 µl of MP lysis buffer. These mixtures were then subjected to a vortex in an Eppendorf tube, left for 10 min at room temperature (prelysis step), and subsequently centrifuged for 2 min at 13,000 rpm in an Eppendorf centrifuge. Thereafter, 490 µl of supernatant was transferred into an MP sample cartridge together with 10,000 copies of IC DNA. Isolation was then performed with the MP system according to the protocol of the manufacturer (Roche Diagnostics, Penzberg, Germany) by using the total nucleic acid kit. The DNA was finally eluted in 100 µl of MP elution buffer.
Competitive TaqMan PCR.
Ten microliters of each eluate, containing 1,000 copies of IC DNA, was used for the TaqMan PCR. The final PCR mixture (25 µl) contained 12.5 µl of TaqMan Universal PCR master mix (ABI), 900 nM forward primer, 900 nM reverse primer, 200 nM target probe, 200 nM IC probe, and 400 ng of
-casein/µl (2). PCR was performed with an ABI Prism 7000 sequence detection system as follows: 2 min at 50°C and 10 min at 95°C, followed by 45 cycles consisting of 15 s at 95°C and 1 min at 60°C. A signal was considered to be relevant if a logarithmic curve was visible above the threshold for the target and/or the IC.
Serial dilutions. Twelve (twofold) serial dilutions of plasmid containing AV2 hexon DNA (AV2-plasmid DNA) and IC DNA in Tris-EDTA (pH 8.0) with 20 ng/µl of calf thymus DNA (Sigma, The Netherlands) in a background of AV-negative throat fluid were made and tested by PCR after the extraction of DNA with the MP system in order to test the lower limit of detection (LLOD) of the AV PCR. Furthermore, 12 (10-fold) serial dilutions of AV2-plasmid DNA in a background of AV-negative plasma, with 104 copies of IC DNA in each dilution, were made in order to investigate whether there was an effect of competition from the IC on the linearity and the LLOD of the assay.
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TABLE 1. LLODs for plasmids containing part of the AV2 hexon gene DNA and IC DNAa
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TABLE 2. Linearity of extraction results for plasmid containing part of the AV2 hexon gene DNA with 104 copies of IC DNA
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FIG. 1. Standard curve for plasmid DNA containing part of the AV2 hexon gene. Twelve series of 10-fold dilutions of extracted plasmid DNA containing part of the AV2 hexon gene, each with a constant level of 104 copies of IC DNA per dilution, were tested by PCR, resulting in a dynamic range of 5 x 103 to 5 x 108 copies/ml, with a regression coefficient of 0.991.
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TABLE 3. Comparison of results from PCR and TCID50 methods
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FIG. 2. Alignments of deduced amplicon sequences from serogroups A to F. Alignments were made using Vector NTI. Primer binding sites are indicated in yellow. The probe binding site is indicated in blue. Redundancies in the primer and probe binding sites are marked in red, whereas dashes represent identical nucleotides. Forward primer sequence, CAGGACGCCTCGGRGTAYCTSAG; probe sequence, CCGGTCTGGTGCAATTCGCCCGC; and reverse primer sequence, TTRGGGTGVCACCGAGG (where R is A or G, S is G or C, V is A, C, or G, Y is C or T, and B is T, G, or C.)
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TABLE 4. Sensitivity of AV PCR for prototype strains of AVa
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TABLE 5. Specificity of AV PCR
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Furthermore, 86 fecal samples were included in the analysis; 36 were AV culture positive, 10 were AV culture negative but AV antigen positive by an enzyme-linked immunosorbent assay (ELISA), and 40 were AV culture and AV antigen negative. Twenty-eight of 40 specimens were completely culture negative, 10 of 40 were EV culture positive, 1 of 40 was rotavirus positive by an ELISA, and 1 of 40 was positive for Clostridium toxin. Two skin swabs were included in the selection, of which one was AV culture positive and one was EV culture positive; one CSF specimen, which was completely culture negative, was also included.
As depicted in Table 6, agreement between the results of virus culture (and antigen detection) and AV real-time PCR was found for 139 of 151 clinical samples (92.1%). Concordant negative results for 31 respiratory samples, 36 fecal samples, 1 skin swab, and 1 CSF specimen (45.7%) were found. Concordant positive results for 23 respiratory samples, 36 fecal samples, and 1 skin swab (39.7%) were found. Discordant results for 12 clinical samples (7.9%) were found. Eight respiratory specimens and four fecal samples (7.9%) were negative by AV culture and positive by the AV real-time PCR. Four of the 12 discrepancies were for samples from AV-infected patients (who had previous samples or other types of specimens that were culture positive); 7 of 12 were for samples that were culture or ELISA positive for another viral pathogen (CMV, rotavirus, or RSV), and 1 of 12 was for a sample positive for Clostridium toxin. In only one case (that of a sputum sample), the patient was not known to have an AV infection detected in other samples or on other test dates and no other pathogen was cultured (Table 6).
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TABLE 6. Comparison of results of AV PCR and virus culture or antigen detection for different clinical specimens
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Various AV PCR assays have been developed up to now; however, none could detect all known AV serotypes in one assay together with an IC in a real-time setting. Various assays were developed which were able to detect a subset of AV types, with or without an IC and either in a real-time setting or not (1, 5, 11, 19, 24). Lion et al. (19) published a description of an AV PCR approach which is able to detect all 51 serotypes; however, six separate assays (six primer-probe combinations) are needed for the detection of all serotypes. Heim et al. (14) and Sarantis et al. (22) describe a TaqMan PCR method which is able to detect all 51 serotypes; however, in this assay, no IC is used. ICs are essential in diagnostic assays, because false-negative results or invalid results can be ruled out (3). Moreover, the diagnosis of AV infections with one set of primers and two probes for the detection of all known AV types and with an IC in a real-time PCR is preferable to the other approaches and to our knowledge not previously documented.
The real-time AV PCR assay described in the present paper is sensitive, has a broad linear range, and is specific. The sensitivity of the PCR assay was evaluated with limiting dilutions of both AV2-plasmid DNA and IC DNA. AV2-plasmid DNA and IC DNA in a background of AV-negative throat fluid were separately extracted by the MP system. Poisson statistics predict that 63% of the reactions will be positive with a single copy of DNA in the PCR mixture (6). The differences observed in the detection rate between AV2-plasmid DNA and IC DNA are therefore probably within the normal test variation.
The AV IC DNA was constructed from an AV2 stock. We evaluated the sensitivity of the PCR for AV serotypes belonging to the six subgroups in serial dilutions in comparison to that of the TCID50 method of determining titers, and no significant differences were found. Table 3 shows results for representative serotypes from the six subgroups in comparison to TCID50 results. In all cases, the PCR was more sensitive. Moreover, the titration of other serotypes showed similar trends, with comparable R2 values. This finding suggests comparable sensitivities of the PCR for the various subgroups and serotypes.
The PCR was tested against a selection of all known 51 prototype strains with alternating negative controls: 6 EDTA plasma samples PCR positive for CMV, 33 plasma samples PCR positive for EBV, 2 plasma samples PCR positive for BK virus, 4 urine samples PCR positive for BK virus, 3 fecal samples PCR positive for EBV, 10 fecal samples PCR positive for CMV, 3 BAL samples PCR positive for EBV, 5 BAL samples PCR positive for CMV, and 151 clinical samples with known culture results. The results for the panel of samples with the 51 prototype strains showed that our PCR detected them all, whereas serotype 52 (17) showed 100% homology to our primer and probe sequences, making it likely to be detected by the AV PCR assay described herein. The specificity of our AV real-time PCR assay was tested with 66 samples positive for other DNA viruses, and 62 of 66 (94%) were AV PCR negative. The four exceptions came from patients with a hematological disease, and other materials from these patients were also positive in the viral culture. Moreover, AV infection in these particular samples was confirmed by sequencing.
Comparisons with virus culture showed good concordance, and in 12 of 151 cases (7.9%), the PCR was positive while virus culture was negative. In 4 of these 12 cases, AV was cultured from another type of specimen from the same patient, earlier or later in the course of the disease. In these cases, it is conceivable that, due to better sensitivity, the PCR detected AV while the virus culture was negative. In 6 of 12 cases, another viral pathogen (CMV or RSV) was cultured; in 1 of 12, the sample was positive for rotavirus antigen; and in 1 of 12, the cells were destroyed by Clostridium toxin. For these eight samples, it is possible that the culture for AV was less sensitive than the AV PCR assay due to the presence of other pathogens (resulting in overgrowth by another pathogen and/or low AV loads in patient samples because of interference).
In this paper, we present a newly developed internally controlled AV real-time PCR assay which is sensitive when tested on serial dilutions as well as when tested on clinical samples. It is specific and able to detect all known AV serotypes with one primer pair-probe set. The assay is easy to use in diagnostic as well as in research settings, because only one test run per sample is required. Since the spectrum of AV disease is not fully known, our AV real-time PCR may be an important tool in further research and diagnostic protocols.
Published ahead of print on 15 October 2008. ![]()
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