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Journal of Clinical Microbiology, April 2009, p. 1025-1030, Vol. 47, No. 4
0095-1137/09/$08.00+0 doi:10.1128/JCM.01920-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Bundeswehr Institute of Microbiology, Munich, Germany,1 National Institute for Communicable Diseases, Sandringham, South Africa,2 Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,3 Health Protection Agency, Porton Down, Salisbury, United Kingdom,4 Unit of Biology of Viral Emerging Infections, Institute Pasteur, Lyon, France,5 Microbiology Department, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece,6 Chipron GmbH, Berlin, Germany7
Received 4 October 2008/ Returned for modification 26 November 2008/ Accepted 23 January 2009
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Due to clinical similarity between CCHF and other diseases, proper triage and isolation of patients depends on laboratory confirmation of the diagnosis (15). Available diagnostic methods include virus culture, antigen-specific enzyme-linked immunoassay, antibody-specific enzyme-linked immunoassay, and reverse transcription-PCR (RT-PCR) (2, 4, 5, 24). Virus detection in the acute stage of disease is necessary, and RT-PCR provides the best sensitivity (8).
Conventional RT-PCR protocols take up to 8 h for cDNA synthesis, amplification, and gel analysis and in some instances a second round of nested amplification (3, 19). Sequencing of RT-PCR products is needed for strain identification. A real-time RT-PCR procedure for CCHF virus is difficult to develop due to remarkable genetic variability among virus strains (11, 25, 26). Current protocols are often not appropriate for field-based outbreak investigations and may be difficult to implement in those countries where CCHF virus is endemic. Simpler, field-compatible assays are required. Such an approach is described here.
A robust one-step RT-PCR assay with an internal control was established, using the most recent genome information. Based on our prior experiences (25), the assay was formulated for compatibility with an inexpensive and simple nonfluorescent DNA macroarray hybridization platform. Detection with the naked eye was possible by using simple and robust biotin/streptavidin-horseradish peroxidase conjugate chemistry in combination with a tetramethylbenzidine substrate, resulting in the formation of a clearly visible dark precipitate at array positions where DNA-DNA hybridizations took place. No gel analysis was necessary. The possible patterns of hybridization spots were sufficiently heterogeneous to facilitate reliable differentiation among virus strains. Validation was done with strain collections from several collaborating biosafety level 4 facilities, covering essentially the full range of global diversity of CCHF virus (see Fig. 3). Clinical evaluation utilized a comprehensive panel of original clinical samples from patients with confirmed cases of CCHF, collected over almost 20 years by a WHO reference facility.
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FIG. 3. (A) Global distribution and phylogenetic relationships of CCHF virus strains selected for the design and validation of the assay. Phylogenetic analysis was based on 450-bp sequences of the CCHF virus S segment available in the NCBI database, and the phylogenetic tree was generated by the neighbor-joining method with TreeCon for Windows, version 1.3b (Yves van de Peer, University Konstanz, Germany). *, these CCHF virus strains were not available for testing with the novel universal CCHF virus quantitative RT-PCR assay, but genetically closely related isolates have been tested. **, strain AP92 has also not been available for testing. It was isolated from a Rhipicephalus bursa tick and has never been associated with human disease. (B) Representative hybridization patterns of CCHF virus strains listed in Table 2. Different strains of CCHF virus show individual hybridization patterns on the macroarray. However, these patterns are based only on sequence variability within an approximately 25-nt region of the CCHF virus S segment. Therefore, they cannot be considered unique for a specific CCHF virus strain, as shown in patterns 5 and 6. Dugbe virus, a nonpathogenic nairovirus closely related to CCHF virus, is not detected by the CCHF virus-specific array. Note that the internal control spots are not visible in the CCHF virus patterns, as the amplification of the internal control RNA is suppressed in the presence of high concentrations of CCHF virus RNA (also compare Fig. 2).
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TABLE 1. CCHF virus strains used for validation of the RT-PCR assay
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RNA standards and internal control. A synthetic RNA standard was generated by amplifying the full small (S) segment of CCHF virus strain BT-958 (EF123122) as described before (13). After TA cloning of the fragment into Escherichia coli plasmid pCR2.1 (Invitrogen, Germany) and sequencing, a clone with a correct insert sequence was selected and the complete insert including a plasmid-derived T7 promoter was amplified by PCR. RNA was transcribed from the purified PCR product with the MegaScript T7 in vitro transcription kit (Ambion). The DNA template was removed by DNase I, and RNA was purified by affinity chromatography with RNeasy columns (Qiagen, Germany) before spectrophotometric quantification. A competitive internal control was constructed by overlap extension PCR as described previously (10). The resulting construct contained a 350-bp fragment of the CCHF virus S segment and 70 bp of an unrelated sequence motif. It was cloned back into pCR 2.1 and transferred into RNA as described above.
RT-PCR. A 50-µl reaction mixture contained 1x reaction buffer from a one-step RT-PCR kit (Qiagen, Germany), 200 µmol/liter deoxynucleoside triphosphate, 200 nM (each) primers as listed in Table 2, 2µl of one-step RT-PCR kit enzyme mix, and 5 µl of RNA extract. For subsequent hybridization to the macroarrays, a preformulated biotinylated primer mixture from a low-cost, low-density (LCD) array kit (Chipron GmbH, Germany) was used instead of the conventional primers. Amplification in a conventional PCR cycler (Primus 25; Peqlab, Germany) comprised 50°C for 30 min, 95°C for 15 min, and 40 cycles of 94°C for 30 s, 55°C for 30 s, and 72°C for 60 s.
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TABLE 2. Primer and probe sequences used for RT-PCR and macroarray hybridization
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FIG. 1. Schematic diagram of the microarray. (A) Illustration of the 50- by 50-mm polymer support with the eight identical, individually addressable array fields. CSNr, chip specification number; ID, identification number. (B) Spotting pattern of one array field. Twenty CCHF virus-specific capture probes were spotted as vertical duplicates in a nine-by-nine pattern with average spot diameters of 325 µm (positions 1 to 20). Four capture probes for the competitive internal control RT-PCR product were included at the bottom of each array (positions 21). Additional functional control probes to visualize successful hybridization and staining were immobilized in three angles of each field (positions C).
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The assay was optimized for sensitivity by the titration of essential RT-PCR mix components. The assay amplified a broad range of CCHF virus strains (Table 1; data not shown). To determine the analytical sensitivity, RNAs from representative strains Bangui BT-958, Turkey 4348/02, and ArD39554 in limiting log10 dilution series were amplified. Viral loads down to 800, 1,000, and 780 genome copies per ml, respectively, could be detected.
To identify samples with RT-PCR inhibition, a synthetic internal control RNA was designed. To ensure amplification of the molecule without additional (possibly interfering) primers, an internal control that contained the same primer binding sites as CCHF virus (a competitive internal control) was chosen (10). To ensure that it did not outcompete even small amounts of virus RNA in the reaction mixture, the control was used at a low concentration (see below) and its length was extended over that of the virus, providing an inherent amplification disadvantage. The construct was 350 bp instead of 280 bp in length, through the insertion of a random sequence by overlap extension PCR.
Functionality was evaluated in cross-titration experiments with mixtures containing different amounts of CCHF virus RNA and internal control RNA. When CCHF virus RNA was absent, the internal control was amplified clearly (Fig. 2). In the presence of increasing concentrations of CCHF virus RNA, the level of amplification of the internal control was either lower or absent because of competitive inhibition by the amplification of the CCHF virus genomic target (Fig. 2). With increasing concentrations of the internal control in reaction mixtures containing constantly low levels of CCHF virus RNA (60 copies per reaction), it was demonstrated that no inhibition of virus amplification was imposed by competitive effects of the internal control. A working concentration of 200 copies of the internal control per reaction was chosen for all further assays.
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FIG. 2. RT-PCR amplification with the CCHF virus-specific assay (280-bp amplicon) and the internal control (350-bp amplicon). (A) Conventional 1.5% agarose gel analysis of the RT-PCR products. (B) Specific hybridization patterns of the same RT-PCR products on the macroarray. Lane M, 100-bp molecular size ladder; lanes/fields 1 to 3, CCHF virus strain BT-958 in vitro-transcribed RNA; lane/field 1, 6 x 106 genome copies per reaction; lane/field 2, 6 x 104 copies per reaction; lane/field 3, 6 copies per reaction; lane/field 4, internal control RNA only; lane/field 5, control to which no RNA was added. Note that both analysis methods visualize the suppression of the internal control amplification by increasing concentrations of CCHF virus target RNA.
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Hybridization to LCD arrays was evaluated next. All 18 virus reference strains listed in Table 1 were amplified and hybridized (Fig. 3). Signals after the hybridization and staining procedures were clearly visible to the naked eye. Repeated testing of a virus sample showed constantly identical hybridization patterns (data not shown). The whole protocol took less than 4 h, and up to 48 samples could easily be analyzed in parallel. Documentation images as shown in Fig. 3 were obtained using a standard slide scanner purchased from a department store. Array hybridization provided the same sensitivity as gel detection, as shown in Fig. 2. However, at virus concentrations below 1,000 copies per reaction, some of the capture probes which generated only weak hybridization signals at higher template concentrations were not visible. This result may limit the ability to discriminate among certain CCHF virus strains in samples with very low viral loads.
The specificity of the RT-PCR assay was verified using purified genomic nucleic acids from culture supernatant or high-titered patient samples containing pathogens that cause diseases resembling CCHF infections: Bacillus anthracis, Bacillus cereus, Bacillus subtilis, Coxiella burnetii, cytomegalovirus, dengue virus types 1 to 4, Dugbe virus, Ebola virus strain Gulu, Epstein-Barr virus, hepatitis C virus, Japanese encephalitis virus, Lassa virus strain AV, Leptospira interrogans, Listeria monocytogenes, monkeypox virus, Neisseria meningitidis, Plasmodium falciparum, poliomyelitis virus types 1, 2, and 3, rabies virus, Rickettsia prowazekii, Rickettsia rickettsii, Rift Valley fever virus, Ross River virus, Sindbis virus, Venezuelan equine encephalitis virus, West Nile virus strain Uganda, and yellow fever virus. None of these materials, including Dugbe virus (strain AF014014), a nonpathogenic nairovirus related to CCHF virus, showed any reactivity. None of the assays with these pathogens showed any random reactivity, i.e., additional nonspecific bands in gel electrophoresis or background hybridization (data not shown).
Clinical application. A total of 63 serum samples from 31 patients with confirmed CCHF, received from 1986 to 2006, were tested after they had been stored at –70°C for up to 20 years. Of the 31 confirmed cases of CCHF included in the study, 27 occurred in widely separated locations in South Africa and Namibia, 3 occurred in Iran, and 1 occurred in Pakistan. Serum had been collected 1 to 18 days (mean, 6 days; SD, 2.8 days) after the onset of disease. Viral loads of the stored samples were quantified by real-time RT-PCR (25) and ranged from 1.6 x 103 to 5 x 108 genome copies per ml (mean, 106 genome copies per ml; SD, 20 genome copies per ml). All samples were positive in all assays. Serial samples from the same patients showed identical hybridization patterns (Fig. 4). All tested clinical samples from different regions where CCHF is endemic could be distinguished on the basis of their hybridization patterns (compare Fig. 3A and B).
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FIG. 4. Serial samples from a patient with an acute case of CCHF. This example shows hybridization patterns obtained from serum samples on days 1, 5, and 8 after the onset of the disease. The viral loads of the samples (in genome copies per reaction [cps/rx]) were quantified by real-time RT-PCR as described before (25).
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Opinions, interpretations, conclusions, and recommendations are those of the authors and are not necessarily endorsed by any governmental agency or department or other institutions.
Published ahead of print on 18 February 2009. ![]()
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