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Journal of Clinical Microbiology, May 2004, p. 1994-1999, Vol. 42, No. 5
0095-1137/04/$08.00+0 DOI: 10.1128/JCM.42.5.1994-1999.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Departments of Zoology,1 Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, Peoples Republic of China2
Received 11 August 2003/ Returned for modification 4 October 2003/ Accepted 26 December 2003
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Recently, a new strain of virus in the family Coronaviridae was discovered in SARS patients admitted to local hospitals (4), and its genome was completely sequenced a few weeks later (3, 7, 12). It is believed that this new virus causes SARS, and current diagnostic tests, including serological and molecular tests, are based on this virus. Reverse transcriptase PCR (RT-PCR) is employed for the rapid detection of virus in clinical samples. Primers amplifying regions within the RNA-dependent RNA polymerase-encoding sequence of the virus are being used for diagnosis in several of the World Health Organization network laboratories (in Germany, the United States, and Hong Kong). In Mouse hepatitis virus, a typical member of the genus Coronavirus, both the genomic RNA and mRNA transcripts are capped and possess common 3' ends and common leader sequences on their 5' ends. With this unique transcription strategy, it is expected that the copy numbers of different viral genes during the replication of the virus are different in the host cells (Fig. 1). The N gene that encodes the nucleocapsid protein has the most abundant copy number during virus replication, as all transcripts may carry the nucleotide sequence from the N gene, although they are not all in frame for translation of the gene product. Recently, Rota et al. (7) showed that when they used a digoxigenin-labeled riboprobe overlapping the 3' untranslated region of the genome in a Northern blot analysis of the SARS-associated coronavirus (SARS-CoV), all transcripts showed a positive signal (7). Therefore, we hypothesized that an RT-PCR assay amplifying the 3' region, including the N gene, of the viral genome would be more sensitive than amplifying the rest of the viral genome for diagnostic purposes. In this study, we report a new and improved RT-PCR assay for the detection of SARS-CoV in clinical samples.
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FIG. 1. Genome organization and transcription strategy of SARS-CoV HK-39. Genomic and mRNA transcripts are capped (black circles), carry leader sequences (vertical lines) at the 5'-proximal end, and are polyadenylated (A15). Arrows point to the positions of the intergenic sequence (CTAAACGAAC). After the release of the positive-sense genomic RNA into the cytoplasm of the host cell, the viral RNA-dependent RNA polymerase, encoded by ORF1a and -1b, is synthesized. It performs transcription of a full-length complementary (negative-sense) RNA, from which new genomic RNA, an overlapping set of subgenomic mRNA transcripts, and leader RNAs are synthesized. Note that all transcripts are preceded with common 5' leader sequences and common 3' ends. ORF1a and -1b, RNA-dependent RNA polymerase; S, the major peplomer glycoprotein; M, transmembrane glycoprotein; N, nucleocapsid protein; X1, X2, and X3, putative uncharacterized proteins.
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First-strand cDNA synthesis and PCR. Reverse transcription was performed with 200 U of Superscript II RT (Invitrogen) in a 20-µl reaction containing 0.15 µg of random hexamers, 1x RT buffer, 10 mM dithiothreitol, and 0.5 mM deoxynucleoside triphosphates. Reactions were incubated in a Peltier thermal cycler (MJ Research) for 50 min at 42°C, followed by 15 min at 70°C. Primers were designed according to the complete SARS-CoV genomic sequence of a local specimen, isolate HK-39, which was described previously (12) (accession no. AY278491). The forward primer (SRS251 [5'-GCAGTCAAGCCTCTTCTCG-3'], corresponding to nucleotides [nt] 28658 to 28676 of the HK-39 SARS-CoV genome) and reverse primer (SRS252 [5'-GCCTCAGCAGCAGATTTC-3'], corresponding to nt 28866 to 28883) amplified a 225-bp fragment from the region of the N gene that showed no homology to other coronaviruses. Primers amplifying the RNA-dependent RNA polymerase gene (1b gene) were used as parallel controls (coro3 [5'-TACACACCTCAGCGTTG-3'] and coro4 [5'-CACGAACGTGACGAAT-3'], corresponding to nt 18041 to 18057 and nt 18207 to 18222, respectively [Department of Microbiology, HKU]). Both amplicons were cloned into the pCR2.1 cloning vector. Serial dilutions of the plasmid, from 106 to 101 copies, were used to determine the dynamic range and optimal conditions for the PCRs. Another set of primers that amplified a 745-bp fragment from the pig ß-actin gene was employed as an internal control for the diagnostic PCR assay (actin F [5'-TGAGACCTTCAACACGCC-3'] and actin R [5'-ATCTGCTGGAAGGTGGAC-3']). A conventional PCR and gel electrophoresis were performed as a preliminary experiment. Briefly, 1 µl of cDNA from a clinical sample was amplified with 0.5 U of recombinant Taq DNA polymerase (Invitrogen Life Technologies) in a 25-µl reaction mixture containing 1x PCR buffer, 1.5 mM MgCl2, 0.1 mM deoxynucleoside triphosphates, and 0.5 pmol each of the forward and reverse primers. The reaction was incubated in a Peltier thermal cycler (MJ Research) for 3 min at 94°C, followed by 50 cycles of 94°C for 10 s, 56°C for 10 s, and 72°C for 10 s and a 10-min final extension step at 72°C. Amplicons were analyzed by 2% agarose gel electrophoresis. Quantitative real-time PCR using the Sybr Green fluorophore was performed for the diagnosis of clinical samples. In a 25-µl reaction, 1 µl of a cDNA template was mixed with 12.5 µl of 2x SYBR Green PCR master mix (Applied Biosystems) and 0.5 pmol each of the forward and reverse primers. The volume of the reaction was adjusted to 25 µl with distilled water. Reactions were performed with the iCycler iQ Real-Time PCR detection system (Bio-Rad) for 3 min at 94°C, followed by 50 cycles of 94°C for 10 s, 56°C for 10 s, and 72°C for 10 s. Fluorescence signals (FAM; excitation wavelength = 490 nm and emission wavelength = 530 nm) were collected at the end of each extension step during the PCR cycles. The threshold cycle (CT) of each sample was determined by the maximum curvature approach. Melting curve analysis was performed after a 10-min final extension. cDNAs from non-SARS patients, including patients suffering from adenovirus (n = 5), respiratory syncytial virus (n = 5), human metapneumovirus (n = 5), influenza A virus (n = 5), and influenza B virus (n = 5) infections, were used as negative controls for the assay.
Northern blot analysis. SARS-CoV HK-39-infected Vero cells were provided by the Department of Microbiology, HKU, and the total RNA was extracted from cells by use of the TRIzol reagent (Invitrogen Life Technologies) according to the manufacturer's protocol. The total RNA (8 µg) was separated by electrophoresis in a 1% agarose gel containing 3.7% formaldehyde, transferred to a positively charged nylon membrane (Roche Diagnostic Corporation) by capillary blotting, and fixed by UV cross-linking. The cDNA synthesized with the same RNA sample was used as a template for probe synthesis. Four pairs of primers, amplifying fragments from the 1b gene (nt 18057 to 18222), the S gene (nt 21920 to 22107), the M gene (nt 26867 to 26996), and the N gene (nt 28658 to 28883), were used for probe synthesis (Table 1). Digoxigenin labeling of the probes and hybridization and detection of the bands were performed with the digoxigenin system, used according to the manufacturer's procedures (Roche Molecular Biochemicals). The signals were then analyzed by chemiluminescence.
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TABLE 1. DNA probes used for Northern blot analysis
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In addition, the current sample collection procedure involves dilution of the virus titer in the samples. This step compromises the sensitivity of the assay because the virus titer is generally low in nasal and throat swab specimens, especially during the early stage of infection (1). It has been suggested that the sensitivity of PCR tests for SARS-CoV depends on the quality of the specimen and the time of testing during the course of the illness (10). In order to increase the sensitivity of the test, we concentrated the total RNAs isolated from clinical samples prior to first-strand cDNA synthesis.
In order to avoid false-negative PCR results due to a failure during the process of RNA isolation and first-strand cDNA synthesis, total RNAs were extracted from clinical samples in parallel with viable PK-15 pig cells. Figure 2 shows the RT-PCR screening results for both NPA and stool clinical samples. Diagnostic PCRs were performed in parallel with ß-actin as a PCR control. All clinical samples were positive by the ß-actin PCR. These results indicate that RNAs and cDNAs were extracted and synthesized successfully from the samples in a single-step protocol. With this amplification control, total RNA isolation and cDNA synthesis from the samples can be ensured and false negatives can be eliminated. Moreover, the 96-well assay format developed for this study was adapted into a high-throughput screening protocol, with which we were able to obtain diagnostic results for >90 clinical samples in 3 h with one clinical technician, while the current protocol, for which samples are processed in individual tubes, can only handle about 30 to 50 samples per day per technician.
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FIG. 2. RT-PCR screening of clinical samples from suspected SARS patients. The upper bands in each row show a 745-bp DNA fragment amplified with actin F and actin R, while the lower bands are the amplicons by primers specific to the N gene of SARS-CoV (225 bp). cDNA samples synthesized from total RNAs extracted from NPA samples (A1 to H1) were used as templates in both N-gene-specific and ß-actin-specific PCRs. The negative control (water) and positive control (cDNA from SARS-CoV-infected Vero cells) for the assay are indicated. Five-microliter samples of PCR products from two separate reactions, i.e., N-gene-specific PCR and ß-actin-specific PCR, were mixed and loaded into the same well in a 2% agarose gel. M, 1 kb Plus molecular marker (Invitrogen).
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TABLE 2. Detection rates of N-gene-specific RT-PCR assay for SARS-CoV
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FIG. 3. Specificity test for N-gene-specific PCR. An amplification plot of fluorescence intensity versus the number of PCR cycles is shown. Black lines show the dynamic range of N-gene-specific PCR with a serially diluted plasmid construct (from 101 to 106 copies). Results for NPA samples from non-SARS patients, including patients suffering from infections with adenovirus (n = 5), respiratory syncytial virus (n = 5), human metapneumovirus (n = 5), influenza A virus (n = 5), or influenza B virus (n = 5), are shown by gray lines. Triangles, SARS-CoV-positive NPA samples. NTC, no-template control. The x axis indicates the cycle number of the quantitative PCR, while the y axis represents the fluorescence intensity (FAM-490) over the background signal. The inset shows a melting curve analysis of the PCR products. Signals from positive (+ve) and negative (ve) samples and from a no-template control are indicated.
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FIG. 4. Comparison of dynamic ranges of N-gene- and 1b-gene-specific PCRs. The dynamic ranges of both N-gene- and 1b-gene-specific PCRs were obtained with the same plasmid construct into which a 1:1 ratio of the corresponding amplicons were subcloned. The serially diluted plasmid, with copy numbers ranging from 101 to 105 copies, was used as a template for both PCRs. Triangles, N-gene-specific PCR; gray lines, 1b-gene-specific PCR. The inset shows CT values for a triplicate set of experiments of both PCRs with different copy numbers of the template. NTC, no-template control. The x axis indicates the cycle number of the quantitative PCR, while the y axis represents the fluorescence.
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FIG. 5. Amplification curve (A) and melting curve (B) of real-time quantitative PCR specific to 1b and N gene of SARS CoV. (A) Amplification plot of fluorescence intensity versus the number of PCR cycles. One-microliter samples of cDNAs from NPA, tracheal dispersion, and lung biopsy samples from patients with clinical symptoms were used as templates for PCRs. Fifty cycles of PCR were performed to achieve the saturation phase of the reaction. The x axis indicates the cycle number of the quantitative PCR, while the y axis represents the fluorescence intensity (FAM-490) above the background signal. The horizontal gray line indicates the threshold value calculated by the maximum curvature approach, and the baseline cycle CT was calculated automatically. The inset shows half-maximal fluorescence values (1/2max) and CT values of both PCRs with cDNAs from various tissues isolated from a key patient (patient A [1]) at three different time points. TW, tracheal wash; LW, lung wash. (B) Melting curves of PCR products. Melting curve analysis was performed after a 10-min further extension step. The Tm rose from 56 to 94°C for 76 0.5-s steps, while each set-point temperature was held for 7 s for data collection and analysis. The Tms of the 1b- and N-gene-specific PCR products were 80.5 and 85.5°C, respectively. The x axis indicates the temperature in degrees Celsius, while the y axis represents the fluorescence intensity (FAM-490) above the background signal. One microliter of water was used as a no-template control in the reaction.
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TABLE 3. Comparison of threshold cycles of 38 SARS-positive samples in N-gene- and 1b-gene-specific PCR assays
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FIG. 6. Northern blot analysis of SARS-CoV total RNA. The total RNA of SARS-CoV was extracted from SARS-CoV-infected Vero E6 cells. The RNA was separated in a 1% denaturing gel containing 6.29% formaldehyde. Afterwards, the RNA was transferred to a positively charged nylon membrane and hybridized with digoxigenin-labeled PCR fragments specific for the 1b, S, M, and N genes. Lane 1, 1b; lane 2, S; lane 3, M; lane 4, N. The vertical bar shows the molecular size reference. Arrows indicated the transcripts hybridized with the N probe. The signals were analyzed by chemiluminescence.
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We thank C. C. Hon, Ken Y. C. Chow, Carol W. M. Chan, and Vince Y. Y. Li (Department of Zoology, HKU) for their efforts in the analysis of the genomic sequence of SARS-CoV strain HK-39. We thank Leo T. O. Lee (Department of Zoology, HKU) for his technical advice on real-time quantitative PCR. We also thank Leo L. M. Poon (Department of Microbiology, HKU) for providing us with clinical samples for this study.
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