Detection of human rotavirus by using an alkaline phosphatase-conjugated synthetic DNA probe in comparison with enzyme-linked immunoassay and polyacrylamide gel analysis

Detection of cilia-associated respiratory bacillus in experimentally and naturally infected mice and rats by the polymerase chain reaction

Cilia-associated respiratory (CAR) bacillus was detected by means of the reverse transcription (RT)-polymerase chain reaction (PCR), and the results were compared with those of indirect immunofluorescence test (IFAT) for the detection of the organism. In the experimental infections, 15 mice were in contact with mice previously inoculated with CAR bacillus. Three mice each were tested at days 3, 5, 7, 12 and 20 postexposure. On day 3 postexposure, CAR bacillus was detected in oral swab samples from all 3 mice by RT-PCR, but was not detected in any sampling sites from the mice by IFAT. Total numbers of positive samples from nasal, oral and tracheal swabs obtained through the test were 6/15, 14/15 and 8/15, respectively, by RT-PCR, and 2/15, 6/15 and 3/15, respectively by IFAT. For the detection of CAR bacillus in samples from 52 rats, 34 serum antibody negative rats by enzyme-linked immunosorbent assay were also negative by RT-PCR and IFAT except for one sample from the oral cavity, and all serum antibody positive rats were positive for the organism by RT-PCR but it could not be detected in five of them by IFAT. By means of RT-PCR, no differences in the positive rates depending on sampling sites were observed except in one rat. The RT-PCR was found to be a specific, highly sensitive and reliable procedure for detecting CAR bacillus in mice and rats. The oral cavity was the most suitable site for the diagnosis of the early stage of this infection by RT-PCR.

Rotavirus detection by dot blot hybridization assay using a non-radioactive synthetic oligodeoxynucleotide probe

A synthetic oligodeoxynucleotide of 40 nucleotides corresponding to nucleotides 33-72 of the gene coding for the viral protein VP7 of rotavirus, was used as a nucleic acid probe to develop a non-radioactive hybridization method for rotavirus detection. The probe was labelled at the 3' end with biotin-7-dATP. The sensitivity and specificity of the dot blot hybridization assay for rotavirus detection was evaluated with 303 stool specimens. The results indicate that the hybridization assay has a higher sensitivity than both PAGE and EIA. Among the rotavirus strains tested 37 different electropherotypes were found. The results suggest that rotavirus diagnosis by dot hybridization using a non-radioactive probe may become routine laboratory procedure because it is simple, highly specific and very sensitive.

Detection of hepatitis B virus DNA in serum with nucleic acid probes labelled with 32P, biotin, alkaline phosphatase or sulphone

To facilitate the clinical application of dot-blot hybridization for assaying hepatitis B virus (HBV) DNA, we compared the ability of nucleic acid probes labelled with 32P or with various non-radioactive markers to detect HBV DNA in patient serum. Cloned HBV DNA was hybridized with (1) 32P-labelled HBV DNA cloned in M13, (2) the 32P-labelled HBV RNA probe included in the HepProbe kit, (3) an alkaline phosphatase-labelled synthetic oligonucleotide of HBV, (4) biotin-labelled HBV DNA, and (5) sulphonated HBV DNA. Detection was either by autoradiography or an enzymatic colour reaction. The lowest level of detection of cloned HBV DNA was achieved with the 32P-labelled HBV RNA probe (0.3 pg HBV DNA, corresponding to 3 x 10(4) genomes in 50 microliters), followed by the 32P-labelled DNA probe (0.3-2 pg), sulphonated DNA (1-2 pg), biotin-labelled DNA (4 pg), and an alkaline phosphatase-labelled synthetic oligonucleotide (30 pg). Subsequently, sera from 159 patients with various constellations of HBsAg, HBeAg, and anti-HBe were tested with the most sensitive radioactive method (HepProbe) and the corresponding nonradioactive method (sulphonation). The overall concordance rate was 71% (r = 0.42). Compared with HepProbe results, sulphonation showed a sensitivity of 80% and a specificity of 67%. We conclude that radiolabelling (in particular 32P-labelling of HBV RNA) still allows the most sensitive and reliable detection of HBV DNA in patient serum using conventional dot-blot hybridization.

Improved detection of rotavirus RNA in dot-blot hybridization assay by chromatographic extraction and acid denaturation of double-stranded RNA

One of the commonest methods of denaturing nucleic acids, denaturation by heat, was found to be ineffective for double-stranded (ds)RNA when RNA preparations contain 200 mM or higher concentrations of NaCl. We report acid denaturation of dsRNA (incubation for 10 min in the presence of 80 mM HCl) was particularly useful for such preparations. When genomic dsRNAs of rotavirus were extracted by ion-exchange chromatography columns (Extractor) and then denatured by acid, the detection of rotavirus RNA in stool specimens by the previously reported dot-blot hybridization assay (Yamakawa, K. et al. (1989). Molecular and Cellular Probes 3, 397-401.) was significantly improved.

Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes

A dot blot hybridization assay is described for the detection and differentiation of porcine rotavirus serotypes. Recombinant complementary DNA (cDNA) representing gene 9 (the gene encoding the neutralization antigens in VP7 glycoprotein) from OSU (porcine rotavirus serotype 1) and Gottfried (porcine rotavirus serotype 2) strains were used to determine the optimal hybridization conditions which allow specific detection of group A porcine rotaviruses. Probes were prepared by excision of the inserts from the recombinant plasmids and radiolabeling of cDNA with 32P by the random primer extension method. Probes were hybridized at various stringencies with viral RNA from different rotavirus serotypes bound to nylon membranes. Hybridization at low stringency (26% base pair mismatch for stable hybrid formation) had high sensitivity but low specificity. Hybridization at high stringency (16% base pair mismatch for stable hybrid formation) produced high specificity but decreased the sensitivity observed at low stringency. Probes were specific for rotavirus at both stringencies and did not hybridize with nucleic acids from other porcine viruses. Subgenomic gene 9 fragments were then tested to provide more specific probes. A 322 bp fragment from OSU gene 9 between nucleotides 382 and 704 and a 266 bp fragment from Gottfried gene 9 between nucleotides 230 and 496 were found to be specific as hybridization probes. These studies demonstrated the feasibility of the dot blot hybridization assay using subgenomic fragments of gene 9 to detect and differentiate serotypes of porcine rotavirus. Additional studies are warranted to further evaluate the sensitivity and the capability of these probes to detect porcine field isolates of the same serotype.

Use of an alkaline phosphatase-labeled synthetic oligonucleotide probe for detection of Campylobacter jejuni and Campylobacter coli

A commercially available synthetic nucleic acid probe (SNAP) conjugated to alkaline phosphatase was compared with standard culture techniques for detecting Campylobacter species. The SNAP was able to detect either 5 ng of C. jejuni DNA or 10(5) CFU of bacteria. The SNAP could also detect DNA extracted from 10(5) CFU in mock-infected stool samples. The SNAP detected C. jejuni and C. coli but showed no reactivity with C. laridis, C. fetus subsp. fetus, C. fetus subsp. venerealis, C. fennelliae, "C. upsaliensis," C. cinaedii, C. fecalis, C. hyointestinalis, C. mucosalis, or Helicobacter (Campylobacter) pylori. The SNAP also showed no cross-reactivity with other enteric pathogens. When applied to pure cultures, the SNAP detected 55 clinical isolates of C. jejuni and 11 clinical isolates of C. coli, with an accuracy of 100%. When applied directly to clinical specimens, the SNAP detected Campylobacter spp. in 19 of 23 culture-positive stool specimens (sensitivity, 82.6%; specificity, 100%). Pure cultures of the Campylobacter strains isolated from the four probe-negative, culture-positive stool specimens gave positive reactions with the SNAP. While the SNAP had excellent sensitivity and specificity for isolated bacterial colony isolates, the main limitation to the Campylobacter probe detection kit may be the sensitivity limit on direct detection of Campylobacter organisms in stools.

Identification of rotaviruses by dot-blot hybridization using an alkaline phosphatase-conjugated synthetic oligonucleotide probe

We have evaluated a recently-developed dot-blot hybridization assay for the detection of human rotaviruses using an alkaline-phosphatase conjugated oligonucleotide probe. The lower detection limit of this assay was 1 ng (approximately 5 x 10(7) copies) of the double-stranded (ds) RNA, when a purified preparation from serotype 1 human rotavirus was used but appeared to be much higher when applied on clinical specimens. This assay could detect dsRNA from rotavirus strains belonging to serotypes 1 through 6, 8 and 9. A total of 235 stool specimens were used to evaluate the oligonucleotide probe assay in comparison with polyacrylamide gel electrophoresis and latex agglutination assay (Rotalex). When polyacrylamide gel electrophoresis was used as a gold standard, sensitivity, specificity and positive and negative predictive values of the probe assay were 84, 100, 100 and 89%, respectively. These values were slightly better than those of Rotalex assay which is commonly used in clinical laboratories in Japan. Although the probe assay requires more hands-on time than the immunoassays, the high specificity of this probe assay recommends it as a confirmatory test in the clinical laboratory setting.