Nonisotopic oligomeric probes for the human enteroviruses

Evaluation of a commercially available reverse transcription-PCR enzyme immunoassay (Enterovirus Consensus kit) for the diagnosis of enterovirus central nervous system infections

A commercial reverse transcription (RT)-PCR amplification method was compared with culture for the diagnosis of enterovirus meningitis. In total, 99 cerebrospinal fluid (CSF) specimens were examined with the Enterovirus Consensus kit and shell vial culture. RT-PCR allowed the amplification of enterovirus cDNA and its detection in a microtitre plate by hybridisation. Clinical information and CSF analysis were used to resolve the discrepancy in results. The detection limit of the RT-PCR assay was determined with the Third European Union Concerted Action Enterovirus Proficiency Panel. There were 34 true-positive CSF specimens. Of these, RT-PCR detected 33 (sensitivity 97%), while culture detected 19 (sensitivity 54.5%). RT-PCR failed to detect one culture-positive specimen that contained inhibitors. When samples from the Third European Union Concerted Action Enterovirus Proficiency Panel were tested, the RT-PCR method gave identical results to those expected. The Enterovirus Consensus kit was rapid and statistically more sensitive than culture (p < 0.01) for the detection of enteroviruses in CSF, and may offer considerable benefits in the clinical management of patients with enterovirus meningitis.

Use of heat labile UNG in an RT-PCR assay for enterovirus detection

A reverse transcription-polymerase chain reaction (RT-PCR) assay was developed to replace the Roche AMPLICOR Enterovirus Test used in our laboratory from 1996 to 1999. The new assay design was optimized to match or exceed the performance of the Roche AMPLICOR Enterovirus test kit with respect to analytical sensitivity and specificity, contamination control, ease of use and availability of reagents. This new assay uses a heat labile form of the enzyme uracil DNA glycosylase (UNG) for amplicon contamination control and an RT-PCR enzyme mixture, enabling a one tube/one step amplification. RNA preparation was undertaken using a commercial extraction kit. End detection was accomplished using a probe-capture enzyme immuno assay (EIA) plate format. This EV RT-PCR assay exceeds the performance of the Roche AMPLICOR Enterovirus assay in a direct comparison. The combined enzymological approach has potential application to a wide variety of assays requiring sensitive RNA detection and stringent contamination control, including those utilizing real time detection methods.

Enhancement of the AMPLICOR enterovirus PCR test with a coprecipitant

The incorporation of a commercially available coprecipitant into the AMPLICOR enterovirus PCR test specimen preparation enhanced the sensitivity and reproducibility of this assay. Fifty-five previously tested archived cerebrospinal fluids (CSF) specimens were tested in a blind study in duplicate with and without Pellet Paint coprecipitant (Novagen, Inc., Madison, Wis.). Of these specimens, 26 had previously been determined to be positive and 29 had previously been determined to be negative. All previously positive CSF specimens were positive when Pellet Paint was used and only 18 were positive without Pellet Paint. No previously negative specimens were positive on repeat testing with or without Pellet Paint. The background signal was not affected by the addition of Pellet Paint. These data support the utility of a coprecipitant in minimizing false-negative results.

Evaluation of an enterovirus group-specific anti-VP1 monoclonal antibody, 5-D8/1, in comparison with neutralization and PCR for rapid identification of enteroviruses in cell culture

We evaluated the usefulness of a commercially available monoclonal antibody (MAb) directed against a group-specific epitope of the capsid protein VP1 of enteroviruses for the rapid identification of these viruses in cell culture. The MAb was assayed in an indirect immunofluorescence test with cultured cells infected by various serotypes of enterovirus; all 39 serotypes tested, including echoviruses 22 and 23, which are considered atypical enteroviruses, were reactive. The MAb was also tested with 61 strains recovered from clinical specimens inoculated into cell cultures in comparison with seroneutralization with intersecting pools of hyperimmune sera and PCR with primers from the 5' untranslated region of enteroviruses. There was total agreement between the results obtained with the MAb and those obtained by PCR, even for those strains of enteroviruses which were found to be untypeable with polyclonal antisera. These data demonstrate the usefulness of the MAb for rapid identification of enteroviruses in cell culture.

Quantitation of enteroviral RNA by competitive polymerase chain reaction

The polymerase chain reaction (PCR) is a new diagnostic technique for the detection of enteroviral infection; however, it currently provides only qualitative results. The aim of this study was to adapt PCR for the accurate quantitation of enteroviral RNA in clinical specimens. For this purpose, we designed a standard RNA which was homologous to sequences at the 5' end of the coxsackie B3 enterovirus genome but contained a single-base-pair mutation which created a novel internal restriction site. Serial dilutions of this standard template RNA were mixed with a fixed concentration of coxsackie B3 enterovirus RNA. The viral and standard templates were reversed transcribed to cDNA and coamplified by PCR, and a comparison of the radioactive PCR products was made. Since the templates were both present in a single reaction tube and competed for the same primers, the ratio of products remained proportional throughout the amplification process. By this approach, a fourfold-difference in viral titer was clearly distinguishable. Moreover, we were able to accurately quantitate as few as 15 50% tissue culture infectious doses, which reflects common clinical viral titers. This study lays the foundation for quantitation of enteroviral RNA in clinical specimens and establishes a technique that can readily be applied to the diagnosis of enteroviral infection.

Nested polymerase chain reaction for high-sensitivity detection of enteroviral RNA in biological samples

A method based on nested polymerase chain reaction was developed for the detection of enteroviral genomes in biological samples. By taking advantage of the conserved 5' noncoding region of the enteroviral RNA, two sets of primers were utilized, enabling the detection either of a broad range of enteroviruses or of group B coxsackieviruses only. The sensitivity of the method is close to the detection of single molecules of viral RNA in as much as 1 mg of tissue sample. A preliminary study showed the usefulness of this technique for the analysis of endomyocardial biopsy samples from patients with idiopathic dilated cardiomyopathy and myocarditis.

A simple, rapid and sensitive presence/absence detection test for bacteriophage in drinking water

A rapid, simple and sensitive direct bacteriophage presence detection method for 500 ml drinking water samples has been developed. The method includes a glass device consisting of a jar containing the water sample and an immersible probe filled with solidified soft agar containing bacterial host cells. Host bacteria in logarithmic phase were added to the experimental volume and the probe was submerged. The entire device was incubated in a water bath at 36 degrees C. Plaques of somatic bacteriophage infecting Escherichia coli strain CN13, could be detected within 3 h. Male-specific bacteriophages infecting E. coli F+ amp were detected within 6 h. Bacteriophage infecting the anaerobe Bacteroides fragilis subsp. fragilis HSP40 were detected after 8 h. Application of this device and the associated technique, enabled a one-step detection of 1 pfu of E. coli or Bact. fragilis specific bacteriophage in 500 ml drinking water samples.

Detection of enteroviral RNA in idiopathic dilated cardiomyopathy and other human cardiac tissues

Enteroviruses have been considered to be a possible cause of idiopathic dilated cardiomyopathy. We used a polymerase chain reaction methodology for the identification of enteroviral RNA in an attempt to provide evidence of a role for enteroviruses in the pathogenesis of idiopathic dilated cardiomyopathy. The methodology was shown to identify a wide variety of enteroviruses with a sensitivity up to 0.1-1 plaque-forming units/gram of tissue. 5 of 11 cases (45%) of idiopathic dilated cardiomyopathy, as well as 9 of 24 cases (38%) of a wide variety of other cardiac conditions (including normal heart), were positive for enteroviral nucleic acid sequences; all eight control cases of breast carcinoma tested were negative. These results suggest that both the normal and abnormal heart may represent a site of latent or low-grade persistent enteroviral infection, and that the mere presence of enteroviral nucleic acid sequences is not specifically associated with idiopathic dilated cardiomyopathy.

Detection of enteroviruses in faeces by polymerase chain reaction

A polymerase chain reaction (PCR) technique for the detection of human enteroviruses in stool specimens was developed. The test was based on the synthesis of cDNA, followed by PCR and slot blot hybridization. The primers used were selected from a highly conserved sequence in the 5'non-coding region of the enteroviral genome. By this method 27 different enterovirus serotypes (15 echo, 6 coxsackie A, 4 coxsackie B, poliovirus type 2 and enterovirus 71) from 89 patients could be detected. Using positive virus culture as reference, the sensitivity of PCR was 69% after 30 cycles of amplification, 91% using 30 + 10 cycles and 100% following 2 rounds of amplification with ensuing hybridization. None of 23 stool samples from healthy individuals or patients with meningitis of proven non-enteroviral etiology were positive by the PCR. By contrast, 13/26 culture-negative, randomly chosen stool samples from patients with suspected enteroviral disease were positive by the test. These findings demonstrate a high sensitivity and an apparently high specificity of PCR for detection of enteroviruses in stool samples. Therefore, the methodology may be useful in the laboratory diagnosis of enterovirus infections.

Nucleic acid detection systems for enteroviruses

The enteroviruses comprise nearly 70 human pathogens responsible for a wide array of diseases including poliomyelitis, meningitis, myocarditis, and neonatal sepsis. Current diagnostic tests for the enteroviruses are limited in their use by the slow growth, or failure to grow, of certain serotypes in culture, the antigenic diversity among the serotypes, and the low titer of virus in certain clinical specimens. Within the past 6 years, applications of molecular cloning techniques, in vitro transcription vectors, automated nucleic acid synthesis, and the polymerase chain reaction have resulted in significant progress toward nucleic acid-based detection systems for the enteroviruses that take advantage of conserved genomic sequences across many, if not all, serotypes. Similar approaches to the study of enteroviral pathogenesis have already produced dramatic advances in our understanding of how these important viruses cause their diverse clinical spectra.

Common and specific sequences in picornaviruses

Enteroviruses and rhinoviruses were studied by nucleic acid hybridization using oligonucleotide probes. The reactivity of these sequences varied from serotype specificity to wide reactivity with nearly all human picornaviruses tested. Widely reactive sequences were from the 5' non-coding region while specific oligonucleotides were found from the coding region. Sequences that were common to both enteroviruses and human rhinoviruses were identified and one of the oligonucleotides reacted with a majority enterovirus serotypes.

Molecular detection and identification of enteroviruses using enzymatic amplification and nucleic acid hybridization

Analysis of enteroviral genomes has revealed that the 5' nontranslated region is highly conserved, providing consensus sequences for the design of oligonucleotides which should anneal to most, if not all, human enteroviral RNAs. We designed and used a pair of such generic primers to enzymatically amplify cDNA from coxsackievirus group B types 1 through 6, poliovirus types 1 through 3, 4 coxsackievirus A types, and 29 echoviruses. The polymerase chain reaction (PCR) products generated with these enteroviral primers were analyzed by agarose gel electrophoresis, Southern blotting, or slot blot hybridization. A genotype-specific PCR was used to detect coxsackievirus B3, to the exclusion of other enteroviruses, by using a coxsackievirus B3 genome-specific primer pair that was derived from sequences coding for part of a capsid protein. A technique is demonstrated by which individual genotypes, for which no sequence information is known, can be identified by high-criterion hybridization analysis following amplification with generic enterovirus PCR primers.

A structural model for the genome of echovirus 22

We have proposed previously that the structural model for the echovirus 22 genome is a single-stranded RNA molecule that has folded back upon itself to form a stable "hairpin" at the 5'-terminus. The vRNA of echovirus 22 has been characterized further by digestion with selective ribonucleases, electrophoresis in composite gels, hydrodynamic studies in density gradients of Cs2SO4 and sucrose, thermal denaturation and 3'-terminal ribonucleotide analysis. Based on these observations, the genome of echovirus 22 is a single-stranded RNA molecule having a region of secondary structure located at the 5'-terminus that may be characterized as a snapback hairpin with hydrogen-bonded base-pairing. In addition, a VPg-like protein is attached (presumably to the 5'-end of the RNA) and the 3'-terminus contains a polyadenylic acid tract [poly (A)].

Enzymatic RNA amplification of the enteroviruses

Enteroviruses are among the most common causes of childhood infection. Current diagnostic techniques are often too slow and too insensitive to benefit the patient optimally. This report describes a modified polymerase chain reaction technique by which enteroviral RNA can be amplified, over a few hours, to a level detectable by agarose mini-gel electrophoresis or nucleic acid hybridization or both. Three oligomeric regions of great homology among the enteroviruses were identified and designated as a potential primer pair and probe. With this combination, all 11 of the enterovirus serotypes tested, representing the major subgroups of these pathogens, were successfully amplified and detected. The sensitivity and rapidity of this new assay speak to its potential clinical applicability in the diagnosis of enterovirus infections.

Identification of human picornaviruses by nucleic acid probes

Human picornaviruses include rhinoviruses and enteroviruses which are responsible for both common and severe clinical diseases. Rhinoviruses are a frequent cause of respiratory infections while members of enterovirus subgroups, polio, coxsackie and ECHO viruses are often responsible for infections of the central nervous system, myocarditis, myositis etc. Human picornaviruses consist of nearly two hundred serotypes and therefore their specific identification after virus isolation, or the diagnosis based on the detection of immune response in patients, is problematic and does not usually provide virological diagnosis at the acute phase of illness. New methods for detection of picornavirus genomic RNA together with increasing knowledge of the nucleotide sequences of this virus group offer interesting possibilities for diagnostic procedures. Spot hybridization, in situ hybridization and enzymatic amplification of specific sequences have successfully been used for this purpose. Probes covering the 5' non-coding part of the genome, and also sequences derived from the region coding for non-structural proteins, can be used as broadly reacting reagents in picornavirus detection. Specific sequences are mainly found in the capsid protein region of the genome. cDNA probes and synthetic oligonucleotides are useful in rapid identification of picornaviruses after amplification in cell cultures and in epidemiological analysis. The biochemical amplification methods may enable recognition of picornaviruses directly in clinical samples in the near future. In situ hybridization methods have been of special interest because they can be used to reveal the presence of enterovirus genomes in biopsy specimens from e.g. affected heart muscle in patients with myocarditis and cardiomyopathy.