Advances in the use of nucleic acid probes in diagnosis of viral diseases of man. Brief review

Human papillomavirus detection in cervical dysplasias or neoplasias and in condylomata acuminata by in situ hybridization with biotinylated DNA probes

Specimens from cervical dysplasias or carcinomas and genital condylomata acuminata were retrospectively analysed by in situ hybridization (ISH) with biotinylated DNA probes for human papillomavirus (HPV) types 6, 11, 16 and 18. In the control group no case was positive for HPV DNA. In mild/moderate dysplasias, 4 cases (14%) were positive for HPV 6 or 11 and 2 cases (7%), for HPV 16. In the severe dysplasia/in situ carcinoma group, 9 cases (31%) showed presence of DNA of HPV types 16 or 18. Six invasive carcinomas (20%) were positive for HPV type 16 or 18. Among condylomata acuminata, 22 cases (73%) were positive for HPV types 6 or 11. In all ISH-positive cases only one viral type was detected. No correlation between HPV DNA positivity and histological findings of HPV infection was observed. Although less sensitive than some other molecular biology techniques, in situ hybridization with biotinylated DNA probes proved to be simple and useful for detecting and typing HPV in samples routinely received for histopathological analysis.

Comparison of four in situ hybridization methods, based on digoxigenin- and biotin-labelled probes, in detecting HPV DNA in male condylomata acuminata

We have compared the efficacy of digoxigenin- and biotin-labelled probes in detecting HPV DNA by in situ hybridization on paraffin-embedded tissue sections of 57 male condyloma-suspect genital lesions. Each biopsy was hybridized with at least three of the following four methods: digoxigenin-labelled HPV DNA probes (Dig-HPV), biotinylated HPV-DNA probes (Bio-HPV), and two commercial methods (ViraType in situ and PathoGene), both based on biotinylated DNA probes. The hybridization products were visualized with colourigenic enzyme substrates. In most biopsies, the 4 methods gave equal results although cross-hybridization was most often found with the low-stringency ViraType method. Dig-HPV 6/11 probes gave positive results about twice as often as either of the commercial methods. No such difference, however, was found for HPV 16/18 probes. DNA of any type of HPV 6/11, 16/18 or 31/33/35 or 51 was detected in 28/43 (65%) of lesions showing condyloma acuminatum histology but in none of the 14 biopsies with no histological signs of HPV infection. In HPV-positive condylomata with no cellular atypia. HPV 6/11 was detected in 87% (13/15), and HPV 16/18 in 27% (4/15). In biopsies with cellular atypia, HPV types 6/11 were detected in 62% (8/13), HPV types 16/18 in 46% (6/13), and HPV types 31/33/35 or 51 in 50% (6/12). In about 50% of the biopsies where at least one hybridization method gave a positive result, either one of the commercial methods gave a negative result.(ABSTRACT TRUNCATED AT 250 WORDS)

Identification of thermotolerant Campylobacter species from poultry using an enzyme-labelled oligonucleotide DNA probe

A commercially available enzyme-labelled DNA probe for human Campylobacter strains has been tested and also found to hybridize with DNA from C. jejuni and C. coli isolates from poultry. DNA from 11 enteric, non-campylobacter organisms, included in the test as negative controls, failed to hybridize with the probe indicating that the probe might be used for identification of campylobacter from poultry too.

Applications of nucleic acid probes in veterinary infectious diseases

Nucleic acid probe technology is increasingly being used in basic research in veterinary microbiology and in diagnosis of infectious diseases of veterinary importance. This review presents an overview of nucleic acid probe methodology and its applications in veterinary infectious diseases. The major applications of nucleic acid probes include detection of pathogens in clinical samples, especially those organisms which are fastidious and difficult to cultivate, differentiation of virulent from avirulent organisms and vaccine strains from wild type isolates, typing of microorganisms, mapping genes, screening libraries of cloned DNA for specific genes, detection of latently infected or carrier animals, study of mechanisms of pathogenesis, epidemiological studies and food safety.

Rapid and simple method for purification of nucleic acids

We have developed a simple, rapid, and reliable protocol for the small-scale purification of DNA and RNA from, e.g., human serum and urine. The method is based on the lysing and nuclease-inactivating properties of the chaotropic agent guanidinium thiocyanate together with the nucleic acid-binding properties of silica particles or diatoms in the presence of this agent. By using size-fractionated silica particles, nucleic acids (covalently closed circular, relaxed circular, and linear double-stranded DNA; single-stranded DNA; and rRNA) could be purified from 12 different specimens in less than 1 h and were recovered in the initial reaction vessel. Purified DNA (although significantly sheared) was a good substrate for restriction endonucleases and DNA ligase and was recovered with high yields (usually over 50%) from the picogram to the microgram level. Copurified rRNA was recovered almost undegraded. Substituting size-fractionated silica particles for diatoms (the fossilized cell walls of unicellular algae) allowed for the purification of microgram amounts of genomic DNA, plasmid DNA, and rRNA from cell-rich sources, as exemplified for pathogenic gram-negative bacteria. In this paper, we show representative experiments illustrating some characteristics of the procedure which may have wide application in clinical microbiology.

Detecting Viruses in Water

Various and divergent approaches that have been used to concentrate and assay viruses from tap water and environmental freshwaters are summarized and briefly explained. The basic principles behind the different methodologies and descriptions of the most recent developments are emphasized. Comparisons help demonstrate the relative sensitivities of different concentration and assay techniques.

Analysis of parvovirus infections using strand-specific hybridization probes

The autonomous parvoviruses cause a broad spectrum of acute and chronic infections of animals and man. The discrimination of sites of viral replication from sites of viral sequestration is an important goal in elucidating the pathogenesis of these diseases. It is possible to employ strand-specific RNA hybridization probes in such analyses because a 'plus' sense probe will react with single stranded virion DNA and duplex replicative form DNA, but a 'minus' sense probe will react preferentially with obligate replicative intermediates (duplex replicative form DNA and mRNA). Strand-specific RNA hybridization probes were developed for the Aleutian mink disease parvovirus (ADV) and were used to study acute and chronic infections of mink. Such probes were capable of differentiating replicative intermediates (duplex replicative form DNA and mRNA) from single-stranded virion DNA in Southern blot analysis and in strand-specific in situ hybridization. ADV infection of seronegative newborn mink kits causes an acute, cytopathic infection of type II alveolar cells. Replication in these cells is highly permissive and is characterized by high levels of replicative intermediates and virion DNA. A fatal respiratory distress syndrome and hyaline membrane formation result from impaired surfactant production by the infected type II cells. On the other hand, ADV infection of adult mink is associated with a persistent infection and a disorder of the immune regulation. The target cells for viral replication in adult mink are confined to the lymphoid system and the bone marrow. Replication in these cells, which are probably lymphocytes, is restricted, and characterized by greatly reduced levels of replicative intermediates and virion DNA. It, therefore, seems that disease in the infected adult mink results from a restricted infection by ADV. Large amounts of virion DNA can also be demonstrated in locations where replication cannot be detected and apparently represents sequestration of virion particles by elements of the reticuloendothelial system. Thus, replication and sequestration can, in fact, be distinguished by the strand-specific in situ hybridization. These studies indicate that strand-specific in situ hybridization is a potentially valuable method for studying the pathogenesis of parvovirus infections.

Detection of parvovirus B19 DNA in fetal tissues by in situ hybridisation and polymerase chain reaction

Attempts were made to detect human parvovirus B19-DNA by in situ hybridisation and the polymerase chain reaction in placental and fetal tissues from a case of intrauterine fetal death. In the in situ hybridisation experiments radioactive and non-radioactive (labelled with 2-acetyl-aminofluorene, AAF) DNA probes were used. B19-DNA was detectable in paraffin wax embedded fetal tissue from the liver, heart, lung, brain and thymus. The resolution with the AAF-labelled probes was higher than with the radiolabelled DNA. Parvovirus B19 DNA sequences were also detected in these tissues by an enzymatic in vitro amplification technique--the polymerase chain reaction. Amplification of a B19-DNA sequence before detection increases the rapidity and sensitivity of detection. The rapid, specific, and sensitive analysis of parvovirus B19 in normal and diseased tissues using these techniques may contribute considerably to determining the role of this virus as a risk factor in the outcome of pregnancy.

Candida albicans- and Candida stellatoidea-specific DNA fragment

DNA was isolated from whole cells of Candida albicans and digested with MspI restriction enzyme. In addition to the expected large number of low-molecular-weight DNA pieces resulting from the digestion, multiple high-molecular-weight (greater than 3.0 kilobase pairs) fragments were generated by this enzyme, which cleaves DNA at CCGG sequences. Some of these fragments appeared highly repeated. An MspI fragment which was similar in size to one of the repeat elements (2.9 kilobase pairs) was cloned into the ClaI site of the plasmid vector pBR322 and replicated in a suitable Escherichia coli host strain. The candidal fragment was radiolabeled and used to probe Southern blots of DNA from several Candida species, various other fungi, and mouse and human cells. Only DNA from C. albicans and a strain of Candida stellatoidea was found to contain sequences of significant homology for hybridization. The cloned fragment may possibly be of use as a DNA probe for detection of the presence of C. albicans.

Synthetic oligonucleotide probes for the detection of human papilloma viruses by in situ hybridisation

Using the published nucleotide sequence data for human papilloma virus (HPV) types 1, 6 and 16, sequences of 30 bases in length from the beginning of the E6 open reading frame (ORF) were selected. Oligonucleotides were synthesised on an Oswel Gene Synthesizer and labelled at the 3' end with biotin using the enzyme terminal transferase. In situ hybridisation was carried out on paraffin sections of wart and cervical tissues mounted on silanated slides. A 2 h hybridisation step allowed the whole process to be completed within one working day. The technique successfully demonstrated the presence of HPV-1 in skin warts, and of HPV-6 and HPV-16 in genital warts and cervical lesions. This simple approach has diagnostic potential for the detection and typing of papilloma viruses in biopsy material.

Bovine herpesvirus 1: rapid diagnosis of infection by direct filter hybridization

Direct filter hybridization (DFH) was applied as a simple method of nucleic acid hybridization to diagnose bovine herpesvirus 1 (BHV-1) infection without previous purification of nucleic acids from the specimens. The DNA of BHV-1 was cleaved with the restriction endonuclease Pst I and randomly cloned into pKH47 plasmids. The clones were labelled with 32P or biotin and selected on uninfected and infected cells for the highest specific activity to detect BHV-1 infection. Two clones, which detected about 10 infected cells, were selected for the diagnosis of BHV-1 in cattle. On specimens collected during experimental and natural disease, the DFH showed to be in concordance with the standard method of virus isolation. This simple hybridization technique proved to be a sensitive and rapid alternative to virus isolation. Specific diagnosis of BHV-1 infection can be made even in simply equipped laboratories within 10 h.