Cytomegalovirus in urine: detection of viral DNA by sandwich hybridization

Transrenal DNA testing: progress and perspectives

Transrenal DNA (Tr-DNA) is a recently discovered class of extracellular urinary DNA that originates from cells dying throughout the body. Postapoptotic DNA is known to appear in the circulating plasma, but it is now recognized that a portion of these fragments cross the kidney barrier and appear in urine in the form of 150-200-bp fragments. Tr-DNA containing fetal sequences has been isolated from the urine of pregnant women, tumor-specific mutations have been detected in Tr-DNA from patients with colon and pancreatic tumors, and donor DNA has been found in Tr-DNA isolated from recipient urine. Furthermore, proviral HIV DNA, bacterial and parasite DNA sequences have been detected in Tr-DNA from infected patients. Potential applications of Tr-DNA-based tests cover a very broad area of molecular diagnostics and genetic testing, including prenatal detection of inherited diseases, tumor diagnostics and therapeutic monitoring and detection of infectious agents. The Tr-DNA test is expected to have utility in treatment monitoring, transplantation monitoring, drug development and broad public health screening, where a noninvasive, common-platform diagnostic technology has particular value. This review describes some of the highlights of Tr-DNA technology applications, advantages over existing technologies and potential problems anticipated in test development.

Bacillus anthracis: toxicology, epidemiology and current rapid-detection methods

B. anthracis, the causative agent for anthrax, has been well studied for over 150 years. Due to the genetic similarities among various Bacillus species, as well as its existence in both a spore form and a vegetative state, the detection and specific identification of B. anthracis have been proven to require complex techniques and/or laborious methods. With the heightened interest in the organism as a potential biological threat agent, a large number of interesting detection technologies have recently been developed, including methods involving immunological and nucleic acid-based assay formats. The technologies range from culture-based methods to portable Total Analysis Systems based on real-time PCR. This review with 170 references provides a brief background on the toxicology and epidemiology of B. anthracis, discusses challenges associated with its detection related to genetic similarities to other species, and reviews immunological and, with greater emphasis, nucleic acid-based detection systems.

Cytomegalovirus infection and viral shedding in the genital tract of infertile couples

The prevalence of cytomegalovirus (CMV) infection and viral shedding in infertile couples in Taiwan and its role in infertility were studied. Two hundred fifty couples were enrolled in this study. Anti-CMV IgG was measured in serum samples from these infertile couples. Viral shedding examined by DNA hybridization was detected in semen from the husband and cervical mucus from the wife. Anti-CMV IgG was detected in 249 (99.6%) of the 250 male serum samples and in 247 (98.9%) of the 250 female serum samples. Viral shedding was detectable in 83 (33.5%) of 248 semen samples and 83 (33.7%) of 246 cervical mucus samples by dot-blot DNA hybridization assay. Semen quality was not apparently affected by the existence of viral shedding. The co-shedding rate in semen and cervical mucus was high (15.9%). It is concluded that the seroprevalence and genital tract viral shedding were relatively high in infertile couples in Taiwan. Viral shedding did not affect the semen quality. Nevertheless, screening of donor semen is recommended.

Specificity of molecular hybridization techniques for the detection of bluetongue virus serotypes in Culicoides variipennis

Direct blot hybridization (DBH) and sandwich hybridization (SH) were evaluated for their ability to detect bluetongue virus (BTV) RNA in the biting midge Culicoides variipennis (Coquillett). Probes were derived from the L3 RNA segment of BTV, serotype 17. RNA of the five BTV serotypes occurring in the USA (BTV-2, BTV-10, BTV-11, BTV-13, and BTV-17) was extracted from pools of varying numbers of infected and uninfected biting midges and assayed by direct blot and sandwich hybridization tests. Direct blot hybridization using an RNA transcript probe or cDNA probe was a fast, efficient and sensitive technique, detecting as few as one midge infected with any BTV serotype in a pool of 50 or 100. Sandwich hybridization was able to detect the homologous serotype, BTV-17, in pools containing a single infected midge in a total of 50 or 100. However, detection of the heterologous serotypes, BTV-10, BTV-11, and BTV-13, was limited to pools containing 5 or more infected midges in a total of 50, and BTV-2 was undetectable by SH. Hybridization techniques provide an alternative to the conventional detection methods of inoculation of cell culture or embryonated chicken eggs for detection of BTV.

Rapid diagnosis of cytomegalovirus infections by direct immunoperoxidase staining with human monoclonal antibody against an immediate-early antigen

Direct immunoperoxidase technique using a horseradish peroxidase (HRP)-conjugated Fab' fragment of human monoclonal antibody (humab C7), designated HRP-C7, was evaluated as a rapid diagnosis of cytomegalovirus (CMV) infection. A total of 138 clinical specimens consisting of 124 urine samples and 14 oral swabs were examined for CMV by the direct HRP-C7 staining in comparison with conventional virus isolation. The number of CMV-positive samples by each method was 40 (29.0%) for the former and 37 (26.8%) for the latter, respectively. By HRP-C7 staining, CMV was identifiable within 24 hr after inoculation. By conventional isolation method, an average of 10.3 days had passed before cytopathic effect characteristic of CMV appeared in the cell culture. Some false-positive and false-negative cases were discussed in relation to toxicity of urine samples, storage of the samples, and amount of CMV in the sample. The sensitivity and specificity of HRP-C7 method against conventional isolation method were 89.2% and 93.1%, respectively. Thus, HRP-C7 staining is useful for a rapid diagnosis of CMV infections.

Preparation of europium-labelled DNA probes and their properties

A chemical method for labelling DNA with a europium chelate is presented. First, primary aliphatic amino groups are introduced onto DNA in a transamination reaction. The transamination reaction is altered by adjusting temperature and duration of the reaction. Subsequently, the modified DNA is reacted with an isothiocyanate derivative of a Eu chelate. The optimum amount of Eu chelates on a DNA probe is 4-8% of total nucleotides. There is a decrease of 0.7 degrees C in the melting temperature of DNA for each incorporated Eu chelate on 100 bases. Hybridization efficiency is lowered by the introduction of Eu chelates but this effect can be partly overcome by using high DNA probe concentrations. The detection limit of the Eu-labelled probe is 0.15 attomoles of target DNA in a mixed-phase hybridization assay on microtitration wells. In addition to high sensitivity the Eu-labelled probes offer convenience in use and results which are quantitative and easy to interpret.

DNA probes: applications of the principles of nucleic acid hybridization

Nucleic acid hybridization with a labeled probe is the only practical way to detect a complementary target sequence in a complex nucleic acid mixture. The first section of this article covers quantitative aspects of nucleic acid hybridization thermodynamics and kinetics. The probes considered are oligonucleotides or polynucleotides, DNA or RNA, single- or double-stranded, and natural or modified, either in the nucleotide bases or in the backbone. The hybridization products are duplexes or triplexes formed with targets in solution or on solid supports. Additional topics include hybridization acceleration and reactions involving branch migration. The second section deals with synthesis or biosynthesis and detection of labeled probes, with a discussion of their sensitivity and specificity limits. Direct labeling is illustrated with radioactive probes. The discussion of indirect labels begins with biotinylated probes as prototypes. Reporter groups considered include radioactive, fluorescent, and chemiluminescent nucleotides, as well as enzymes with colorimetric, fluorescent, and luminescent substrates.

A rapid solution hybridization method for detection of human papillomaviruses

Nucleic acid hybridization methods in routine diagnosis of micro-organisms have been limited by the tedious assay procedures. We have previously described the sandwich hybridization method which allows convenient testing of biological specimens. In this paper we describe the adaptation of the solution hydridization method into the microtitre plate format using 35S-isotope as label. Using 3-hour hybridization followed by 2-hour collection of the hybrids a sensitivity of 5 x 10(5) target DNA molecules was achieved. The method was applied for identification of human papillomaviruses in crude gynaecological specimens. A simple 1-day assay protocol was achieved with high HPV type specificity. The specificity was confirmed by testing a variety of unrelated micro-organisms, none of which gave a positive signal in the test. Results, obtained as numerical values, were easy to interpret; positive and negative samples gave clearly distinguishable signals.

Detection of bluetongue virus serotype 17 in Culicoides variipennis by nucleic acid blot and sandwich hybridization techniques

Molecular hybridization techniques were developed for the detection and surveillance of bluetongue virus (BTV) serotype 17 in the insect vector Culicoides variipennis, a biting midge. Radiolabeled RNA and cDNA probes were generated from sequences of the L3 segment of BTV serotype 17. These probes were used to detect BTV RNA in pools of infected C. variipennis by hybridizing the probes directly to analyte immobilized on nylon membranes or by using a nucleic acid sandwich hybridization test. Hybridization procedures were able to detect 1 infected C. variipennis in a pool of 50 and as little as 3.55 log10 50% tissue culture infective doses per ml of virus. These hybridization techniques provide an alternative to virus isolation for the surveillance of BTV in vector populations.

Affinity-based collection of amplified viral DNA: application to the detection of human immunodeficiency virus type 1, human cytomegalovirus and human papillomavirus type 16

We have devised a sensitive and convenient hybridization technique by combining the polymerase chain reaction (PCR) with affinity-based hybrid collection. In this method 5'-biotinylated primers are used to introduce biotin residues into the DNA fragments during the amplification. The amplified DNA fragments are detected by liquid hybridization using a 32P- or 35S-labelled oligonucleotide as probe. For measurement the hybrids are collected on polystyrene microparticles or onto microtitre wells taking advantage of the biotinavidin interaction. The method is highly sensitive allowing the detection of 30 molecules of DNA. It involves few and simple operations, and is thus suitable for routine diagnostics. The applicability of the method to the detection of HIV-1 DNA from blood, HCMV DNA from urine and HPV-16 DNA from cervical scrapes was evaluated.

Detection of human cytomegalovirus early and late antigen and DNA production in cell culture and the effects of dimethyl sulfoxide, dexamethasone, and DNA inhibitors on early antigen induction

Recently a conventional method for the laboratory diagnosis of human cytomegalovirus (HCMV) infection was improved by using centrifugation culture to enhance viral adsorption and by detecting HCMV early antigen and DNA. Comparison of the sensitivity of three rapid methods using commercial diagnostic reagents for the detection of HCMV early antigen (EA), late antigen (LA), and DNA was quantitatively evaluated in centrifugation cultures of human fibroblast cells (MRC-5) infected with HCMV. HCMV-EA was first detected 4 hours after infection, and the number of antigen-positive cells increased rapidly thereafter. Using biotinylated DNA probe, viral DNA was first detected 12 hours postinfection; the number of DNA-positive cells increased slowly. HCMV-LA was first seen 48 hours postinfection, and the number of LA-positive cells also increased thereafter. Thus detection of HCMV-EA was the most rapid and sensitive method for HCMV diagnosis. Several chemical compounds have been used to enhance HCMV replication. The effect of dimethyl sulfoxide (DMSO), dexamethasone (DEX), 5-bromo-2-deoxyuridine (BrdU), 5-fluoro-deoxyuridine (FdU), and cytosine arabinoside (Ara-C) on HCMV-EA induction was evaluated in centrifugation cultures of MRC-5 cells infected with HCMV. Infected cells treated with 1% DMSO alone or with DMSO plus DEX (10(-5) M) have been shown to increase the number of HCMV-EA-positive cells three- to fivefold over the untreated control cultures. The enhancing effects of Ara-C, BrdU, and BrdU plus FdU were demonstrated only occasionally.

Primer-mediated enzymatic amplification of cytomegalovirus (CMV) DNA. Application to the early diagnosis of CMV infection in marrow transplant recipients

A nucleic acid amplification procedure, the polymerase chain reaction (PCR), has been used to establish a diagnostic assay for the identification of cytomegalovirus (CMV) immediate-early sequences in clinical specimens. Preliminary testing against virus-infected cell cultures indicated that the PCR assay was highly CMV-specific, recognizing both wild-type and laboratory strains of CMV. There was no cross-reactivity with human DNA or with DNA from other herpes viruses. The sensitivity of the assay, using cloned CMV AD169 Eco RI fragment-J as template, was 1 viral genome per 40,000 cells. In a prospective study of CMV infection in bone marrow transplant recipients, the PCR assay correctly identified four patients with confirmed CMV infection. In three of these patients who were followed longitudinally, correlation of DNA reactivity with CMV culture and CMV antibody status over time indicated that DNA was the most sensitive marker for the diagnosis of CMV infection.

Cytomegalovirus detection by biotinylated DNA probes

Clinical specimens from 317 patients suspected of cytomegalovirus infection were examined by immunofluorescence (IF) using monoclonal antibodies and by a biotinylated DNA probe kit after cell culture isolation. Of the 317 samples, 68 were positive by culture isolation. Of these 67 were IF positive when the cytopathic effect (CPE) was 1+ or less, whereas 56 gave positive results with DNA probes when the CPE was 2+. A further 83 specimens were examined directly by immunoperoxidase histopathology (IHP), IF and the DNA probe kit: 26 of these were positive by IHP examination, 25 by IF and only 6 by DNA probes. The sensitivity of the DNA probe kit was not satisfactory when the clinical tissue specimens were directly examined. However, the sensitivity improved considerably to 82% if the specimens were propagated first in cell culture. The IF method detected the virus before and after cell culture isolation equally well (96%-98.5%). Compared to the IF method, the DNA probe kit is costly and requires more labor and time.

Rapid and accurate viral diagnosis

In recent years, there has been increased recognition of the importance of viral infections. In addition, new antiviral agents have become available. These factors have led to a marked increase in utilization of viral diagnostic services. In this review, both conventional and rapid methods for viral diagnosis are presented, with emphasis on recent advances. The antiviral agents currently available and the major drugs under investigation are also briefly discussed. It is hoped that this review will serve as a useful adjunct for the management of patients with virus infections.

Nucleic acid analysis by sandwich hybridization

One of the most significant achievements of the biochemist during the past two decades is the use to which immunologically based assays have been put in clinical diagnosis (Hood et al.: Immunology, 1984). The problem faced and surmounted by immunologists in effecting the transition from research tool to routine clinical assay bears a remarkable similarity to that confronting the molecular biologist today; i.e., how can nucleic acid hybridization, a technique of obvious potential (Meinkoth and Wahl: Anal Biochem 138:267-284, 1984; Syvanen: Med Biol 64:313-324, 1986; Matthews and Kricka: Anal Biochem 169:1-25, 1988), be modified in order to fulfill all necessary parameters of a routine diagnostic assay? There are several such requirements, and the importance placed on each depends on the objectives of the assay: the technique must be sensitive, specific, and reproducible. Other advantages would be cost-effectiveness, ease of manipulation, and amenability to automation. Ideally, the signal detection should be based on a non-radioactive system, because of the instability of probes labelled with isotopes like 32p, and the potential hazards involved in their handling and disposal. The sandwich hybridization for the analysis of nucleic acid sequences was first used in 1977 (Dunn and Hassell: Cell 12:23-36, 1977), but its potential as a diagnostic assay was not realized until 1983, when it was applied to the detection of adenovirus DNA in nasopharyngeal aspirates from children with acute respiratory infection (Ranki et al: Gene 21:77-85, 1983). It has since been modified and used not only for the detection of microbial infection (Virtanen et al.: Lancet i:381-383, 1983; Ranki et al.: Cur Top Microbiol Immunol 104:307-318, 1983; Lehtomaki et al.: J Clin Microbiol 24:108-111, 1986; Virtanen et al.: J Clin Microbiol 20:1083-1088, 1984; Palva and Ranki: Clin Lab Med 5:475-490, 1985; Polsky-Cynkin et al.: Clin Chem 31:1438-1443, 1985; Parkkinen et al.: J Med Virol 20:279-288, 1986; Palva: FEMS Microbiol Lett 28:85-91, 1985; Palva et al: FEMS Microbiol Lett 23:83-89, 1984; Zolg et al.: Mol Biochem Parasitol 22:145-151, 1987; Palva: J Clin Microbiol 18:92-100, 1983), but also for the analysis of nucleotide sequence variations (Langdale and Malcolm: Gene 36:201-210, 1985). We will discuss the development of the sandwich technique and the advantages it conveys over the more conventional nucleic acid hybridization formats, together with new developments which will ensure that it earns a place alongside immunoassay in the diagnostic laboratory.

Quantification of polymerase chain reaction products by affinity-based hybrid collection

We have used oligonucleotides modified with biotin in the 5'-end as primers in the polymerase chain reaction (PCR)-amplification. This results in the synthesis of 5'-biotinylated DNA molecules, which are detected by hybridization to a labelled probe in solution. The formed hybrids are collected on an avidin-matrix by mediation of the biotin residue of the target molecules. The affinity-based hybrid collection method is quantitative and makes it possible to measure the amount of DNA produced in the PCR-amplification. At low concentrations of template the efficiency of the process is close to 100%, making it possible to detect the presence of a few molecules of target DNA in 25 cycles. With high template concentrations the efficiency of the process is low.

Nucleic acid sandwich hybridization: enhanced reaction rate with magnetic microparticles as carriers

A method for the detection of nucleic acid hybrids using the sandwich hybridization technique with magnetic polystyrene microparticles as the solid support is described. The capture DNA is coupled to the polystyrene-hydroxy surface of the particles through p-toluenesulfonyl chloride activation. The use of microparticles results in a substantial increase in the reaction rate compared to filter hybridization, without decreasing the sensitivity of detection. Polyethylene glycol additionally enhances the reaction rate. The use of magnetic microparticles allows rapid and convenient collection of the formed hybrids.

DNA hybridization assay for congenital cytomegalovirus infection

An in vitro DNA hybridization assay was used to test 281 newborns for congenital infection with cytomegalovirus. The assay utilized an abbreviated method for DNA preparation and a dot blot assay that provided good sensitivity (100%) and specificity (98.9%) when compared with standard tissue culture, yet substantially reduced the total time of analysis. This assay would be a useful adjunct to tissue culture to diagnose newborns with congenital infection with cytomegalovirus.

Detection of cytomegalovirus by dot-blot DNA hybridization using probes labelled with 32P by nick translation or random hexanucleotide priming

A DNA hybridization assay for the detection of human cytomegalovirus (HCMV) DNA was developed using random hexanucleotide-primed 32P-labelled Hind III restriction fragments of HCMV DNA as probes, and compared with a DNA hybridization assay using probes labelled with 32P by nick translation. Nick-translated probes were shown to be able to detect between 1 and 10 pg of homologous DNA or the DNA of 10-50 HCMV-infected fibroblasts. Random hexanucleotide-primed DNA probes lowered these detection limits to 0.1-0.5 pg of homologous DNA or one to five HCMV-infected fibroblasts. An increase in the autoradiographic exposure time from 18 h to 4 days increased the level of detection for homologous DNA or HCMV-infected fibroblast DNA by approximately five-fold. Preliminary screening of 35 urine samples by DNA hybridization using a random hexanucleotide-primed probe correctly identified three samples positive by virus isolation in tissue culture or immediate-early nuclear antigen detection and 29 of 32 samples negative by tissue culture.

Screening of premalignant cervical lesions for HPV 16 DNA by sandwich and in situ hybridization techniques

A series of 97 cervical smears and 69 directed punch biopsies derived from 84 consecutive women prospectively followed-up for cervical HPV (human papillomavirus) infections were studied using the sandwich hybridization and in situ hybridization techniques with HPV 16 DNA probes. The aim was to test the sensitivity and applicability of these two techniques in routine diagnosis of cervical HPV infections from smears. As a measure of specimen adequacy, the number of cells recovered in the cervical scrape was determined along with HPV 16 DNA in the sandwich hybridization test using human pro-alpha 2(I)-collagen gene probe. CIN (cervical intraepithelial neoplasia) was suggested in 56% of the patients by the Pap smear, and disclosed in 65% of the biopsies. HPV 16 DNA was present in 57% of cervical scrapes consistent with CIN, i.e., were of Pap smear classes III or IV. Forty percent of the scrapes not suggestive of CIN, i.e., Pap smear classes I or II, also contained HPV 16 DNA. The detection rate for HPV 16 DNA of the sandwich hybridization method was 89% of that of the in situ method in adequate scrapes, but only 43% in cell-poor specimens. The number of HPV 16 DNA-positive scrapes as compared with the total number of diagnoses obtained by studying also the biopsies was 31/36 (69 patients). The results indicate that the cervical scrape as a noninvasive specimen is applicable for screening of cervical HPV infections, and it can be studied with acceptable sensitivity by the rapid sandwich hybridization technique. However, if a punch biopsy is indicated it should be studied using the in situ hybridization technique that allows more sensitive detection of HPV DNA than any other hybridization method and enables the analysis of several HPV types in the same sample instead of only one HPV type in the scrapes.

Detection of herpes simplex virus in conventional tube cell cultures and in shell vials with a DNA probe kit and monoclonal antibodies

Specimens submitted for diagnosis of herpes simplex virus (HSV) infection were inoculated into shell vials and reacted with a commercial DNA probe kit (Pathogene; Enzo Biochem, Inc., New York, N.Y.) and an immunofluorescence assay at 16 h postinoculation. The results were compared with isolation of the virus in conventional tube cell cultures. Of 504 specimens, 105 (20.8%) were positive for HSV. Of the 105, 93 HSV-positive specimens (89%) were detected by all three assay systems. Maximum detection of HSV (100 of 105 [95%]) was obtained by probe or monoclonal antibody assay in shell vials, which had sensitivities of 98 and 97%, respectively, compared with viral recovery in conventional tube cell cultures (mean time for recognition of cytopathic effects, 2 days). Both shell vial assays were 99% specific. The DNA probe kit may be used as an alternative to a monoclonal antibody and fluorescence assay in shell vials as a diagnostic method for rapid laboratory detection of HSV infection.

Diagnostic deoxyribonucleic acid probes for infectious diseases

Virtually all microorganisms contain some unique nucleotide sequences which can be the target of deoxyribonucleic acid probes. Probes have been used successfully to identify a wide variety of pathogens from the simple ribonucleic acid-containing polioviruses to the complex filarial worms Brugia malayi. Probe technology offers the clinical laboratory the potential both to extend the types of pathogens that can be readily identified and to reduce significantly the time associated with the identification of fastidious microorganisms. Over a dozen commercially prepared deoxyribonucleic acid probe tests are now available. This article explores the development of deoxyribonucleic acid probe tests and reviews the sensitivity, specificity, and predictive values of many of the diagnostic probes developed during the last several years. Prospects for newer, more sensitive detection systems for the products of hybridization reactions are also reviewed.

Rapid methods for the molecular diagnosis of infectious diseases: current trends and applications

Methods for the rapid diagnosis of infectious diseases have become increasingly common in the last decade. The impetus for the development of such techniques has stemmed from the need to provide clinically relevant information without the length of time and complexity inherent to traditional cultivation methods. This is particularly important in high-risk populations for which more effective antibiotics and antiviral compounds are now available. Assay systems for the immunological detection of microbial agents occupy a central role in the molecular diagnosis of infectious diseases and are rapidly appearing on the market. Novel methods of organism detection by nucleic acid hybridization, long considered usable only in highly specialized laboratories, have the potential for use in routine microbiological laboratories and some systems are now commercially available. As more efficient and rapid diagnostics systems are being developed, the selection of the optimal method will depend on the environment in which the system is to be used. Rapid methods for the detection of infectious agents might markedly improve health care in a variety of clinical, laboratory and epidemiologic situations.

The use of DNA probes in dental diagnosis and therapy

Recombinant DNA technology now allows for the development of genetic probes specific for a growing number of etiologic disease agents, including those suspected pathogens in the oral environment. The increasing refinement of DNA probe methodologies and sensitivities will ultimately permit their commonplace use with clinical samples for the rapid identification of their bacterial compositions. The use of probe technology potentially offers a much more facile, accurate, and less time-consuming mechanism for the identification of fastidious micro-organisms from the oral cavity, many of which are laborious and difficult to cultivate.

Problems in detection of cytomegalovirus in urine samples by dot blot hybridization

A hybridization assay for the detection of cytomegalovirus (CMV) in urine specimens was established. Two different DNA fragments were used as hybridization probes: the HindIII L fragment (11.7 kilobases) and the EcoRI J fragment (10.6 kilobases) of the human CMV strain AD169. These probes were used in an isolated and highly purified form and therefore did not cross hybridize with vector sequences. As shown by hybridization with DNA from CMV-infected and uninfected cells, the assay was highly CMV specific and sensitive (detection limit, 750 to 500 fg of CMV DNA). A total of 122 urine specimens were examined by DNA hybridization, virus isolation, and the detection of CMV-induced early nuclear protein. The results coincided in 91% of the samples. The application of DNA hybridization to urine samples, however, is not without problems, and some of the pitfalls and drawbacks are discussed.

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

A variety of methods are now available for the preparation and labelling of viral nucleic acids for use as probes in diagnostic virology. Some of these are assessed including the use of synthetic oligonucleotides in place of molecularly cloned nucleic acids, and alternatives to labelling with radioactive isotopes such as biotin, enzymes and fluorochromes. Dot blot, sandwich, indirect sandwich and in situ hybridization are covered, and examples given of the current use of nucleic acid probes in detection of human viral infections. The potential and limitations of nucleic acid hybridization are discussed in the light of these new methods.

Sensitive detection of genes by sandwich hybridization and time-resolved fluorometry

Europium has been used as a non-radioactive marker in immunoassays as this metal can be detected with high sensitivity by time-resolved fluorometry. In this work streptavidin labeled with europium was used to detect biotinylated probes in a sandwich nucleic-acid hybridization assay with microtitration strips as the solid phase. pBR 322 plasmids were detected with a sensitivity of 4 x 10(5) molecules. As the sample is added in solution in sandwich hybridization, fast and simple sample pre-treatment can be used without encountering background problems. The method was applied to test bacterial samples of uropathogenic Escherichia coli strains for the presence of the beta-lactamase gene.

[Technic of nucleic acid hybridization and its significance for diagnostic problems]

Nucleic acid hybridization techniques (e.g., Southern blotting and in situ hybridization) gain increasing importance in laboratory medicine, as demonstrated by examples in this paper. The molecular basis of this approach to detect nucleic acids homologous to known DNA probes is explained. It is concluded that this technique has advantages in the detection of pathogens compared to other methods used in laboratory medicine.

Sensitivity and specificity of enzyme immunofiltration and DNA hybridization for the detection of HCMV-infected cells

The sensitivity and specificity of enzyme immunofiltration and DNA hybridization were compared in human cytomegalovirus (HCMV) (AD 169)-infected MRC-5 cells. The enzyme immunofiltration was carried out on glass fiber filters in microplates, using an HCMV (AD 169) monoclonal antibody and a peroxidase conjugate. The DNA hybridization was carried out with a microfiltration apparatus, using a 32P-labelled HCMV (AD 169) Eco R1 D fragment probe. The sensitivities of enzyme immunofiltration and DNA hybridization were 1.82 X 10(3) and 1.13 X 10(3) infected cells, respectively. Both methods were highly specific, but enzyme immunofiltration was faster and simpler.

Nucleic acid probes in clinical microbiology

The infectious disease applications of nucleic acid probe have been described. In addition, the basic procedures of nucleic acid probe technology have been discussed, as have the factors affecting implementation of probe technology in diagnostic laboratories. Despite the questions raised, nucleic acid probes will become part of the diagnostic laboratory in the near future. Commercial interests are developing and marketing new probes, reagents, and kits which will expedite the employment of this technology. High-volume reference laboratories will first use probes as part of a battery of tests which will include ELISA and monoclonal antibody methods. In all probability, probes will replace methods: that have proven to be ineffective, difficult, or costly such as culturing for some enteric pathogens and Legionella, that require long incubation periods, such as mycobacteria, or that have high costs and low yields, such as virology.

Detection of varicella-zoster virus in lymphocytes by DNA hybridization

The availability of cloned varicella-zoster virus (VZV) DNA probes allows rapid detection of viral-specific DNA by "dot-blot" hybridization in lymphocytes or in lesion aspirates. Thirty-six blood specimens were obtained from 25 patients with suspected varicella or zoster. VZV-specific DNA was demonstrated in 15 lymphocyte preparations of nine patients with varicella and in one with disseminated zoster out of five patients with zoster. VZV-specific DNA was detected prior to rise in antibodies, indicating early viremia in these patients. Virus isolation from lesions and serological tests confirmed VZV infections. VZV-specific DNA was detected in lymphocytes of three patients out of six with active herpetic lesions, whereas it was not detected in lymphocyte specimens from two patients with undiagnosed rash or four with lymphoproliferative diseases, who did not present varicella or zoster, or from 18 healthy controls. No signal was obtained in herpes simplex virus (HSV)-infected and -uninfected cell lines. The hybridization assay proved that specific and viral or cellular DNAs other than VZV did not cross-hybridize with the probe. The sensitivity limit of detection was 4-15 pg of homologous DNA, and the assay was accomplished within 72-96 hr. These results point to the possible rapid diagnosis of VZV infection in patients suspected of varicella or generalized zoster. In addition, simultaneous infection with both VZV and HSV seems to occur in some patients.

Detection of human papillomavirus DNA by the nucleic acid sandwich hybridization method from cervical scraping

Cervical scrapes collected from 100 consecutive patients participating in a prospective follow-up study for cervical human papillomavirus (HPV) infections were tested for the presence of HPV 11 DNA by the nucleic acid sandwich hybridization method, which allows testing the specimens in a crude form. Part of each specimen was processed through phenol extraction and DNA purification to a dot blot hybridization assay. The dot blots were serially hybridized with HPV 6, 11, 16, and 18 probes as well as with an Alu-repeat probe to estimate the number of cells in the specimen. In PAP smears, HPV-infection was suspected in 63 patients whereas in 37 patients the smear was negative. In the first group, the dot blot assay revealed three cases of HPV 11, two of HPV 16, and one of HPV 18 infection. In the second group with normal PAP smear, one additional HPV 18 infection was found. The sandwich hybridization assay detected 5 HPV 11 infections, including the three mentioned above. All HPV DNA-positive samples contained at least 1.6 X 10(6) cells. Since we considered this a prerequisite for successful diagnosis, only 25 specimens in the first group and 15 in the second were adequate specimens. Thus the HPV-DNA detection rate was 32% (8/25) in the first group and 1/15 in the second. This study demonstrates that sandwich hybridization, detecting 1-3 X 10(5) HPV 11 molecules is a reliable diagnostic method. Cervical scrape is a valuable alternative to punch biopsy, but the number of cells collected is critical for the outcome of the assay.

The vector homology problem in diagnostic nucleic acid hybridization of clinical specimens

Nucleic acid hybridization techniques using cloned probes are finding application in assays of clinical specimens in research and diagnostic laboratories. The probes that we and others have used are recombinant plasmids composed of viral inserts and bacterial plasmid vectors such as pBR322. We suspected that there was material homologous to pBR322 present in many clinical samples. because hybridization occurred in samples which lacked evidence of virus by other techniques. If the presence of this vector-homologous material was unrecognized, hybridization in the test sample might erroneously be interpreted as indicating the presence of viral sequences. In this paper we demonstrate specific hybridization of labeled pBR322 DNA with DNA from various clinical samples. Evidence is presented that nonspecific probe trapping could not account for this phenomenon. In mixing experiments, it is shown that contamination of clinical samples with bacteria would explain such a result. Approaches tested to circumvent this problem included the use of isolated insert probes, alternate cloning vectors, and cold competitor pBR322 DNA in prehybridization and hybridization mixes. None proved entirely satisfactory. We therefore emphasize that it is essential that all hybridization detection systems use a control probe of the vector alone in order to demonstrate the absence of material with vector homology in the specimen tested.

Fast quantification of nucleic acid hybrids by affinity-based hybrid collection

A hybridization technique for the quantification of nucleic acids is described. In the method a probe pair is allowed to form hybrids with the target nucleic acid in solution. One of the probes has been modified with an affinity label, by which the formed hybrids can be isolated after the reaction. Streptavidin-agarose was used to capture hybrids containing biotinylated DNA. The hybrids were measured using radioiodine as label on the second probe. The rate of the hybridization reaction in solution is fast, allowing the whole procedure to be carried out in 3 h. The method is quantitative with a detection limit of 4 X 10(5) molecules (0.67 attomoles) target DNA. The test is insensitive to impurities in biological samples, which are analyzed without purification of the target DNA. Non-isotopic measurement of the hybrids can also be applied. In this case the hybrids are bound to microtitration wells and detected spectrophotometrically by peroxidase-catalyzed colour development.

Time-resolved fluorometry: a sensitive method to quantify DNA-hybrids

Europium and other lanthanides can be excitated with UV-radiation, whereafter the energy is released as fluorescence, delayed in time up to 1 ms after the excitation. Eu can be used as a sensitive label in biological assays. Here we report on the application of time-resolved fluorometry to detect nucleic acid hybrids. The probe DNA was tagged with a hapten, either a fluorene or a sulfone group. After hybridization the probe DNA was detected by a two-step immunological assay with the second antibody labelled with Eu. The method is quantitative with a detection limit of 0.3 pg of actual target regions of immobilized adenovirus genomic DNA. The label was also used in sandwich hybridization, which allowed analyzing nasopharyngeal mucus for the presence of adenovirus.