Detection of dengue virus RNA using nucleic acid hybridization

Seroprevalence of asymptomatic dengue infection in children in Lahore

Dengue has become a global problem in past few decades, with half of the world's population at risk of infection. For some countries of Asia and Latin America, severe dengue is a major cause of serious illness and even death in children. Pakistan has been reported as a hyperendemic area for dengue infection. Our study aimed to find seroprevalence of past dengue infection in asymptomatic children of Lahore with no previous history of dengue infection. A total of 400 samples were collected from children aged 1-12 years in Lahore using random sampling. The inclusion criteria were children aged 1-12 years, who had no previous symptoms of dengue fever during their lives. Children with known immunodeficiency status or fever at the time of recruitment were excluded from the study. Commercially available ELISA kits were used to determine the IgG status in sera of children. The data obtained was entered and analysed using SPSS v. 20.0. The overall prevalence of asymptomatic dengue infection was found to be 25%. There was no statistically significant difference between prevalence of infection in male and female children. There was, however, a strong relationship between increasing age of the child and number of cases with infection, with low incidence in children aged ⩽5 years.

Trends in dengue diagnosis

The conventional diagnosis of dengue virus infections includes the detection of the virus in serum or tissue samples, both by isolation in culture or through detection of specific viral molecules (genome RNA or dengue antigens) and detection of specific anti-dengue antibodies (serology). Isolation of dengue virus provides the most direct and conclusive approach to diagnosis, despite the demand for high-level equipment, technical skills and manpower. However, it is useless in early diagnosis because several days are required to isolate and classify the virus. Serology, despite being simpler, is not able to afford an accurate early diagnosis in primary infections because 4-5 days are required for the immune system to produce a sufficient amount of antibodies. Moreover, it leads to misleading results in secondary infections owing to cross-reactivity among serotype-specific antibodies and with other flavivirus antibodies. The RT-PCR and other PCR-based techniques are fast, serotype-discriminating, more sensitive and easier to carry out than conventional nucleic-acid hybridisation, but are handicapped by easy sample contamination and high technological demands. Recently, advances in bioelectronics have generated commercial kits and new techniques for detection of dengue antibodies and RNA, based on biosensor technology. Most of them are rapid, easy to operate, reusable, cheap, sensitive and serotype-specific. Nevertheless, their accuracy is still questionable because most still lack validation and standardisation. This review summarises and describes the techniques currently employed and anticipated in the near future for diagnosis of dengue disease.

Detection of dengue viral RNA by microplate hybridization

Dengue virus infection is a major public health problem throughout tropical countries. In endemic areas, dengue hemorrhagic fever (DHF) or dengue shock syndrome (DSS) are common complications resulting in death. However, serological confirmation of dengue-related illness is often complicated and time-consuming. Detection of dengue viruses in clinical or field samples usually depends on virus isolation in susceptible cell lines or in mosquitoes, followed by viral protein identification using polyclonal or monoclonal antibodies. The increasing incidence of dengue virus infections has prompted increased efforts to develop rapid and reliable diagnostic techniques. A simple microplate hybridization method was developed for identification of viral RNA. Microplate hybridization is simpler than enzyme-linked immunosorbent assay and has several advantages over the conventional dot-blot hybridization method: (1) radioisotopes are not necessary; (2) synthetic oligonucleotide for the probe is not needed; (3) the time required for washing of the solid phase is greatly reduced; and (4) baking is eliminated. The results show that this procedure is sensitive, rapid and easy to perform.

Detection of dengue-2 viral RNA by reversible target capture hybridization

A reversible target capture (RTC) sandwich hybridization technique has been developed for the detection of dengue-2 viral RNA. The RTC is a form of sandwich hybridization that utilizes two probes: a poly(dA)-tailed capture probe and a labeled detector probe. Following hybridization of both probes to the analyte in solution, the poly(dA)-tailed capture probe is used to selectively remove the hybrids by capture on oligo(dT)-coated paramagnetic beads. AFter elution from the beads, the presence of specific hybrids is revealed by detection of the labeled probe. After optimization of all parameters by using 32P-labeled probes, digoxigenin was used as a label to preclude the use of radioisotopes. The sensitivity of the developed RTC procedure was determined. The lowest amount of virus detectable in cell culture lysates by using 32P-labeled probes was 20 PFU, while with digoxigenin-labeled probes, 200 PFU was detectable. The RTC procedure also detected dengue-2 virus in infected mosquitoes, both individually and in pools. The RTC has the advantage of being performed directly on crude samples, eliminating the need for phenol extraction and purification of target nucleic acids. These results indicate that the RTC procedure is sensitive, rapid, and easy to perform and that its use in surveillance programs will allow detection of dengue virus in pools of mosquitoes more rapidly than current procedures.

Use of NS3 consensus primers for the polymerase chain reaction amplification and sequencing of dengue viruses and other flaviviruses

Consensus primers for the polymerase chain reaction were designed based on conserved motifs within the serine protease and RNA helicase domains encoded by the NS 3 genes of dengue and other flaviviruses. Target fragments of 470 bp were amplified on cDNA templates synthesized from RNAs of dengue types 1, 2, 3, and 4, Japanese encephalitis, Kunjin, and yellow fever viruses using random or specific downstream primers. PCR of oligo(dT)-primed cDNAs from Japanese encephalitis and Kunjin viral RNAs did not yield target bands. As few as 10(3) copies of dengue viral RNA could be detected. Direct DNA sequencing of PCR products of reference strains of dengue 2 (NGC), Kunjin (MRM 61C) and yellow fever (17 D) viruses demonstrated complete concurrence with published data. However, 2 nucleotide differences were observed between our data for dengue 3 H87 strain and the published sequence, resulting in a single amino acid disparity. Differences at 21, 16, and 11 nucleotide positions were noted between dengue 1 Hawaii and S 275/90; dengue 4 H 241 and 814669; Japanese encephalitis Nakayama and JaOArS 982 viral strains, culminating in only 4, 1 and 1 amino acid residue differences, respectively. These amino acid disparities occurred outside putative active sites of the enzymatic domains, emphasizing the important role of the NS3 protein in flaviviral replication. This RNA-PCR consensus primer strategy coupled with DNA sequencing represents a valuable tool for the molecular diagnosis and epidemiology of dengue and other flaviviral infections.

Detection of dengue virus by in situ hybridization

A non-radioactive in situ hybridization protocol was developed for the detection of dengue virus RNA in fixed tissues and cells. For this purpose a riboprobe was constructed from a 39 base sequence, from the capsid protein coding region of the genome, which is conserved in the four dengue serotypes. The ability of this probe to specifically detect dengue RNA from each serotype was confirmed on brain sections from infected mice. Dengue viral RNA was also detected in in vitro infected human primary endothelial cells which release infectious virus without showing gross cytopathic effect. With clinical samples dengue viral RNA was detected in some preparations of white blood cells from dengue fever patients and in thymus autopsy sections following suspected death from dengue shock syndrome. For dengue samples of undetermined serotype the sensitivity of the short probe was compared to that of an equimolar mixture of long (260 base) probes from the envelope coding region of the four dengue serotypes, provided by Dr. V. Deubel. In those samples examined, sensitivity of the long probe mixture was greater and higher numbers of infected cells were detected.

Amplification of viral RNA for the detection of dengue types 1 and 2 virus

In vitro DNA amplification by means of the polymerase chain reaction (PCR) was used to amplify dengue types 1 and 2 viral genomes in cultured cells and in the serum of persons infected with dengue virus. Results of the present investigation suggest that the PCR method is type-specific in detecting dengue virus and has a detection sensitivity of less than 100 plaque-forming units (pfu) for both serotypes of the virus. The PCR method may be useful for detecting and typing dengue virus in clinical and epidemiological specimens.

Identification of dengue sequences by genomic amplification: rapid diagnosis of dengue virus serotypes in peripheral blood

Polymerase chain reaction (PCR) was developed for the in vitro amplification of dengue virus RNA via cDNA. A fraction of the N-terminus gene of the envelope protein in the four dengue serotypes was amplified using synthetic oligonucleotide primer pairs. Amplified products were cloned and used as dengue type-specific probes in gel electrophoresis and dot-blot hybridization. We detected and characterized dengue virus serotypes in blood samples by the three-step procedure DNA-PAH consisting in cDNA priming (P), DNA amplification (A) and hybridization (H) using specific non-radiolabelled probes. Our findings showed that DNA-PAH was more rapid and sensitive in the identification of the infecting serotype than the mosquito cell cultures. Moreover, the failure of cultures to detect virus particles in sera containing few copies of viral genome or anti-dengue antibodies justified the approach of DNA-PAH to the dengue identification in clinical specimens.

The dengue viruses

Dengue, a major public health problem throughout subtropical and tropical regions, is an acute infectious disease characterized by biphasic fever, headache, pain in various parts of the body, prostration, rash, lymphadenopathy, and leukopenia. In more severe or complicated dengue, patients present with a severe febrile illness characterized by abnormalities of hemostasis and increased vascular permeability, which in some instances results in a hypovolemic shock. Four distinct serotypes of the dengue virus (dengue-1, dengue-2, dengue-3, and dengue-4) exist, with numerous virus strains found worldwide. Molecular cloning methods have led to a greater understanding of the structure of the RNA genome and definition of virus-specific structural and nonstructural proteins. Progress towards producing safe, effective dengue virus vaccines, a goal for over 45 years, has been made.

Detection of dengue viral RNA in mosquito vectors by mixed phase and solution hybridization

A mixed phase hybridization technique was developed to detect dengue virus type 2 (DEN-2) RNA in pools of infected Aedes albopictus mosquitoes using radiolabelled RNA probes. This technique used a guanidine thiocyanate extraction procedure to simplify analyte preparation. The probes contained sequences complementary to portions of the NS-1 or NS-5 genes of the DEN-2 viral genome. One infected mosquito in a pool of 25 could be detected in approximately 48 h. RNAs from DEN serotypes 1-4 were extracted from cultured mosquito (C6/36) cells. The NS-1 RNA probe was highly specific for DEN-2 RNA. The NS-5 RNA probe detected both DEN-2 and DEN-4 RNA. DEN-2 RNA was also detected by molecular hybridization in concentrated solutions of guanidine thiocyanate using the NS-1 probe. Solution hybridization was 10-fold more sensitive when detecting RNA from purified DEN-2 virus than the mixed phase assay and could detect one infected mosquito in a pool of 25 within 6-8 h. Solution hybridizations were performed in 2-3 h vs 16-20 h for mixed phase hybridizations, and solution hybridizations required 5-10 times less mosquito RNA than mixed phase hybridizations to attain comparable sensitivities. However, solution hybridizations did result in a broader probe specificity than mixed phase hybridizations.

Rapid detection of herpes simplex virus DNA by in situ hybridization with photobiotin-labelled double-stranded DNA probes

An assay for rapid detection of herpes simplex virus in infected cells is described. The assay utilizes in situ hybridization with photobiotin-labelled double-stranded DNA probes prepared from HSV-1 DNA cloned in plasmid vectors. The assay provided an alternative method for earlier detection of virus in cell cultures with the ease of preparation of photobiotin-labelled double-stranded DNA.

Detection of dengue virus type 2 in Aedes albopictus by nucleic acid hybridization with strand-specific RNA probes

A molecular hybridization technique with radiolabeled, strand-specific RNA probes was developed to detect dengue virus type 2 RNA in pools of infected Aedes albopictus mosquitoes. One infected mosquito in a pool of 25 could be detected, corresponding to a dengue virus type 2 titer of 2.75 log10 50% tissue culture infectious doses.

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.