A reverse-transcription competitive PCR assay based on chemiluminescence hybridization for detection and quantification of hepatitis C virus RNA

Development and validation of an RT-qPCR assay for rapid detection and quantification of hepatitis C virus RNA for routine testing in Moroccan clinical specimens

A one-step reverse transcription quantitative PCR (RT-qPCR) assay in combination with rapid RNA extraction was evaluated for routine testing of hepatitis C virus (HCV) RNA. Specific primers and probes were designed for the detection of a 150 bp sequence located in the 5'untranslated region (5'UTR) of HCV RNA. The target sequence was selected as the most conserved region between the six known HCV subtype sequences following an alignment. The assay was able to quantify a dynamic linear range of 10⁸ to 10¹ plasmid copies/reaction (r²  = 0.98) containing the target sequence. Two copies of this HCV plasmid corresponds to one international unit (IU) measured using a standard obtained by serial dilutions of the World Health Organization (WHO) standard. The detection limit of the assay was about 10 IU/mL of HCV RNA (20 copies/mL) in plasma samples. The assay was comparable to Cobas AmpliPrep/Cobas TaqMan® HCV Test, v2.0 Quantitative assay (Roche Molecular Systems, Inc., Branchburg, NJ) with correlation coefficient r²  = 0.98. The present assay could be completed within 3 hours from RNA extraction to data analysis of at least 30 plasma samples. Our test provides sufficient sensitivity, specificity, and reproducibility and proved to be fast, labor-saving, and cost-effective. Indeed, our system will definitely allow low-income countries to monitor accurately this viral infection and to efficiently treat their infected patients.

Oligonucleotide-based biosensors for in vitro diagnostics and environmental hazard detection

Oligonucleotide-based biosensors have drawn much attention because of their broad applications in in vitro diagnostics and environmental hazard detection. They are particularly of interest to many researchers because of their high specificity as well as excellent sensitivity. Recently, oligonucleotide-based biosensors have been used to achieve not only genetic detection of targets but also the detection of small molecules, peptides, and proteins. This has further broadened the applications of these sensors in the medical and health care industry. In this review, we highlight various examples of oligonucleotide-based biosensors for the detection of diseases, drugs, and environmentally hazardous chemicals. Each example is provided with detailed schematics of the detection mechanism in addition to the supporting experimental results. Furthermore, future perspectives and new challenges in oligonucleotide-based biosensors are discussed.

Detection of short oligonucleotide sequences of hepatitis B virus using electrochemical DNA hybridisation biosensor

A novel, sensitive and selective electrochemical hybridisation biosensor was developed for the detection of the hepatitis B virus (HBV) using a manganese(II) complex as electrochemical indicator and a DNA probe-modified carbon paste electrode as the biosensor (DNA/CPE). The results showed that this complex could be accumulated electrochemically the immobilised dsDNA layer rather than in the single-stranded DNA (ssDNA) layer. On the basis of this, the manganese complex was used as an electrochemical hybridisation indicator for the detection of oligonucleotides related to HBV. The hybridisation event was evaluated on the basis of the difference between the reduction signals of the manganese(II) complex with the probe DNA prior to and post hybridisation with a target sequence using a differential pulse mode. Several factors affecting the immobilisation and hybridisation of oligonucleotides as well as the indicator’s accumulation were investigated. Experiments with a noncomplementary and mismatch sequences demonstrated the good selectivity of the biosensor. Using this approach, the HBV target oligonucleotide’s sequence could be quantified over arange from 0.22 ng L

Rapid detection of hepatitis C virus RNA by a reverse transcription loop-mediated isothermal amplification assay

The usefulness of reverse transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid diagnosis of hepatitis C virus (HCV) RNA was evaluated. This assay showed higher sensitivities than that of nested RT-PCR, with a detection limit of 600 IU mL(-1) , and no cross-reactivity was observed with hepatitis A virus, hepatitis B virus and hepatitis E virus. Furthermore, 106 stored sera from recently diagnosed cases were retrospectively investigated with real-time RT-PCR, the nested RT-PCR, in parallel with this new assay. The general detection rates of HCV RT-LAMP, real-time PCR and the nested RT-PCR for 106 stored sera samples were 95%, 96% and 88%, respectively. This study provides the first data on the usefulness of HCV RT-LAMP in the diagnosis of HCV RNA, especially in the early clinical diagnosis of acute HCV infection.

Nanoparticle-based electrochemical detection of hepatitis B virus using stripping chronopotentiometry

A selective and sensitive gold nanoparticle-based electrochemical method for detection of hepatitis B virus DNA sequences was used. This method relies on the hybridization of amplified hepatitis B virus DNA strands with probes that are extended on paramagnetic beads. After separation of noncomplementary sequences, hybridized magnetic beads were treated with streptavidin-modified gold followed by silver enhancement. High selectivity and high sensitivity were obtained using electrochemical stripping detection of silver ions that were deposited on gold nanoparticles. With a signal/noise ratio of approximately 4.6, the detection limit was estimated to be 0.7ng/ml.

A chemiluminescence-based assessment of androgen-binding activity in a large pedigree affected with androgen insensitivity syndrome

We report a novel chemiluminescence (CL)-based method for assaying the ligand-binding activity of the androgen receptor. The central parts of this method are the utilization of the steroid CL marker as the replacement of the radioactive label in the conventional ligand-binding assay and the determination of the binding activity by the light measurement of the bound CL-label under an H(2)O(2)-microperoxidase system. The properties and reliability of this assay were investigated and verified using genital skin fibroblasts (GSF) from seven normal males. The method is precise (CV < 7% for both B(max) and K(d)) with high correlation coefficients (r > 0.93) in each Scatchard linear regression analysis. This assay can determine the androgen binding properties using only a quarter of the cells (approximately 40 000 cells/data point) of that required by the radiolabelling approach. The utility of the method was illustrated by binding experiment on the GSFs of several patients from a large Chinese family affected with androgen insensitivity syndrome. The familial distinct feature is that all patients shared an identical Arg840Cys substitution in the androgen receptor but displayed high phenotypic variation in disorders of male sexual development. The patients selected for the present study represent a wide spectrum of this phenotypic variation. This study thus provides insights on the pleiotropic effects of the mutation. In conclusion, the CL-based method can serve as an effective, precise and reliable replacement for the radiolabelling approach and has the advantages of simplicity, cost-effectiveness and health and environmental safety over the counterpart.

Identification of novel defective HCV clones in liver transplant recipients with recurrent HCV infection

Patients with recurrent hepatitis C after liver transplantation usually have a high viral load and are generally resistant to interferon (IFN)-alpha2b plus ribavirin (RBV) therapy. However, it remains unclear whether pretreatment viral titre determines the effectiveness of combination therapy, especially in patients with a high viral load. The aim of this study was to identify the viral factors associated with a sustained virological response (SVR) to antiviral therapy in patients with recurrent hepatitis C after living-donor liver transplantation. Twenty-three patients with recurrent hepatitis C received combination therapy of IFN-alpha2b plus RBV. SVR was achieved in 7 of the 23 patients (30.4%). Predictive factors for SVR included a 2 log10 decline in Hepatitis C virus (HCV) RNA at 2 weeks after the start of therapy and disappearance of HCV RNA at 4 or 24 weeks after the start of therapy. As the pretreatment high viral load showed no association with SVR, we asked whether other viral factor was associated with the response to the combination therapy in transplant recipients. We found the several novel defective HCV clones in 4 of 12 recipients' sera. All defective HCV clones had deletions in the envelope region. Interestingly, no patients with defective clones showed a prompt decrease in HCV RNA after the start of IFN-alpha2b plus RBV therapy. Thus, early decline in serum HCV RNA after treatment was closely associated with SVR. The circulating defective HCV clones are present and might be associated with the response to the combination therapy in patients with recurrent hepatitis after liver transplantation.

Improvement of Potato virus Y (PVY) detection and quantitation using PVY(N)- and PVY(O)-specific real-time RT-PCR assays

A Potato virus Y (PVY) single nucleotide polymorphism (A/G(2213)), recently identified as a molecular determinant of the tobacco leaf necrosis symptom induced by PVY(N) isolates, has been used as a target to develop two PVY group-specific (PVY(N) and PVY(O)) fluorescent (TaqMan-based) real-time RT-PCR assays. These procedures allow detection, characterisation, and quantitation of a wide range of PVY isolates in samples containing 10(3)-10(8) viral transcripts. Moreover, the high specificity of these two new assays make the simultaneous detection and the reliable quantitation of PVY(N) and PVY(O) isolates in mixed solutions, regardless of the Y(N)/Y(O) ratio, feasible. The high sensitivity (threshold of 10(3) copies per reaction) and the PVY group specificity of these two new PVY detection tools clearly improve previously published PVY detection tests and offer new opportunities for PVY research programs.

Analytical performance of and real sample analysis with an HBV gene visual detection chip

A novel hepatitis B virus (HBV) gene detection chip has been developed. The HBV-specific probes immobilized on glass slides were hybridized with polymerase chain reaction (PCR) products of different serum samples. The hybridization signal can be easily visualized upon a sandwich assay with nanoparticle amplification. The analytical performance (e.g., specificity, sensitivity, and accuracy) of this method has been evaluated. The chip-based detection method possesses a greater sensitivity and a better reproducibility than some of the conventional immunological or molecular biological methods (e.g., enzyme-linked immunosorbent assay, ELISA) and is simple, cost-effective, and highly selective.

Selective labeling and detection of specific mRNA in a total-RNA sample

We report a unique approach to selectively label and detect specific RNA using its internal sequence, without separation, reverse transcription, and/or polymerase chain reaction. This approach is especially useful for individual mRNA labeling and detection. To expose mRNA internal sequence for selective labeling and detection, RNase H digestion is used to remove the 3(')-common sequences. We have designed a DNA-2(')-O-Me-RNA hybrid as the template for both RNase H digestion and Klenow extension and have found buffer conditions for both enzymes. Sharing the same template and buffer by these two enzymes largely simplifies experimental procedures. Using this approach, lacZ mRNA was selectively labeled and detected in the presence of thousands of mRNAs. We have successfully demonstrated for the first time the direct labeling and detection of an individual mRNA in a total-RNA sample. The detection sensitivity can reach up to attomole level (5 x 10(-18)mole). This method has great potential in RNA decay and metabolic regulation studies via individual mRNA labeling and in methodology of mRNA direct detection on microchip and direct gene expression profiling, without reverse transcription and polymerase chain reactions.

Selective labeling and detection of specific RNAs in an RNA mixture

We report here a unique approach to selectively label and detect specific RNA in an RNA mixture (without separation or purification) using DNA polymerase, dNTP labels, and a short synthetic DNA template complementary to the 3(')-terminus of the RNA. The detection sensitivity is high, at attomole level (10-18 mole). The selective principle was demonstrated by individually labeling and detecting RNAs in a RNA mixture when different templates were provided. By taking advantage of the template-directed selectivity, poly(A) tail-containing mRNA in total RNA was detected and labeled at the 3(')-terminal on a poly(T) template. Nonradioactive labels, such as fluorophore and antigen labels, may also be used; this method can be applied in methodology for direct detection and quantification of viral RNAs.

Variation of hepatitis C virus load, hypervariable region 1 quasispecies and CD81 hepatocyte expression in hepatocellular carcinoma and adjacent non-cancerous liver

Hepatitis C virus (HCV) infection is etiologically associated with the development of hepatocellular carcinoma (HCC) worldwide. HCV has been reported to exist and replicate in both HCC and adjacent non-cancerous liver tissue, but limited information was available on HCV viral load and quasispecies composition in HCC relative to adjacent non-cancerous hepatocytes. Previous study has also suggested CD81, a surface hepatocyte protein, as a receptor for HCV. To clarify the above, HCV-RNA and CD81-RNA titers in 20 paired hepatectomized liver and serum were quantitatively measured by chemiluminescent RT-cPCR. Hypervariable region 1 (HVR-1) variations of parallel specimens were analyzed after subcloning in 6 patients. HCV-RNA levels in serum and non-cancerous liver were markedly higher for HCV genotype 1 than genotype non-1. HCV levels were markedly higher in non-cancerous liver than in HCC (P = 0.001) in a genotype-independent manner, with a mean ratio of 56:1 for non-cancerous tissue to HCC. Both non-cancerous and HCC tissues had the same level of CD81-RNA expression, which was not linked to HCV load. HCV-RNA quantity in both HCC and non-cancerous liver correlated with the number of HVR-1 quasispecies in the tissue, and distinct HVR-1 subclones existed.