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PubMed1991

Hepatitis delta virus RNA detection in chronic HBsAg carriers with and without HIV infection.

Hepatitis delta virus (HDV) RNA detection was carried out, using a full-length HDV RNA probe, in serum of 43 patients with chronic HDV infection. Among them, 30 cases (70%) were HDV RNA-positive. With respect to other HDV markers, serum HDAg (detected by immunoblot) was found in 33 patients (77%) and IgM anti-HD in 29 (67%). A similar percentage of HDV RNA-positive patients with and without circulating hepatitis B virus (HBV) DNA (32.5 vs. 37%, respectively) was found. Antibodies against the human immunodeficiency virus (HIV) were detected in 15/43 subjects studied. The presence of HDV RNA was significantly higher (p less than 0.05) in anti-HIV-seropositive cases (93%) than in the HIV-seronegative ones (57%). Moreover, simultaneous HDV and HBV replication was found more frequently (60 vs. 18%, p less than 0.05) and at higher levels among the anti-HIV-positive patients than in the rest. In addition, in most of the anti-HIV-positive subjects, HDV RNA and HBV DNA were constantly positive during a whole year of follow-up.

Acquired Immunodeficiency Syndrome↗
PubMed2002

Two-round rapid-cycle RT-PCR in single closed capillaries increases the sensitivity of HCV RNA detection and avoids amplicon carry-over.

BACKGROUND: For the detection of hepatitis C virus (HCV) specific nucleic acids the polymerase chain reaction (PCR) is widely used. Rapid-cycle PCR is performed in glass capillaries with the LightCycler instrument and allows PCR including product analysis to be performed within a closed system in about 1 h. Thus, rapid-cycle PCR appears especially suitable for routine diagnostic applications. However, the volume of the PCR vessel is restricted to about 20 microl, which may limit the sensitivity of the PCR. To increase its sensitivity two-round or nested primer PCR protocols have been developed. In rapid-cycle PCR first-round PCR products are usually collected from the capillaries by centrifugation, a procedure prone to cross-contamination. OBJECTIVES: Development of a two-round rapid-cycle reverse transcription-polymerase chain reaction (RT-PCR) in single closed LightCycler capillaries for the sensitive detection of HCV RNA in serum or plasma. STUDY DESIGN: A set of two pairs of nested primers was selected. The first-round RT-PCR reaction mixture was separated from the second-round PCR mixture by silicone oil. Reverse transcription followed by the first-round PCR was performed. Then, the second-round mixture was combined with first-round products by a centrifugation step followed by second round PCR during which fluorescence intensities were recorded and used for quantification. RESULTS: To establish the sensitivity of this novel assay a serial dilution of HCV reference standard was used. In plasma samples about 100 IU/ml HCV were consistently detected using the high pure viral RNA kit for nucleic acid purification. This detection limit was found to be about 20 fold increased compared with single-round RT-PCR and corresponded to 3.4 IU of HCV per capillary. Using a panel of HCV genotype standards the novel assay exhibited similar sensitivity for all HCV genotypes. The applicability for clinical routine testing was demonstrated by examining 156 clinical samples. CONCLUSION: Two-round RT-PCR with the LightCycler instrument using a single closed capillary throughout the procedure was found ideally suited for rapid (100 min), accurate and sensitive molecular diagnosis of active HCV infections. Since the capillaries remained closed during the procedure carry-over contamination was precluded.

Base Sequence↗
PubMed1993

Simple technique for detecting RNA viruses by PCR in single sections of wax embedded tissue.

The detection of specific RNA species in wax-embedded tissue sections using the polymerase chain reaction (PCR) means that gene expression can be studied and RNA viruses detected in stored histological tissue samples. This technique potentially allows the distribution of gene expression and viral replication to be studied in finely subdivided tissues. A technique is presented that has been used successfully to detect short RNA target sequences (130-420 bases) from proto-oncogene Abelson, human enteroviruses, and the sheep retrovirus Maedi-Visna virus using RNA PCR in single wax sections (20-30 microns). Various tissues were used which had not been deliberately prepared for this purpose. In a simple procedure hot xylene dewaxing is followed by acid phenol extraction of RNA and RNA PCR.

Abelson murine leukemia virus↗
PubMed1998

A sensitive and robust method for measles RNA detection.

The aim of this study was to compare measles RNA amplification methods and to develop and select the most rapid, sensitive and robust procedure. The use of hybrid capture for measles RNA isolation was evaluated, and three RNA amplification detection techniques were compared. These were: (a) reverse transcription followed by nested polymerase chain reaction (RT-PCR) with MMLV reverse transcriptase and Taq polymerase; (b) a combined RT-PCR reaction using rTth polymerase; and (c) NASBA. An internal positive control was also developed. The sensitivities of the detection methods were quantified by using a dilution series of a known amount of total RNA from measles-infected Vero cells or by calculation of the number of transcript molecules (produced from a recombinant plasmid containing an insert measles nucleoprotein DNA) present in each amplification reaction, respectively. The results indicated that hybrid capture followed by combined RT-PCR with rTth polymerase was the most reproducibly robust and sensitive protocol and could detect as few as 10(4) synthetic measles RNA transcripts added to tissue homogenates. However, NASBA proved to be the most sensitive method for measles RNA detection in water.

Animals↗
PubMed1999

The effect of saliva specimen collection, handling and storage protocols on hepatitis C virus (HCV) RNA detection by PCR.

OBJECTIVES: Commercial assays can now be adapted to detect salivary anti-hepatitis C virus (HCV) antibodies, increasing the potential of saliva as a non-invasive diagnostic specimen suited to surveillance and epidemiological studies. However, current diagnostic algorithms involve confirmation of HCV infection by RT-PCR. Manipulation and storage conditions of serum can influence the stability of viral RNA. This study examined whether varying specimen collection, handling and storage protocols also affected subsequent HCV RNA detection by RT-PCR applied to saliva specimens. METHODS: Whole unstimulated saliva, together with saliva samples collected in two commercially available devices (Salivette and Omnisal) were obtained from 50 HCV seropositive intravenous drug users. The specimens were subjected to a number of handling and storage conditions, including heat treatment and prolonged storage, then examined for HCV RNA by RT-PCR using primers derived from the 5' non-coding region (5'NCR). RESULTS: HCV RNA was detected in saliva samples from 25 (50%) of the patients. No single collection device or handling procedure identified all the subjects with HCV RNA positive saliva though whole saliva yielded the greatest number of positive results. CONCLUSIONS: Collection and processing of saliva specimens for RT-PCR analysis is complex. At present, detection of salivary HCV RNA by PCR is not sufficiently sensitive for use as a diagnostic tool in epidemiological studies.

Adult↗
PubMed2003

Approaches to messenger RNA detection - comparison of methods.

Detection of messenger RNA is an important part of current biomedical research, although utilized for decades. This communication endeavors to compare three most commonly used techniques of mRNA detection, i.e. Northern blot, ribonuclease protection assay (RPA), and real-time polymerase chain reaction (RT-PCR). Principles and general procedures of these methods are described, and advantages and weaknesses of each are discussed in terms of their specificity, sensitivity, difficulty, time and material demands as well as health and environmental risks. We conclude that choice of any method discussed depends on particular purpose, experience of the researcher, and on laboratory equipment and organization.

Blotting, Northern↗
PubMed2001

Utility of HHV8 RNA detection for differentiating Kaposi's sarcoma from its mimics.

BACKGROUND: The diagnostic distinction of atypical vascular lesion or angiomatoid/hemosiderotic dermatofibroma and Kaposi's sarcoma can be difficult, especially in AIDS patients. Given the strong association between human herpes virus 8 (HHV8) and Kaposi's sarcoma, this study attempts to determine if HHV8 RNA detection by reverse transcription (RT) in situ polymerase chain reaction (PCR) could help in differentiating these entities. METHODS: Twenty-three Kaposi's sarcoma cases, 13 dermatofibromas, including 7 angiomatoid or hemosiderotic variants and eight atypical vascular lesions were tested for HHV8 by RT in situ PCR; five of the patients in the latter two groups were known to have AIDS. RESULTS: HHV8 RNA was detected in each of the 23 cases considered on histologic grounds to represent Kaposi's sarcoma; viral RNA and DNA localized to the majority of the endothelial and stromal spindle cells. None of the cases of dermatofibroma were HHV8 positive, whereas two of the atypical vascular lesions were viral positive, leading to a final diagnosis of Kaposi's sarcoma. CONCLUSIONS: RT in situ PCR for HHV8 RNA is a useful tool in the differential diagnosis between Kaposi's sarcoma and its mimics.

Acquired Immunodeficiency Syndrome↗
PubMed1993

Plasma collected from heparinized blood is not suitable for HCV-RNA detection by conventional RT-PCR assay.

Detection of hepatitis C virus-RNA (HCV-RNA) in serum or in plasma is considered a reliable marker for ongoing HCV infection. HCV-RNA was measured routinely in plasma collected from heparinized blood of patients with chronic hepatitis C and varying results were found. In this study, HCV-RNA was detected in peripheral blood mononuclear cells (PBMCs) and in serum of 16 out of 17 anti-HCV positive patients with chronic hepatitis C. In contrast, HCV-RNA was found in plasma collected from heparinized blood of only one of these seventeen patients. The addition of heparin to known HCV-RNA containing solutions before reverse-transcription and separately before PCR, demonstrated the inhibitory effect of heparin on the reverse transcription and amplification reaction. Furthermore, evidence is provided that plasma for PCR should be collected preferably into EDTA vacutainers. It is concluded, therefore, that plasma collected from heparinized blood is not suitable for HCV-RNA determination by RT-PCR. In addition, PBMCs might play an important role in the pathobiology of hepatitis C virus, since HCV-RNA was easily detected in PBMC of patients with chronic hepatitis C.

False Negative Reactions↗
PubMed1991

3'-end fluorochromized and haptenized oligonucleotides as in situ hybridization probes for multiple, simultaneous RNA detection.

We have used fluorescein-, digoxigenin- and biotin-(di)deoxyXTPs and terminal deoxynucleotidyl transferase for small scale labeling of synthetic oligonucleotide probes and here we show the applicability of such probes for the in situ detection of multiple RNA sequences. The enzymatic 3'-end-labeling methods proved to be good alternatives for the chemical fluorochrome and hapten labeling of 5'-end alkylamino-derivatized oligonucleotides. By combining 3'-end fluorescein-, biotin-, and digoxigenin-labeled oligonucleotides, double and triple hybridizations are feasible. For example, we demonstrated simultaneously mRNAs coding for caudodorsal cell hormone, a molluscan insulin-related peptide, and 28 S ribosomal RNA in cryostat sections of the cerebral ganglia of the pond snail Lymnaea stagnalis.

Animals↗
PubMed1986

In situ hybridization--application to gene localization and RNA detection.

In situ hybridization offers a direct approach for localization and quantitation of nucleic acid sequences in cellular preparations. Recent improvements in technology and methodology make possible the detection of DNA and RNA of relatively low copy number. For example, development of in situ hybridization methods for detection of single copy DNA sequences on mitotic chromosomes has led to general use of this technique for gene mapping of the human genome. More recently, improvements in methodology for detection of low abundancy RNA make possible a facilitated analysis of gene expression, both from cellular genes and exogenous sequences, such as viral genomes. In situ hybridization is now a powerful method for studying nucleic acid organization and function in normal cells, as well as in malignant cells, which should contribute to better understanding of the cell transformation process.

Acquired Immunodeficiency Syndrome↗
PubMed1994

Comparative analysis of the 5' non-coding region of pestivirus RNA detected from live virus vaccines.

Comparative analysis of nucleotide sequences in the 5' non-coding region (NCR) of pestivirus RNA detected from live porcine and human virus vaccines indicated that the contaminants are of bovine viral diarrhea virus (BVDV), and that there are at least three genotypes, which are distinct from hog cholera virus, among the BVDV strains. Most of the nucleotide changes in variable regions of the 5' NCR were covariant, with complementary substitutions at other positions for secondary structures. The proposed secondary structure in the 5' NCR was similar to the prokaryotic rho independent terminator. Short open reading frames in the 5' NCR were well conserved among pestiviruses.

Animals↗
PubMed1996

Is hepatitis C virus-RNA detection by nested polymerase chain reaction clinically relevant in hemodialysis patients?

We have prospectively studied in hemodialysis (HD) patients the evolution of hepatitis C virus (HCV) viremia and the putative relationships between the viremia and the biological markers of liver disease. For each of 22 HD patients having detectable antibodies to HCV (anti-HCV+), we looked four times for serum HCV-RNA by nested PCR (N-PCR), in April and November 1992, November 1993 and May 1994. We checked the transaminases (Trans) and the gamma glutamyl transpeptidase (gamma(GT)) levels on the same day as blood tests for the N-PCR. Abnormal Trans or gamma(GT)++ values were considered if they exceeded the upper limit of the normal level for our laboratory. Fifteen patients (68%) were intermittently N-PCR positive (N-PCR+): 3 patients were N-PCR+ at three determinations, 7 were N-PCR+ at two determinations and 5 only one time. Two patients (9%) were always N-PCR+ and five (23%) always negative. No correlation between an abnormal value of either Trans or gamma(GT) and viremia was evidenced at successive determinations. In conclusion, the majority (68%) of the anti-HCV+ patients had intermittent HCV N-PCR+. Among the anti-HCV+ patients, 77% were viremic. Since HCV viremia is often transitory and since there is no correlation between N-PCR positivity and the increase in Trans or gamma(GT) activities, HCV-RNA detection by N-PCR is probably not clinically relevant in anti-HCV+ HD patients.

Alanine Transaminase↗
PubMed1998

Sensitivity and specificity of a qualitative RNA detection assay to diagnose HIV infection in young infants. Perinatal AIDS Collaborative Transmission Study.

OBJECTIVE: To evaluate the sensitivity and specificity of an RNA detection assay for diagnosing perinatal HIV infection. METHODS: Plasma and serum specimens taken during the first 3 months of life from HIV-infected and uninfected children enrolled in a cohort study were assayed for HIV RNA using the qualitative nucleic acid sequence-based amplification (NASBA) kit. Sensitivity, specificity, and predictive values were calculated. NASBA results from infected children were compared with DNA PCR results from the same blood samples. Autoantibody patterns of suspected false-positive specimens were compared with those of subsequent specimens from the same child to exclude specimen labelling errors. RESULTS: Amongst 131 specimens from 105 HIV-infected children, the sensitivity of the qualitative NASBA assay was 13 out of 34 [38%; 95% confidence interval (CI), 22-56] at < 7 days, 56 out of 58 (97%; 95% CI, 88-100) at 7-41 days, and 37 out of 39 (95%; 95% CI, 83-99) at 42-93 days of life. Of 252 specimens from 206 uninfected children, six tested positive and one tested indeterminate by NASBA. Four of these positive specimens had discordant autoantibody patterns suggesting mislabelling; excluding these, the test specificity was 245 out of 248 (99%; 95% CI, 97-100). Amongst 128 paired specimens from infected children, NASBA results were more often positive than those from DNA PCR (103 versus 92; P=0.01). Amongst infants with specimens drawn in the first week of life, the proportion born after > 4 h of membrane rupture was greater amongst those testing negative (81%) than those testing positive (46%; P=0.05). CONCLUSIONS: The qualitative NASBA RNA assay is highly specific and more sensitive than DNA PCR. Qualitative RNA assays may be useful for diagnosing and excluding perinatal HIV infection in children after the first week of life for such purposes as initiating antiretroviral therapy and other treatment, resolving parental uncertainty, determining timing of transmission, and providing endpoints for intervention trials.

Cohort Studies↗
PubMed2003

[The rate of HCV-RNA detection in the serum, saliva, and tissue of the minor salivary glands in chronic hepatitis C with Sjogren's syndrome].

The trial enrolled 38 patients with chronic HCV-infection and Sjogren's syndrome (mean age 44.3 +/- 13.7 years). Biopsy of the minor salivary glands (MSG) was made in 20 patients. Polymerase chain reaction was used to study 20 MSG biopsies, 38 samples of native saliva for HCV-RNA. Saliva samples were also studied for Herpes virus DNA (EBV, CMV, HHV-VI type). All the patients with VHC appeared to have signs of xerostomia, 24 (63.2%) patients had xerophthalmia. MSG pathohistological changes were found in 19 (95%) patients. In the majority of cases (86.9%) they were characterized by mild infiltration and advanced fibrosis. HCV-RNA was found in the saliva of 23 (57.5%) patients, in MSG tissue--in 9 (39.1%) patients. HCV-RNA detection in the saliva did not depend on the degree of viremia, viral RNA in MSG correlated with viral load. EBV and HHV-VI, HHV-VI only and EBV were detected only in 7 (18.4%), 10 (26.3%) and 6 (15.8%) patients, respectively. Xerostomia occurred with the same rate (26.1 and 31.3%) in patients with and without herpes viruses in the saliva. Detection rate for HCV-RNA in the saliva was not related with viremia degree. Sjogren's disease symptoms in CHC patients did not depend on the presence or absence of DNA of herpes viruses in the saliva.

Adult↗
PubMed2006

Nanostructured probes for RNA detection in living cells.

The ability to visualize in real-time the expression level and localization of specific RNAs in living cells can offer tremendous opportunities for biological and disease studies. Here we review the recent development of nanostructured oligonucleotide probes for living cell RNA detection, and discuss the biological and engineering issues and challenges of quantifying gene expression in vivo. In particular, we describe methods that use dual FRET (fluorescence resonance energy transfer) or single molecular beacons in combination with peptide-based or membrane-permeabilization-based delivery, to image the relative level, localization, and dynamics of RNA in live cells. Examples of detecting endogenous mRNAs, as well as imaging their subcellular localization and colocalization are given to illustrate the biological applications, and issues in molecular beacon design, probe delivery, and target accessibility are discussed. The nanostructured probes promise to open new and exciting opportunities in sensitive gene detection for a wide range of biological and medical applications.

Animals↗
PubMed2006

Immunosuppression and GB virus C-RNA detection among HIV-infected patients in Cambodia.

In this survey, 213 patients in an antiretroviral treatment programme in Phnom Penh, Cambodia, were tested for GB virus C (GBV-C) RNA before treatment initiation. Most had advanced HIV infection, only 34 having CD4 cell counts > 200 cells/microl. GBV-C-RNA was detected in 35 patients. The proportion with positive GBV-C-RNA decreased dramatically with CD4 cell counts < 100 cells/microl. In multivariate analysis, low CD4 cell counts, tuberculosis, anaemia, and traditional medicine were independently and negatively associated with GBV-C-RNA detection.

AIDS-Related Opportunistic Infections↗