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PubMed2000

Efficacy of HCV core antigen detection during the preseroconversion period.

BACKGROUND: The purpose of this study was to compare the performances of HCV core antigen (HCV Ag) testing with HCV RNA detection during the preseroconversion period. STUDY DESIGN AND METHODS: Six HCV antibody (HCV Ab)-negative and HCV RNA-positive blood samples from 6 donors and 135 serial samples from 28 patients who had undergone hemodialysis, collected a mean of 90 days before the detection of HCV Ab, were tested by ELISA for the detection of HCV Ag and by PCR to quantify HCV RNA. RESULTS: Five of the six donors were positive for HCV Ag. The donor with a negative HCV Ag test had the lowest viral load. In the hemodialysis patients, the 43 first specimens of the series were HCV RNA negative. Of the 92 specimens that were HCV RNA positive, 81 (88%) were positive for HCV Ag. Among the 74 samples with more than 10(5) RNA copies, 71 (96%) were HCV Ag positive. Average time from first viremic bleed to first HCV Ag-positive bleed was estimated at 2.0 days and that to first HCV Ab-positive bleed at 50.8 days. CONCLUSION: HCV Ag testing permits the detection of an HCV infection about 1.5 months earlier than the HCV Ab screening tests and an average of only 2 days later than quantitative HCV RNA detection in individual specimens.

Antibodies, Viral↗

PubMed2001

Virus-like particles in a case of acute hepatitis with human GB virus-C viraemia.

BACKGROUND/AIMS: It is still controversial whether the human GB virus-C can cause liver injury, as in situ demonstration of the virus is still inconclusive. METHODS: Here we describe the case report of a patient with two episodes of severe acute hepatitis, who had a meticulous clinical, immunological and microbiological work-up, including human GB virus-C RNA detection by in situ hybridization and electron microscopy. RESULTS: Human GB virus-C viraemia was found as the only potential cause of hepatitis in this patient. Furthermore, virus-like particles could be demonstrated in the cytoplasm of single hepatocytes by electron microscopy and human GB virus-C RNA was detected in the liver by in situ hybridization. CONCLUSION: The presence of human GB virus-C RNA in serum together with the demonstration of human GB virus-C RNA in the liver, favour acute human GB virus-C infection as the cause of liver injury in this patient. Thus virus-like particles and hepatic human GB virus-C RNA should be specifically looked for by electron microscopy and in situ hybridization, especially during the diagnostic work-up of patients with unexplained hepatitis.

Acute Disease↗

PubMed1993

Hepatitis C virus RNA in serum of blood donors with or without elevated transaminase levels.

The pattern of hepatitis C virus (HCV) viremia in blood donors who are positive for antibody to HCV (anti-HCV) according to the level of transaminase activity is unclear. A polymerase chain reaction-based HCV RNA detection method was used to study two clearly defined groups of anti-HCV-positive blood donors with repeatedly normal (n = 27) and elevated (n = 17) alanine aminotransferase (ALT) levels. HCV RNA was detected in only 4 of 27 blood donors with normal ALT values and 15 of 17 with elevated ALT values. These results indicate that anti-HCV-positive blood donors with normal ALT levels constitute a heterogeneous group, as HCV viremia is detectable in only a small proportion of cases. Polymerase chain reaction should be useful in the surveillance of anti-HCV-positive blood donors with normal ALT levels, by identifying those who might benefit from further investigation and treatment.

Alanine Transaminase↗

PubMed1973

Detection of avian tumor virus RNA in uninfected chicken embryo cells.

Uninfected chicken embryo cells were analyzed for the presence of viral ribonucleic acid (RNA) by molecular hybridization with the single-stranded deoxyribonucleic acid (DNA) product of the RNA-dependent DNA polymerase contained in avian sarcoma-leukosis virions. Viral RNA was detected in all cells which contained the avian tumor virus group-specific antigen and the virus-related helper factor. The amounts of viral RNA in these cells ranged from approximately 3 to 40 copies of viral-specific sequences per cell. In general, the viral RNA content correlated with the level of helper activity in the cells. Cells infected with Rous-associated virus 2 contained 3,000 to 4,000 copies of viral RNA per cell. RNA from these infected cells hybridized with nearly 100% of the viral (3)H-DNA. By contrast, a maximum of less than 50% hybridization was obtained with RNA from the uninfected helper-positive cells, suggesting that not all of the viral RNA sequences were present in these cells. No viral RNA was detected in cells which lacked group-specific antigen and helper activity. Under the conditions used in these studies, less than 0.3 viral genome equivalents of RNA per cell would have been detected.

Animals↗

PubMed1975

Separation of sarcoma virus-specific and leukemia virus-specific genetic sequences of Moloney sarcoma virus.

We have studied the nucleic acid sequences in nonproducer cells transformed by Moloney sarcoma virus or Abelson leukemia virus (two types of replication-defective, RNA-containing, viruses isolated by passage of Moloney leukemia virus in BALB/c mice). DNA probes from the Moloney leukemia in virus detect RNA in both Abelson virus-transformed nonproducer cells and Moloney sarcoma virus-transformed nonproducer cells. A sarcoma-specific cDNA, prepared from the Moloney sarcoma virus, has extensive homology to RNA found in heterologous nonproducer cells transformed by Moloney sarcoma virus, has little homology to RNA in cells producing Moloney leukemia virus, and no detectable homology to RNA in nonproducer cells transformed by the Abelson virus. By analogy to earlier data on avian and mammalian sarcoma viruses, these results suggest that the Moloney sarcoma virus arose by recombination between a portion of the Moloney leukemia virus genome and additional sarcoma-specific information, and indicate that the expression of this information in not essential for Abelson virus-mediated fibroblast transformation.

Cell Line↗

PubMed2005

Detection of hepatitis C virus (HCV) in serum and peripheral-blood mononuclear cells from HCV-monoinfected and HIV/HCV-coinfected persons.

It has been speculated that hepatitis C virus (HCV) replicates in peripheral-blood mononuclear cells (PBMCs), which, therefore, may be a site for interaction with human immunodeficiency virus (HIV). We used strand-specific real-time polymerase chain reaction to detect HCV RNA in 28 HCV-monoinfected and 20 HIV/HCV-coinfected women. At the first visit, positive-strand HCV RNA was detected in serum samples from 89% of the women, whereas positive-strand HCV RNA was detected in PBMC samples from 32% and 55% of the HCV-monoinfected and HIV/HCV-coinfected women, respectively. After initiation of antiretroviral therapy, the HIV/HCV-coinfected women were significantly more likely to have detectable positive- and negative-strand HCV RNA in the PBMC compartment than were the HCV-monoinfected women. HIV and HCV RNA levels were not correlated. Serum HCV RNA levels were correlated over time; HCV RNA levels in the serum and PBMC compartments were not. These data suggest differential regulation of HCV RNA in the serum and PBMC compartments and may partially explain the limited HCV antiviral response rates observed in coinfected persons.

Adult↗

PubMed1999

Expression of beta-defensin genes by human salivary glands.

This study investigated expression of genes encoding human beta-defensins 1 and 2 by human salivary glands. Tissues from surgical biopsies were collected fresh onto ice and stored in liquid nitrogen. Total RNA was extracted using Trizol reagent and human beta-defensin messenger RNA detected by reverse transcriptase polymerase chain reaction amplification. DNA sequencing of amplified fragments, after ligation into pGEM-T Easy vector and transformation of competent Escherichia coli, confirmed identities of cloned fragments. Human beta-defensin 1 messenger RNA was detected in all 25 samples that generated amplifiable cDNA, as assessed using abl-specific primers. Three of 13 submandibular gland samples (two normal, one chronically inflamed), and 2 of 2 minor salivary gland samples (one normal, one chronically inflamed) expressed human beta-defensin 2 messenger RNA. All six parotid gland samples studied were negative for human beta-defensin 2 messenger RNA. Thus, human beta-defensin 1 gene expression occurred in all human major and minor salivary glands studied, whereas human beta-defensin 2 expression occurred only in a small number of gland samples.

Defensins↗

PubMed1998

Negative-strand HCV RNA was not detected in bone marrow cells of patients with HCV infection.

To determine whether hepatitis C virus (HCV) replicates in bone marrow, we investigated positive- and negative-strand HCV RNA in bone marrow cells and fluids, and sera from patients with HCV infection. The study population consisted of 15 patients positive for antibodies to HCV (anti-HCV). Positive- and negative-strands HCV RNA were detected using highly strand-specific rTth reverse transcription-polymerase chain reaction (rTth RT-PCR) followed by Southern blotting analysis. Positive-strand HCV RNA was detected in 12 (80%) serum samples, in 13 (86.7%) bone marrow fluid specimens, and in 6 (40.0%) bone marrow cell samples. Negative-strand HCV RNA was detected in 9 (60.0%) serum samples, 11 (91.7%) fluid specimens, while it was not detected in bone marrow cells. The absence of negative-strand HCV RNA in bone marrow cells suggested that HCV does not replicate in these cells. Negative-strand HCV RNA detected in serum and bone marrow fluid samples may have been due to contamination with circulating HCV RNA from hepatocytes.

Adult↗

PubMed1995

Role of hepatitis C virus in chronic liver disease occurring after orthotopic liver transplantation.

Paediatric orthotopic liver transplant recipients may develop chronic hepatitis after surgery. To investigate the role of hepatitis C virus in this pathology a cohort of 249 paediatric orthotopic liver transplant recipients was studied. Sixteen children (6.4%) were found to have chronic hepatitis C virus hepatitis after orthotopic liver transplantation. All but one of them had serum transaminase values which were persistently raised two to eight times the upper limit of normal. Thirteen were positive for both serology and serum hepatitis C virus RNA. Serum hepatitis C virus RNA detection occurred five to 33 months before hepatitis C virus antibodies. Liver tissue hepatitis C virus RNA and hepatitis C virus core antigen were detected in five. In one patient, tissue hepatitis C virus core antigen was detected when other tests for hepatitis C were negative. Two patients had positive human cytomegalovirus serum antibodies and RNA before transplantation. Although serum hepatitis C virus RNA was not detected after transplantation, serum enzyme immunosorbent assay and tissue core antigen were still detectable in both patients. In another child, serum hepatitis C virus RNA was positive and hepatitis C virus core antigen was found on a liver biopsy specimen but antihepatitis C virus antibodies were negative as well as liver hepatitis C virus RNA. No patient developed severe liver disease or cirrhosis during a follow up of up to 72 months. It is concluded that hepatitis C virus is a significant cause of morbidity after paediatric orthotopic liver transplantation. Diagnosis cannot rely on serological testing only. The patients remained stable on follow up, but longer prospective histological studies remain necessary to establish prognosis.

Antigens, Viral↗

PubMed1998

Effect of interferon therapy on hepatitis C virus RNA in whole blood, plasma, and peripheral blood mononuclear cells.

Fifty-two patients with chronic hepatitis C virus (HCV) infection were treated with standard doses of interferon alfa-2b. During treatment, HCV RNA detection was studied in samples of whole blood (WB), plasma (Pl), and peripheral blood mononuclear cells (PBMCs). Individuals were classified as sustained responders (SRs), complete responders with relapse (CRs), partial responders (PRs), or nonresponders (NRs) according to normalization of serum alanine transaminase (ALT) during treatment and follow-up. Before treatment, 100% of WB samples and more than 95% of Pl and PBMC samples were positive for HCV RNA. During treatment, there was progressive clearance of HCV RNA from Pl and PBMCs in SRs and CRs, but CRs had significantly more positive WB samples during and following treatment (P <.0001). At 6 months, only 10% of CR patients were positive by Pl assay, but 50% were positive by WB assay (P <.01). In the PR group, all WB samples remained positive throughout treatment, although 25% to 40% of PBMC and Pl samples became negative for HCV RNA during the first 2 months of therapy (WB > Pl or PBMC; P < .001). However, at later times during treatment most Pl and PBMC samples in the PR group were positive. Samples from the NR group showed no clearance of HCV RNA from WB, Pl, or PBMC fractions. These data document the increased sensitivity of WB assays for detecting HCV RNA in the peripheral blood of patients during interferon therapy. Furthermore, our findings suggest that WB analysis of HCV RNA may be a useful parameter to monitor in determining the end point of interferon therapy.

Adult↗

PubMed2026

MAJIQ-CLIN: A novel tool to help identify Mendelian disease-causing variants from RNA-seq data.

PURPOSE: The current diagnostic rate for patients with suspected Mendelian genetic disorders is low, despite exome/genome sequencing being the standard of care. One reason for this low diagnostic rate is that traditional exome/genome sequencing analysis methods struggle to detect RNA splicing aberrations. Causative variants often involve splicing changes, with numerous splice-altering variants being responsible for known Mendelian disorders. Therefore, it is crucial to develop reliable tools to detect, quantify, prioritize, and visualize RNA splicing aberrations from patient RNA sequencing data. METHODS: We developed Modeling Alternative Junction Inclusion Quantification for Clinical Applications (MAJIQ-CLIN), a method to identify RNA splicing aberrations in patients' RNA sequencing data compared with a cohort of control samples. MAJIQ-CLIN can efficiently process large datasets, avoiding reprocessing when new data are added, while effectively detecting local splicing variations with deviations in a given patient, termed outlier local splicing variation, or unique to the patient, termed private local splicing variation. RESULTS: We performed a systematic evaluation of the accuracy of tools for detecting patients' RNA splicing aberrations from RNA sequence using synthetic data across several aberration types and transcript inclusion levels. Then, we used several real datasets to assess MAJIQ-CLINs ability to identify solved test cases and control for the effect of confounders such as batches. We showed that MAJIQ-CLIN compares favorably to existing tools in both accuracy and efficiency. We also used MAJIQ-CLIN to investigate several unsolved patient cases from the Undiagnosed Diseases Network. CONCLUSION: MAJIQ-CLIN offers an efficient, accurate, and user-friendly tool to aid in diagnosing Mendelian disease-causing variants from RNA sequence data.

Bioinformatics↗

PubMed1993

Detection of hepatitis delta virus RNA in human liver tissue by non-radioactive in situ hybridization.

Several studies have demonstrated the presence of serum HDV-RNA by molecular hybridization in patients with chronic D infection, but there is scarce information about the presence of HDV-RNA in hepatic tissue. The presence of HDV-RNA by in situ hybridization (ISH) with a non-radioactive probe in paraffin-embedded hepatic tissue was studied in 29 patients with chronic delta hepatitis (20 with and 9 without intrahepatic delta antigen) and correlate their presence with the expression of hepatic delta antigen and serum HDV-RNA by dot-blot hybridization. HDV-RNA was detected by in situ hybridization in 18 cases: 16 of the 20 (80%) biopsies with intrahepatic delta antigen and 2 of the 9 (22%) without. HDV-RNA was not detected in any of the control cases. Serum HDV-RNA was found in 19 cases: 18 (90%) of 20 chronic delta hepatitis cases with tissular delta antigen and one of the 9 without intrahepatic delta antigen. All patients except one, who was positive for intrahepatic HDV-RNA, showed serum HDV-RNA. However, in two cases ISH detected hepatic HDV-RNA without tissular HDAg; one of these also had serum HDV-RNA and in the other positivity for hepatic HDV-RNA by ISH was the only marker of viral delta replication. In conclusion, detection of HDV-RNA in hepatic tissue by in situ hybridization with a digoxygenin-labelled probe is a rapid and sensitive method that could be a useful tool for diagnosis of HDV infection in clinical laboratories.

DNA Probes↗

PubMed2000

Detection of hepatitis C virus RNA sequences in B-cell non-Hodgkin lymphoma.

Serologic testing shows that hepatitis C virus (HCV) may have a role in the pathogenesis of B-cell non-Hodgkin lymphomas (B-cell NHLs). We tried to demonstrate HCV RNA sequences in paraffin-embedded tissue from B-cell NHLs by reverse-transcription double polymerase chain reaction (RT-PCR) and Southern blotting. We studied 31 consecutive cases of B-cell NHLs; lymph nodes from 32 patients with diseases other than B-cell NHL were negative controls. Positive-strand HCV RNA was tested with primers for the 5' untranslated region. Replicative negative strand HCV RNA was tested with strand-specific RT-PCR for the 5' untranslated region. Immunohistochemical staining for HCV was done using an antibody to HCV core protein. Positive-strand HCV RNA was detected in 8 patients with B-cell NHL; negative-strand HCV RNA was detected in 6 of these cases, indicating viral replication. All control cases were negative for HCV RNA. Immunohistochemistry showed no staining of lymphoma cells for HCV core proteins in any case. HCV and B-cell NHLs may be associated. RT-PCR on paraffin-embedded lymphoma tissue is an alternative method of testing for HCV. The value of immunohistochemistry could not be ascertained. The exact role of HCV in the pathogenesis of B-cell NHL needs to be studied further.

Adolescent↗

PubMed2001

Mosquito cells bind and replicate hepatitis C virus.

Several studies have demonstrated some hepatitis C virus (HCV) replication in lymphocyte and hepatocyte cell lines such as in African green monkey Vero cells. The aim of the present study was to select other cell lines able to bind and replicate HCV. Human hepatoma PLC/PRF/5 cells, human lymphoma Namalwa cells, Vero and mosquito AP61 cells were inoculated with HCV-positive plasma, washed six times and examined for the presence of the viral genome at different times post infection, using an RT-PCR method. Binding of HCV to cells was estimated by HCV RNA detection in cells 2 hr after inoculation and in the last wash of these cells. Successive virus passages in cells were carried out. All the cells studied were able to bind HCV but only AP61 and Vero cells provided evidence of replication and production of infectious virus: virus RNA was detected during 28 days post-infection in four successive virus passages. CD81 molecules, a putative HCV receptor, were detected by cytofluorometric analysis. Vero cells express CD81 molecules whereas these molecules were not detected on AP61 cells. It is suggested that other receptors are involved in HCV binding to Vero and AP61 cells.

Adult↗

PubMed1996

Detection of hepatitis C virus RNA from the heart of patients with hypertrophic cardiomyopathy.

We investigated hepatitis C virus (HCV) infection in 35 patients with hypertrophic cardiomyopathy and 40 patients with ischemic heart disease who were consecutively admitted to our hospital. Frequency of positive anti-HCV antibody was significantly higher in patients with hypertrophic cardiomyopathy (6 of 35 patients, 17.1%) than that in patients with ischemic heart disease (1 of 40 patients, 2.5%, p = 0.036). In three of these six patients with hypertrophic cardiomyopathy, HCV RNA was detected in myocardial tissue. In two of these three patients, HCV RNA was detected from biopsy and autopsy specimens of the ventricles, but not in the serum, suggesting that HCV may replicate in myocardial tissue and may be relevant to ventricular hypertrophy. Thus, HCV infection may play a role in the development of hypertrophic cardiomyopathy.

Adolescent↗

PubMed2004

Microbead-based affinity chromatography chip using RNA aptamer modified with photocleavable linker.

A microbead-based affinity chromatography chip (micro-BACC) controlling hundreds of nanoliters of reaction volume was developed to separate and analyze hepatitis C virus (HCV) RNA polymerase protein by immobilization of an RNA aptamer on beads. A photocleavable linker was conjugated in between the beads and the aptamer to elute the bound RNA polymerase from the RNA aptamer in one step by UV irradiation, resulting in an efficient method to elute and identify the target molecule bound on RNA using a mass spectrometer. This linker showed a cleavage activity over 70% upon UV irradiation at 1050 mW/cm2 for more than 5 min. The photoelution method could prevent the target molecule from contaminations in affinity chromatography caused by elution solutions of high salt concentration, extreme pH and detergent, respectively. In this chip, sample reagents up to 800 nL could be metered quantitatively into the bead chamber using a nanoliter dispenser working, based on surface-guided flow control and pneumatic control by external air pressure on the chip. RNA polymerase eluted after UV irradiation was successfully analyzed by trypsin treatment without additional purification. As a result, using the aptamer, we could detect RNA polymerase from 800 nL hepatitis C patient serum containing 96 fmol HCV RNA polymerase. The detection limit of this system was estimated to be 9.6 fmol HCV RNA polymerase.

Chromatography, Affinity↗

PubMed1984

[Activation of cellular genes as affected by Rauscher leukemia virus].

The methods of hybridization in solution and blot hybridization have shown that the BALB/c mice spleen cells contain "silent" genes which can amplificate and change their structure following the infection by the Rauscher leukemia virus (RLV). The product of these gene activation is nuclear 35S RNA detectable by the comparative electrophoretic analysis of heterogeneous nuclear RNA of leukemic and normal cells. The expression of complete copies of 35S RNA was observed in nuclei of RLV-infected cells, while in cytoplasm this RNA is represented by incomplete copies. The expression of the sequences homologous to this 35 S RNA in normal mice spleen cells was not detected.

Animals↗

PubMed1996

Human immunodeficiency virus in plasma and genital secretions during the menstrual cycle.

Six human immunodeficiency virus (HIV)-positive women were studied weekly over 8 weeks to detect HIV RNA in plasma and cervical secretions and proviral DNA in cervical, vaginal, and cervicovaginal lavage samples by polymerase chain reaction (PCR) amplification techniques. In cervical swab samples, cell-free HIV RNA was detected more frequently than cell-associated HIV proviral DNA (22/48 vs. 7/48, respectively). Cervical HIV RNA was consistently detected in 2 women with plasma HIV RNA > 100,000 copies/mL but was not detected in 2 women with plasma HIV RNA < 10,000 copies/mL, regardless of menstruation status. HIV-specific IgA was detected in the plasma of 2 women and in at least 1 cervicovaginal lavage sample from all 6 women. Thus, quantitation of cervical HIV RNA can be accomplished by PCR techniques and may be useful in evaluation genital viral shedding.

Adult↗