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Rhinovirus detection using probes from the 5' and 3' end of the genome.

This study investigated the abilities of cDNA probes from the 5' and 3' ends of the genome of human rhinoviruses (HRV-) 14, 9, and 1B to detect RNA from 59 rhinovirus serotypes. The results show that probes from the 5' end of the genomes of HRV-14, 9, and 1 B detected a large number of serotypes but the detection rate was variable and depended on the degree of homology with the particular probe. In contrast, all the 3' end probes were specific for the homologous virus. However, a long HRV-9 probe detected a large number of serotypes. It was concluded that such cDNA probes would not detect all serotypes with equal efficiency. Synthetic oligonucleotides corresponding to short but highly conserved regions in the 5' non coding region may overcome this problem.

DNA Probes↗

Hepatitis C virus type I(1a) in northern China.

Twenty-four patients with hepatitis C virus (HCV) antibody from the Chinese North Western province of Jilin were further analysed by the immunoblot assay-2 (RIBA-2), reverse transcription-polymerase chain reaction (RT-PCR) for serum HCV RNA detection, and direct sequence-genotyping. Good concordance was found between the original second generation HCV antibody ELISA, RIBA-2, and serum HCV RNA. The occurrence of genotype I (1a), a genotype not previously reported in China, is described in 5(20.8%) of 24 cases, in association with genotypes II(1b) and III(2a) which were found in 16(66.7%) and 3(12.5%) of 24 cases, respectively. Imported blood products were unlikely to be the source of infection with genotype I (1a) but could not be definitively ruled out.

Base Sequence↗

Hepatitis C viraemia and liver disease in symptom-free individuals with anti-HCV.

There is controversy about clinical management of patients who persistently have antibodies to hepatitis C virus (anti-HCV) but who have no symptoms and signs of liver disease. We have taken liver biopsy samples from 23 such patients (16 of whom had normal alanine aminotransferase [ALT] values) to assess prevalence of liver disease and to see whether anti-HCV and HCV-RNA correlated with histological findings. 16 patients had histological evidence of chronic hepatitis, which was not predicted by serum ALT or by the pattern of specificity of anti-HCV. All 16 cases with hepatitis C viraemia (HCV-RNA detected by polymerase chain reaction), including 9 with normal ALT, had chronic hepatitis on biopsy (p less than 0.001), whereas 7 HCV-RNA-negative cases had normal liver histology. These findings indicate that serum HCV-RNA is a sensitive and specific marker of liver disease in anti-HCV-positive subjects, independent of ALT values, and challenge the idea of the existence of "true" healthy carriers of HCV.

Antibodies, Viral↗

Intercalation activating fluorescence DNA probe and its application to homogeneous quantification of a target sequence by isothermal sequence amplification in a closed vessel.

We developed a completely homogeneous and isothermal method of detecting RNA sequences and demonstrated ultrarapid and direct quantification of pathogenic gene expression with high sensitivity. The assay is based on performing isothermal RNA sequence amplification in the presence of our novel DNA probe, an intercalation activating fluorescence DNA probe, and measuring the fluorescence intensity of the reaction mixture. When detecting mecA gene expression of methicillin-resistant Staphylococcus aureus, we quantified starting copies ranging from 10 to 10(7) copies within 10min. The primer sequences were designed to bind to secondary structure-free sites of the target RNA, which enabled a totally isothermal protocol to quantify mRNA specifically in a sample of existing genomic DNA. When we applied this to quantifying the expression of marker genes of Vibrio parahaemolyticus and Mycobacterium bovis BCG strain, the results correlated well with the viability of each bacterium. We also demonstrated monitoring Pab gene expression of M. bovis BCG during cultivation with antibiotics. The present method can potentially realize rapid antimicrobial susceptibility testing of slowly growing organisms, such as tuberculosis.

Base Sequence↗

Detection of viral RNA by electron microscopic in situ hybridization (ISH-EM) in the germinal epithelium of mice infected with encephalomyocarditis (EMC) virus.

Electron microscopic in situ hybridization (ISH-EM) was first applied to the detection of viral RNA in the germinal epithelium of mice inoculated i.p. with 10(5) plaque-forming units/mouse of the D variant of encephalomyocarditis virus (EMC-D). Signals of viral RNA were first detected in a small number of Sertoli cells showing mild degeneration at 2 days post inoculation, and 2 days later, they were also detected in germinal cells and spermatogonia when Sertoli cells showed prominent degeneration. The results clearly demonstrated that the first site of viral attack in the germinal epithelium was Sertoli cell in the case of EMC-D-induced mouse orchitis.

Animals↗

PCR detection of dengue virus using dried whole blood spotted on filter paper.

Whole blood dried onto filter paper constitutes a potentially useful material for molecular testing of viruses, including dengue. In order to assess the stability of viral RNA, we carried out dengue-RNA detection in whole blood infected with dengue virus that had been previously spotted onto filter paper. Filter papers were stored at room temperature, 4 and -70 degrees C and processed for PCR assay at intervals of 2, 4, 6 and 9 weeks. Our results demonstrated that dengue-RNA was stable in filter paper for 9 weeks at all tested temperatures. Furthermore, we evaluated these conditions using frozen sera and dried blood samples onto filter paper from 52 patients with confirmed clinical diagnosis of dengue infection. PCR results showed a 100% specificity and 93% sensitivity for dried blood samples. This storage method facilitates the transportation and analysis by nucleic acid amplification techniques even when freezing conditions are not available.

Blood↗

Analysis of expression of prgX, a key negative regulator of the transfer of the Enterococcus faecalis pheromone-inducible plasmid pCF10.

Conjugative transfer of pCF10, a plasmid found in Enterococcus faecalis, is induced by the peptide pheromone cCF10 and the donor-recipient aggregation is mediated by PrgB. Expression of prgB in pCF10 is negatively regulated by PrgX. The prgX gene is adjacent to prgQ which provides the promoter for prgB expression. The prgX and prgQ genes are transcribed in opposite directions. A deletion spanning nucleotides+259 to +398 from the prgQ transcription initiation site abolished the prgX gene products at both RNA and protein levels. An RNA, named Qa, was found to be transcribed in the antisense direction in the prgQ region. The transcription start site and the promoter were found to be almost identical with those of the traD determinant in pAD1, another pheromone-responsive plasmid. The first inverted repeat sequence in prgQ, IRS1, was required for the full activity of the Qa promoter. Although the size of the major Qa RNA detected by Northern blot analysis was too short (ca 120 nt) to be an mRNA for PrgX protein, the transcription from the Qa promoter was shown to proceed through to prgX. Transcriptional fusion analyses showed that the transcription of prgX requires one or more trans elements. Moreover, deletion of prgX greatly reduced the level of the Qa RNA and abolished transcription of prgX. Although transcription initiation from the Qa promoter was not increased by PrgX, transcriptional readthrough to prgX was increased by the protein. Based on these data, we conclude that transcription of prgX is initiated from the Qa promoter in prgQ, and PrgX autoregulates its transcription either by mediating transcriptional readthrough or increasing mRNA stability. The PrgX protein, prgX RNA, and the Qa RNA were downregulated by cCF10 induction; however, prgX gene products were still detected for at least 40 minutes after induction.

Amino Acid Sequence↗

Purification of Xenopus transcription factor IIIA and 5 S RNA from 7 S ribonucleoprotein particle by ammonium sulfate precipitation.

A simple and efficient method for purifying Xenopus transcription factor IIIA from the 7 S particle has been developed by taking advantage of the differential solubilities of the protein factor and 5 S RNA in ammonium sulfate solution. Conditions under which ammonium sulfate dissociates the 7 S particle and selectively precipitates factor IIIA while the 5 S RNA moiety remains in the supernatant were found. The method simultaneously purifies, in a nondestructive manner, both factor IIIA and 5 S RNA in high yield. Purification proceeds through several ammonium sulfate precipitations of the 7 S particle. Factor IIIA obtained by this method contains no detectable RNA and is highly active as judged by DNase I footprinting and in vitro transcription of the 5 S RNA gene, as well as reconstitution with 5 S RNA to form the 7 S particle. The molar extinction coefficients of factor IIIA at 205 and 280 nm were determined from the ultraviolet absorption spectra measured with the purified protein.

Ammonium Sulfate↗

Degradation of apolipoprotein II mRNA occurs via endonucleolytic cleavage at 5'-AAU-3'/5'-UAA-3' elements in single-stranded loop domains of the 3'-noncoding region.

Degradation intermediates of the estrogen-regulated apolipoprotein (apo) II mRNA were identified by S1 nuclease mapping and primer extension analysis. S1 mapping of poly(A)-RNA detected a series of mRNAs truncated at specific sites in the 3'-noncoding region. Many of these sites were also detected by primer extension analysis indicating that truncated molecules resulted from endonucleolytic cleavage in the 3'-noncoding region. Identical cleavage sites were seen with RNA from estrogen-treated animals or from animals withdrawn from hormone under conditions where apoII mRNA degraded in the slow (t1/2 = 13 h) or rapid (t1/2 = 1.5 h) decay mode. No differences were seen in poly(A) tail length or heterogeneity among these conditions. These results indicate that the estrogen-induced alteration in apoII mRNA turnover does not involve a new pathway of degradation, but, more likely, involves an increased targeting of the mRNA for degradation by a preexisting pathway. These data are consistent with a mechanism in which the initial step in apoII mRNA degradation is an endonucleolytic cleavage in the 3'-noncoding region without prior removal of the poly(A) tail. The endonucleolytic cleavage sites occurred predominantly at 5'-AAU-3' or 5'-UAA-3' trinucleotides found in single-stranded domains in a secondary structure model of the naked mRNA (Hwang, S-P. L., Eisenberg, M., Binder, R., Shelness, G. S., and Williams, D. L. (1989) J. Biol. Chem. 264, 8410-8418). The structure of the 3'-noncoding region in polyribosomal messenger ribonucleoprotein was examined by titrations of liver homogenates with dimethyl sulfate and cobra venom RNase. The results suggest that the typical cleavage site is a 5'-AAU-3' or 5'-UAA-3' trinucleotide in an accessible single-stranded loop domain. Single-stranded domains alone or accessible domains alone are not sufficient for cleavage. Similarly, 5'-AAU-3' or 5'-UAA-3' trinucleotides alone are not sufficient for cleavage. Localization of these trinucleotides to accessible single-stranded domains in the polyribosomal messenger ribonucleoprotein may provide the specificity for cleavage during targeted degradation.

Animals↗

Detection of hepatitis C virus RNA in serum of patients with chronic hepatitis C treated with interferon-alpha.

We tested serial serum samples for hepatitis C virus RNA from patients undergoing treatment for chronic hepatitis C with interferon-alpha using an assay that combined reverse transcription and polymerase chain reaction. The subjects studied were 20 patients with chronic hepatitis who had serum antibody to hepatitis C virus (anti-C100-3). Before therapy, hepatitis C virus RNA was detected in 18 (90%) and 20 (100%) patients using primer sets derived from the NS3 region or the 5'-noncoding region of hepatitis C virus, respectively. Hepatitis C virus RNA became undetectable in all patients whose ALT level fell into the normal range during therapy. However, hepatitis C virus RNA reappeared in all patients whose ALT levels rose again after therapy, usually before the relapse. In patients whose ALT levels did not become normal, hepatitis C virus RNA did not disappear during therapy. Thus therapy with interferon-alpha appears to be beneficial in chronic hepatitis C because of its suppressive effects on hepatitis C virus replication. Detection of hepatitis C virus RNA in serum is useful for evaluating the antiviral effect of interferon.

Adult↗

Neuropathological changes in transgenic mice carrying copies of a transcriptionally activated Mos protooncogene.

Independent transgenic mouse lines carrying the mouse Mos protooncogene linked to a retroviral transcriptional control sequence display behavioral abnormalities including circling, head tilting, and head bobbing. This dominant phenotype shows various degrees of penetrance in different transgenic founder animals and lines. Neuronal and axonal degeneration, gliosis, and inflammatory infiltrates are found in all transgenic mouse lines in which behavioral traits are present. Recordings of auditory-evoked potentials in mice of one of these lines demonstrate that transgenic mice are deaf; in these mice spiral ganglia degenerate and most of the cochlear hair cells are absent. By using an S1 nuclease protection assay, we have detected RNA expression of the transgene in all tissues examined and, in particular, at high levels in brain. In situ hybridization experiments show that Mos expression can be detected in specific areas of the central nervous system. Lesions are present in areas with demonstrable overexpression of Mos.

Animals↗

Saponin pre-treatment in pre-embedding electron microscopic in situ hybridization for detection of specific RNA sequences in cultured cells: a methodological study.

We describe a method for detection of specific RNA targets in cultured cells at the electron microscopic (EM) level using pre-embedding in situ hybridization (ISH). The specimens were monitored by reflection-contrast microscopy (RCM) before processing for EM. A good balance between preservation of ultrastructure and intensity of hybridization signals was obtained by using mild aldehyde fixation followed by saponin permeabilization. Digoxigenin-labeled probes were used for detection of human elongation factor (HEF) mRNA in HeLa cells, immediate early (IE) mRNA in rat 9G cells, and 28S rRNA in both cell lines. The hybrids were detected immunocytochemically by the peroxidase/diaminobenzidine (DAB) method or by ultra-small gold with silver enhancement. Comparison of these methods favored the peroxidase/DAB system. The accessibility of RNA in the different cell compartments was dependent on the extent of cross-linking during primary fixation even after permeabilization with saponin. By using the most optimal ISH protocol and the peroxidase/DAB system, we detected 28S rRNA over all ribosomes in the cytoplasm but not in the nucleoli, and IE mRNA in a large spot with many smaller spots around it in the nucleoplasm as well as in speckles over the cytoplasm. The sensitivity of the method is such that HEF housekeeping gene transcripts were detected in the cytoplasm.

Animals↗

Laboratory diagnosis of enteroviral infections of the central nervous system by using a nested RT-polymerase chain reaction (PCR) assay.

Enteroviruses are the most common pathogens identified in infants hospitalized for suspected aseptic meningitis. Rapid detection of enterovirus infection is essential in taking the decision for treatment with antiviral agents and applying infection control measures in hospitalized pediatric patients. The purpose of this study was to compare the results of conventional virus isolation with those of enteroviral RNA detection by reverse transcription (RT)-PCR method in identical specimens from cases of suspected aseptic meningitis. Cerebrospinal fluid (CSF) samples were collected for viral examination from 68 pediatric patients with suspected aseptic meningitis from 1999 to 2002. These samples were inoculated in HeLa, Hep-2 and RD cell culture. The viral RNA was investigated by in-house RT-PCR method. The isolated viruses were typed by neutralization test. 36 of the 68 specimens were detected to be enterovirus positive by culture method, while 43 of them yielded positive results when RT-PCR method is used. Discrepancies occurred between the two methods in 15 specimens. While 11 specimens were positive by RT-PCR, these are found to be culture-negative. The isolated viruses were typed as Echovirus 30 (n: 30), Group B coxsackievirus (n: 5) and one isolate could not be typed by neutralization. Because of higher sensitivity and rapidity of RT-PCR, it is superior (p = 0.016) to virus culture of CSF for the diagnosis of enterovirus meningitis. Although the clinical usefulness of viral culture from CSF is limited, the final laboratory identification needs cultural techniques.

Adolescent↗

Calibration of target amounts of DNA in hybridization experiments using monoclonal anti-nucleoside antibodies.

Two anti-nucleoside monoclonal antibodies (A-16 and G-K21) were raised after immunizing mice with adenosine or guanosine coupled to bovine serum albumin by periodate oxidation. They were selected for their ability to detect these immunogens and single-stranded DNA in an enzyme-linked immunosorbent assay test. The antibodies were purified from ascitic fluids, their isotypes were determined and their ability to detect DNAs and RNAs on nitrocellulose membranes was tested. They belonged to the IgG1 subclass and were both able to recognize picogram amounts of single-stranded DNAs on nitrocellulose sheets, whatever the origin of the nucleic acid, but were unable to detect RNA efficiently. The same monoclonal antibodies were used to estimate minute amounts of target staphylococci DNAs to permit standardization of non-radioactive hybridization experiments for detection of antibiotic resistance genes.

Adenosine↗

Differences between interferon-alpha and -beta treatment for patients with chronic hepatitis C virus infection.

To compare virological, biochemical, and immune responses to human lymphoblastoid interferon (IFN-alpha) and human fibroblast interferon (IFN-beta) in patients with chronic hepatitis C virus (HCV) infection, 120 patients were randomly assigned to three groups (group A, 60 patients receiving IFN-alpha, 6 million units (MU) once a day, daily for one month and thrice weekly for five months; group B, 40 patients receiving 6 MU IFN-beta once a day daily for two months; and group C, 20 patients receiving 3 MU IFN-beta twice a day (6 MU/day) daily for two months). Serum soluble interleukin-2 receptor (sIL-2R) and interleukin-6 (IL-6) levels were measured by enzyme-linked immunosorbent assay. Patients with sustained clearance of serum HCV RNA detected by polymerase chain reaction (PCR) at six months after IFN treatment were defined as having complete response to IFN treatment. A low level of HCV RNA (< or = 10(4) copies/50 microl, measured by competitive PCR) and HCV RNA of genotype 2a were favorable factors for a complete response to both IFNs. Complete response in group A treatment was strongly associated with early HCV RNA clearance, in contrast with group B. A significantly higher HCV RNA negativity at the second week from start of treatment was noted in group C (80.0%), compared with groups A (41.6%) and B (27.5%). sIL-2R levels rose in each group during IFN administration. In group C, alanine aminotransferase (ALT) and IL-6 levels were remarkably elevated. These findings indicate that timing of serum HCV RNA negativity in sustained response differs between IFN-alpha and IFN-beta administrations and that early HCV RNA clearance was induced by twice-a-day IFN-beta treatment.

Antiviral Agents↗

Evaluation of HIV-1 p24 antigenemia and level of CD8+CD38+ T cells as surrogate markers of HIV-1 RNA viral load in HIV-1-infected patients in Dakar, Senegal.

Alternative, affordable, and simple assays to monitor antiretroviral therapy (ART) in resource-poor settings are needed. We have evaluated and compared a heat-denatured (HD) HIV p24 amplified enzyme-linked immunosorbent assay from Perkin-Elmer and CD38CD8 T-cell levels, determined by flow cytometry, for their capacity to predict viral load (VL) in HIV-1-infected patients from Senegal. Median fluorescence intensity (MFI) of CD38 expression on memory (CD45RO) CD8 T cells correlated better with RNA VL than HD p24 antigenemia (R = 0.576, P < 0.0001 vs R = 0.548, P < 0.0001). MFI of CD38 expression on memory CD8 T cells could predict detectable RNA VL (VL = 2.6 log10) with a sensitivity of 87% and a specificity of 74%. A comparable sensitivity (89%) could be reached for HD p24 assay, but only to predict RNA VL of more than 5 logs, which might lead to unacceptable delays in clinical decision making. The clinical use of the HD p24 assay to monitor ART in Senegal would require more comparative data about the kinetics of p24 antigen and HIV RNA in peripheral blood as well as further evaluation regarding its sensitivity toward subtype A and CRF02. MFI of CD38 expression on memory CD8 T cells appeared to be a better alternative to monitor ART in HIV-infected patients from Senegal.

ADP-ribosyl Cyclase 1↗

Nipah virus-associated encephalitis outbreak, Siliguri, India.

During January and February 2001, an outbreak of febrile illness associated with altered sensorium was observed in Siliguri, West Bengal, India. Laboratory investigations at the time of the outbreak did not identify an infectious agent. Because Siliguri is in close proximity to Bangladesh, where outbreaks of Nipah virus (NiV) infection were recently described, clinical material obtained during the Siliguri outbreak was retrospectively analyzed for evidence of NiV infection. NiV-specific immunoglobulin M (IgM) and IgG antibodies were detected in 9 of 18 patients. Reverse transcription-polymerase chain reaction (RT-PCR) assays detected RNA from NiV in urine samples from 5 patients. Sequence analysis confirmed that the PCR products were derived from NiV RNA and suggested that the NiV from Siliguri was more closely related to NiV isolates from Bangladesh than to NiV isolates from Malaysia. NiV infection has not been previously detected in India.

Adolescent↗

Evaluation of antibody-dependent enhancement of feline infectious peritonitis virus infectivity using in situ hybridization.

Infection of primary macrophages in vitro by feline infectious peritonitis virus (FIPV) was used as a model system to study the kinetics of Fc receptor-mediated antibody-dependent enhancement (FcR-ADE) of virus infectivity at the single cell level. Cells were examined for evidence of viral RNA synthesis at various times points after infection, using 35S-labeled riboprobes and in situ hybridization. At each time point, infection of macrophages with FIPV in the presence of enhancing antiserum was compared to infection with FIPV alone. Both positive- and negative-sense FIPV RNA synthesis began at the same time point after infection in each case. In addition, the level of enhancement was the same from the earliest time of detectable RNA synthesis onward. Therefore, the degree of enhancement appears to be determined at an early point in the infection cycle. These results indicate that Fc-ADE does not induce more rapid viral RNA synthesis compared to infection with FIPV alone. Our results are compared to those of recent work concerning ADE of human immunodeficiency virus (HIV) in the presence of complement.

Animals↗