A novel strand-specific RT-PCR for detection of hepatitis C virus negative-strand RNA (replicative intermediate): evidence of absence or very low level of HCV replication in peripheral blood mononuclear cells

Hepatitis C virus (HCV) is reported to be lymphotropic under certain circumstances. In order to evaluate viral replication in peripheral blood mononuclear cells (PBMCs), a novel strand-specific RT-PCR was developed for the determination of HCV negative-strand RNA. The detection limit of this strand-specific RT-PCR was 100 copies of HCV negative-strand RNA in the presence of 1 μg liver RNA and 10⁷–10⁸ copies of positive-strand RNA. False positive PCR signals occurred only when HCV positive-strand RNA exceeded 10⁹ copies. With this RT-PCR, the replicative-intermediates could be detected specifically in eight of ten liver tissues, but not in any samples of serum or plasma (0/65) of patients with chronic hepatitis C. When examining the PBMCs of 46 hepatitis C patients, including 12 patients who had undergone orthotopic liver transplantation, HCV negative-strand RNA was detected in only one patient (1/46). In addition, HCV replicative intermediates were not detected in PBMCs of patients using immunosuppressive agents. It is concluded that the replication of HCV in PBMCs is very unusual.     

The effects of gamma interferon on replication of foot-and-mouth disease virus in persistently infected bovine cells

Summary.  Foot-and-mouth disease virus (FMDV) causes a highly contagious viral disease of cloven-hoofed animals, which has a considerable socio-economic impact on the countries affected. In addition, persistent infection can occur following clinical or sub-clinical disease in either vaccinated or non-vaccinated cattle. The mechanism(s) by which FMDV persistence is established and maintained is not fully understood. To better understand the basic mechanisms controlling the virus infection in cattle, the effects of interferon gamma (IFN-γ) on the replication of FMDV was evaluated in vitro in persistently infected-epithelial cells isolated from FMDV infected cattle. Initially primary bovine thyroid (BTY) cells were treated with varying doses of bovine recombinant IFN-γ. The cytokine activity was measured by detection of viral antigen in cell supernatants and viral RNA expression compared with cells without INF-γ treatment. Pretreatment with IFN-γ profoundly affected FMDV growth in BTY cells. The replication of FMDV was affected in the presence of more than 2.5 u/ml of IFN-γ and the effect was both dose-dependent and related to the time of exposure. Analysis of the mechanism of inhibition suggests that IFN-γ did not inhibit the viral replication through induction of nitric oxide. More interesting is the finding that continuous treatment with IFN-γ severely restricts FMDV replication or even cures persistently infected bovine epithelial cells, indicating that a cytokine-mediated pathway may be involved in the in vivo clearance of persistent FMDV. Received June 27, 2001; accepted June 11, 2002     

Highly sensitive TaqMan RT-PCR assay for detection and quantification of both lineages of West Nile virus RNA.

BACKGROUND: Starting in 1999, the West Nile virus (WNV) epidemic represents the largest outbreak of arboviral encephalitis ever recorded in the U.S. The effective means to determine an infection are detection of viral nucleic acid and/or viral specific immunoglobulin, IgM and/or IgG. OBJECTIVE: To develop a highly sensitive and specific TaqMan RT-PCR assay for the detection and quantification of WNV RNA of lineage 1 and lineage 2. STUDY DESIGN: A TaqMan RT-PCR primer-probe was designed to perfectly match target sequences of all sequenced WNV strains and isolates, which added a layer of protection against false-negative results due to strain variability. In addition, the inclusion of a low level RNA internal control (IC) in the assay increased the precision and accuracy of the assay. RESULTS: By optimizing the RNA preparation procedure for increased WNV RNA recovery, together with optimizing the primer-probe and TaqMan conditions for improved amplification efficiency, we developed a highly sensitive assay with the detection limit of 10 copies/mL. To evaluate the assay, we tested plasma samples from 12 transfusion-transmitted implicated cases in 2002 and from 68 positive blood donors in 2003. All tested specimens were WNV positive. The viral load of 68 positive blood donor samples collected in 2003 ranged from 10 copies/mL to 67,000 copies/mL with a mean of 8100 copies/mL. Furthermore, high sensitivity of the assay was achieved without compromising specificity. All 100 routine donor samples tested negative. CONCLUSIONS: The assay results demonstrate that our in-house TaqMan RT-PCR procedure can detect and quantify WNV RNA of lineage1 and lineage 2 in human plasma with high sensitivity and specificity.     

In vitro viral RNA synthesis by a subcellular fraction of TMV-inoculated tobacco protoplasts

A subcellular fraction which can synthesize viral RNA and subgenomic RNA in vitro was prepared from tobacco mosaic virus (TMV)-inoculated tobacco protoplasts. S(1)-Resistant fragment analysis with strand specific TMV cDNA showed that a large amount of plus-stranded and a small amount of minus-stranded, genome-size RNA was synthesized by this subcellular fraction. Plus-stranded subgenomic RNA of coat protein mRNA size was also synthesized. The time course of the appearance of viral RNA synthetic activity was consistent with that of the appearance of TMV infectivity in vivo.     

丙型肝炎病毒在人T淋巴细胞中的体外感染

用丙型肝炎病毒（ＨＣＶ）ＲＮＡ阳性的血清感染人类Ｔ淋巴细胞（Ｍｏｌｔ－４），１２小时后继续孵化１～２８天，将感染后的产物用聚合酶链反应（ＰＣＲ）测定，于第１、２、３天和第８天发现ＨＣＶ－ＲＮＡ的正链，第２和第８天发现ＨＣＶ－ＲＮＡ的负链。     

Development and validation of a duplex quantitative real-time RT-PCR assay for simultaneous detection and quantitation of foot-and-mouth disease viral positive-stranded RNAs and negative-stranded RNAs

A simplified, cost-effective, two-step duplex quantitative real-time RT-PCR assay was shown to detect and quantify foot-and-mouth disease virus positive-stranded RNAs and negative-stranded RNAs simultaneously for improved investigation of the state of virus infection and replication. The primers and Taqman probes were selected from the coding regions of 2B gene and 3D gene respectively, which have the least variations among serotypes. Cells infected acutely, tissue samples and single cell samples were used for evaluation of the assay. At the early stages of virus infection in vitro, the replication level reached a peak at 9 h.p.i. and the negative strands were detectable until 3 h.p.i. The kinetics of ratios of positive strands to negative strands (+RNA/−RNA) in vivo in the liver, kidney and spleen were similar, which demonstrated that the replication dynamics were similar in the three organs. 55 single cell samples out of 187 were positive by both positive strands qPCR and negative strands qPCR, the ratios (+RNA/−RNA) ranged from 15.6 to 1463.4 which showed considerable difference among single cell samples, indicating that active viral replication differs greatly in single cells. A duplex quantitative real-time RT-PCR was validated as effective and reliable.     

Viral genome synthesis in BHK 21 cells persistently infected with Sendai virus

We have carried out daily analysis of the viral RNA species replicated by nucleocapsids present in the cytoplasm of two different BHK 21 cell lines persistently infected with Sendai virus. At each day of analysis (both before and after crises of cytopathology, and during long periods of stable growth) DI particle size RNA was the major species of viral RNA replicated within these nucleocapsids. The molar ratio of DI RNA to standard virus (50 S) RNA species within intracellular nucleocapsids was always extremely high (from 10/1 to 340/1). Thus, there is no evidence for cyclic variations in relative predominance of standard virus and DI nucleocapsids in populations of these persistently infected cells, although “cycling” could occur at the individual cell level at infrequent intervals. Furthermore, challenge of persistently infected cultures with standard Sendai virus or incubation at 33° also failed to significantly decrease the ratio of DI nucleocapsids to standard virus nucleocapsids. It was also found that multiple DI RNA species are present (most are not resolvable by sucrose gradient analysis), and that these evolve with time—some arising and increasing with time, while others are outcompeted. No selective advantage for DI RNA of any particular size was observed. Finally, by measuring the total amount of nucleocapsids present in these persistently infected cells (as estimated by level of NP protein in purified nucleocapsids), and the degree of synthesis of viral nucleocapsid (as determined by [³H]uridine incorporation in the presence of actinomycin D), we found that the rate of viral genome replication was 30- to 40-fold lower in the persistently infected cells than it was in St acutely infected cells. These findings may indicate that the accumulated nucleocapsids in persistently infected cells are built up over a period of many weeks of slow synthesis, although turnover times for NP protein and RNA of nucleocapsids have not yet been determined in persistently infected cells.     

A comparative study of tick-borne encephalitis virus RNA synthesis in acutely and persistently infected cells

Summary Rate zonal and buoyant density gradient centrifugation did not reveal any difference between tick-borne encephalitis virus virions released from acutely or persistently infected cells. All three RNA species characteristic for flavivirus replication were found both in acutely or persistently infected cells, but increased levels of intracellular 42S RNA polyadenylation was observed in persistently infected cells.With 2 Figures