Quantitation of hepatitis C virus genome molecules in plasma samples

Lack of Hcv Infection in Malignant, Cells Refutes the Hypothesis of a Direct Transforming Action of the Virus in the Pathogenesis of Hcv-Associated B-Cell Nhls

Aims and background

Preliminary evidence suggests that hepatitis C virus (HCV) might play a pathogenetic role in autoimmune-related, non-malignant B-cell lymphoproliferation, as well as in a subset of B-cell non-Hodgkin's lymphomas (NHLs). With regard to the mechanism(s) by which HCV might favor B-cell expansion and malignant transformation, most data support an indirect pathogenetic role of the virus as an exogenous trigger. A direct oncogenetic role of HCV by direct cell infection and deregulation has only been hypothesized on the basis of the lymphotropism of the virus.

Methods

In this study we investigated the possible HCV infection of NHL B cells by means of sensitive and quantitative polymerase chain reaction (PCR) on affinity-purified neoplastic cells, and by HCV-specific immunohistochemistry and in situ hybridization.

Results

HCV infection of neoplastic B cells was documented in only three cases, namely the low-grade B-cell NHLs that arose in the course of mixed cryoglobulinemia syndrome (MC). HCV infection, below one viral genome per cell, was detectable only by PCR. All the remaining low-grade (one case) and high-grade B-cell NHLs (two cases) were HCV uninfected. Previous immunoglobulin gene analyses were consistent with an antigen-driven B-cell lymphoproliferation in the studied cases.

Conclusions

Overall, our data are consistent with an indirect oncogenetic role of HCV in B-cell lymphomagenesis as an exogenous trigger. Infection of B cells by HCV appears possible in some NHL subsets, but the implications remain unknown.

Performance evaluation of ExiStation HBV diagnostic system for hepatitis B virus DNA quantitation

•

The new real-time quantitative PCR system for hepatitis B virus was evaluated.

•

This system showed satisfactory analytical sensitivity, excellent reproducibility, no cross-reactivity, no interference and high correlation with other real-time PCR assays.

•

The assay is a useful tool for the detection and monitoring of hepatitis B virus infection.

The performance of a recently developed real-time PCR system, the ExiStation HBV diagnostic system, for quantitation of hepatitis B virus (HBV) in human blood was evaluated. The detection limit, reproducibility, cross-reactivity, and interference were evaluated as measures of analytical performance. For the comparison study, 100 HBV-positive blood samples and 100 HBV-negative samples from Korean Blood Bank Serum were used, and the results of the ExiStation HBV system showed good correlation with those obtained using the Cobas TaqMan (r² = 0.9931) and Abbott real-time PCR systems (r² = 0.9894). The lower limit of detection was measured as 9.55 IU/mL using WHO standards and the dynamic range was linear from 6.68 to 6.68 × 10⁹ IU/mL using cloned plasmids. The within-run coefficient of variation (CV) was 9.4%, 2.1%, and 1.1%, and the total CV was 11.8%, 3.6%, and 1.7% at a concentration of 1.92 log₁₀ IU/mL, 3.88 log₁₀ IU/mL, and 6.84 log₁₀ IU/mL, respectively. No cross-reactivity or interference was detected. The ExiStation HBV diagnostic system showed satisfactory analytical sensitivity, excellent reproducibility, no cross-reactivity, no interference, and high agreement with the Cobas TaqMan and Abbott real-time PCR systems, and is therefore a useful tool for the detection and monitoring of HBV infection.

Molecular and cellular determinants of cell-to-cell transmission of HCV in vitro

It was reported previously that HCV can be transmitted from persistently infected human bone-marrow-derived B-lymphoblastoid cells (TO.FE(HCV)) to human hepatoma cells by cell-to-cell contact. The present study confirms and characterize further such type of HCV infection in vitro. TO.FE(HCV) cells were co-cultured with 2.2.15 hepatoma cells, that are not susceptible to cell-free infection by sera containing HCV of 1b genotype. By this co-cultivation system it was demonstrated that HCV transmission to recipient cells requires de novo virus RNA replication. Several factors may favor HCV-transmission, evidence is provided that TO.FE(HCV) cells were able to select HCV-quasispecies. 5'-UTR and core sequence analysis revealed differences in the HCV-quasispecies composition in serum inoculum and in infected TO.FE B-cells at 4 months post-inoculation. It is considered that the latter may be more successful in replicating HCV in vitro and used to express surface molecules which may be involved in cell-to-cell contact. In TO.FE(HCV) cells replicate distinct, or few close related, HCV-variants correlated with those of serum inoculum. Comparative analysis of tetra-spans and integrins expression undertaken by cytofluorimetry displayed higher level of expression for TO.FE cells in comparison to other human bone-marrow-derived B-cell lines. Overall, the observed persistent in vitro HCV replication is mediated by a continuous cell-to-cell reinfection that may be favored by selection of viral variants and expression of molecules involved in cell adhesion. These observations may provide an explanation for the establishment of HCV infection, the occurrence of chronic infection and HCV-related lymphoproliferative diseases.

Transmission in vitro of hepatitis C virus from persistently infected human B-cells to hepatoma cells by cell-to-cell contact

Virus cell-to-cell spread has been reported for many different viruses and may contribute to pathogenesis of viral disease. The role played by cell-to-cell contact in hepatitis C virus (HCV) transmission was studied in vitro by cell co-cultivation experiments. A human lymphoblastoid B-cell line, infected persistently with HCV in vitro (TO.FE(HCV)), was used as HCV donor [Serafino et al., 2003]; recipient cells were the human hepatoma HepG2 cell line. Both cell types were co-cultured for 48 hr to allow the cell-to-cell contacts. The hepatoma HepG2 cells are not permissive to free-virus infection, but they were infected successfully using TO.FE(HCV) cells as source of virus. The kinetics of viral RNA synthesis and the percentage of infected cells were compared in cell-mediated-and cell-free-viral infection. After co-cultivation, a consistent proportion of hepatoma cells replicated HCV and stably expressed viral antigens. Virus produced was infectious as demonstrated by the ability to reinfect fresh B-cells. This cell model shows that permissiveness to HCV infection can be achieved in vitro in non-permissive hepatoma cells by direct cell-to-cell contacts with infected human B-cells. This mechanism of virus spread may also play a pathogenic role in vivo.

An in vitro system combined with an in-house quantitation assay for screening hepatitis C virus inhibitors

Hepatitis C virus (HCV) infection is a serious global health problem. Interferon-alpha (IFN-alpha) and ribavirin have demonstrated efficacy in the treatment of HCV infection; however, these therapies display many side effects. To screen the anti-HCV compounds from plants, we established an in vitro model for inoculation of HCV by centrifugation-facilitated method. The HCV RNA molecules were then quantitated by nested competitive reverse transcription-polymerase chain reaction (cRT-PCR) using fluorescein-labeled primers, and analyzed by ABI Prism 310. The positive and negative strands of HCV RNA were detectable in Vero cells on Day 7 post-infection, suggesting that the HCV RNA was present in the cell model system. The cell culture system was further used to screen the anti-HCV activities of 4 Chinese herbal formulas and 15 formula components. IFN-alpha showed an antiviral effect. The formulas exhibited no anti-HCV activities, while Arnebia euchroma, Thlaspi arvense, and Poncirus trifoliata displayed anti-HCV activities. Therefore, these results pointed out the possibility by using the cell culture system established in this study to screen the herb extracts for their anti-HCV activities.

Antimicrobial activity of a new intact skin antisepsis formulation

Different antiseptic formulations have shown limitations when applied to disinfecting intact skin, notably short-term tolerability and/or efficacy. The purpose of this study was optimizing a new antiseptic formulation specifically targeted at intact skin disinfection and evaluating its in vitro microbicidal activity and in vivo efficacy.

METHODS

The biocidal properties of the antiseptic solution containing 0.5% chloramine-T diluted in 50% isopropyl alcohol (Cloral; Eurospital SpA Trieste, Italy) were measured in vitro versus gram-positive-, gram-negative-, and acid-alcohol-resistant germs and fungi with standard suspension tests in the presence of fetal bovine serum. Virus-inhibiting activity was evaluated in vitro against human cytomegalovirus, herpes simplex virus, poliovirus, hepatitis B virus, and hepatitis C virus. Tests used different methods for the different biologic and in vitro replication capacity of these human viruses. Lastly, Cloral tolerability and skin colonization retardation efficacy after disinfection were studied in vivo.

RESULTS

The antiseptic under review showed fast and sustained antimicrobial activity. The efficacy of Cloral against clinically important bacterial and viral pathogens and fungi was highlighted under the experimental conditions described in this article. Finally, microbial regrowth lag and no side effects were documented in vivo after disinfection of 11 volunteers.

CONCLUSIONS

A stable chloramine-T solution in isopropyl alcohol may be suggested for intact skin antisepsis.

Molecular testing in the diagnosis and management of hepatitis C virus infection

OBJECTIVES

To review hepatitis C virus (HCV), describe the types of molecular-based tests available for the diagnosis and management of HCV infection, and discuss the appropriate utilization of these tests.

DATA SOURCES

Current information is presented from the published literature, as well as new information where available.

STUDY SELECTION

A major cause of posttransfusion and community-acquired non-A, non-B hepatitis worldwide is HCV. Approximately 4 million people in the United States are infected with HCV, resulting in 8000 to 10,000 deaths annually. Because HCV is not readily cultured, in vitro molecular-based tests have been developed for use in the diagnosis and treatment of HCV-infected patients. Molecular tests include qualitative and quantitative nucleic acid amplification tests, branched DNA tests, and HCV genotyping assays. Qualitative HCV nucleic acid amplification tests are used routinely in association with serologic tests to help make a diagnosis of infection with HCV. Quantitative HCV testing and genotyping methods have been found to be valuable tools in the treatment of infected patients. A patient's pretreatment HCV viral load and the rate of virus decline during therapy have been shown to correlate with the likelihood of long-term response to antiviral therapy. Information pertaining to the genotype of HCV infecting patients has been shown to be helpful in making recommendations regarding treatment. Certain genotypes of HCV are much more responsive to therapy, allowing a shorter course of treatment.

CONCLUSIONS

Molecular tests are valuable tools for use in the diagnosis and treatment of patients infected with HCV.

Transmission of hepatitis C virus in a gynecological surgery setting

A cluster of hepatitis C virus (HCV) infections among gynecological patients who underwent surgical intervention in the same setting is described. An epidemiological investigation was conducted to identify the cases, the likely source of infection, and the route of transmission. Four recent HCV infections were identified. Based on molecular fingerprinting analysis and epidemiological investigation, transmission between the putative source patient (an HCV-positive woman who was the first patient of the surgical session) and outbreak patients was highly suggestive. All patients, including the source patient, were infected with HCV type 1b. Molecular characterization of HCV clones by sequence analysis of both structural envelope regions (20 clones from the source patient and 58 from the outbreak patients) and the nonstructural NS5 region of the viral genome (12 clones from the source patient and 32 from the outbreak patients) showed close homology between the viral isolates from the source and those from the outbreak patients that was higher than that observed between the viral isolates from the source and those from four unrelated, HCV type 1b-infected patients from the same geographical area (in the latter case, 33 clones were sequenced for the envelope regions and 30 were sequenced for the NS5 region). The mean percent divergence between clones was 4.69 for the envelope and 3.71 for the NS5 region in the source patient and the outbreak patients compared with 6.76 (P = 0.001) and 5.22 (P = 0.01) in the source patient and control patients, respectively. Among the risk factors investigated, only that of having undergone surgery in the morning session of the same day reached statistical significance (P = 0.003). The investigation showed that the source patient and outbreak patients shared only the administration of propofol in multidose vials. The study documents the risk of nosocomial transmission of HCV and the importance of infection control procedures in the operating room and highlights the crucial role of molecular strategies, especially sequence-based phylogenetic analysis of cloned viral isolates, in the investigation of HCV outbreaks.

Stability of HCV-RNA level and its lack of correlation with disease severity in asymptomatic chronic hepatitis C virus carriers

This study examines the relationship between HCV-RNA levels and disease severity in 60 individuals with chronic hepatitis C virus infection. HCV-RNA levels were quantified by the branched DNA (bDNA) assay in 445 samples (median: eight samples per patient) obtained over a median of 40.4 months (95% confidence interval (CI): 37.0-42.5). The median log HCV-RNA level was 6.77 (95% CI: 6.62-6.92) molecular equivalents/mL (MEQ/mL). The median log range of HCV-RNA levels in individual patients over the course of the study was 0.89 (95% CI: 0.69-1.16). HCV-RNA level varied over time by less than one log in 62% of patients, by 1-1.5 logs in 22% and by greater than 1.5 logs in only 17%. Univariate analysis, revealed an inverse association between HCV-RNA levels and ALT levels (P=0.037). Univariate and logistic regression analysis showed no significant association between HCV-RNA levels and either the degree of inflammation or fibrosis. In contrast, there was a significant positive association between alanine aminotransferase (ALT) levels and histological activity especially in individuals with ALTs> 100 IU/L. Hence, HCV-RNA levels: (i) almost always fell within the dynamic range of the bDNA assay; (ii) were stable in asymptomatic chronically infected patients, with only a small proportion of patients exceeding a range of 1.5 logs; (iii) did not correlate with either the extent of inflammation or degree of fibrosis. In contrast, there was a strong association between ALT level and the histological severity of liver disease.

Quantitative PCR-ELAHA for the Determination of Retroviral Vector Transduction Efficiency

Current methods to detect transduction efficiency during the routine use of integrating retroviral vectors in gene therapy applications may require the use of radioactivity and usually rely upon subjective determination of the results. We have developed two competitive quantitative assays that use an enzyme-linked, amplicon hybridization assay (ELAHA) to detect the products of PCR-amplified regions of transgene from cells transduced with Moloney murine leukemia virus vectors. The quantitative assays (PCR-ELAHA) proved to be simple, rapid, and sensitive, avoiding the need for Southern hybridization, complex histochemical stains, or often subjective and time-consuming tissue culture and immunofluorescence assays. The PCR-ELAHA systems can rapidly detect proviral DNA from any retroviral vector carrying the common selective and marker genes neomycin phosphotransferase and green fluorescent protein, and the methods described are equally applicable to other sequences of interest, providing a cheaper alternative to the evolving real-time PCR methods. The results revealed the number of copies of retrovector provirus present per stably transduced cell using vectors containing either one or both qPCR targets.

Long-term beneficial effects in sustained responders to interferon-alfa therapy for chronic hepatitis C

BACKGROUND/AIMS

Assessment of chronic hepatitis C outcome in sustained responders to interferon requires prolonged observation and close monitoring. We prospectively studied the impact of sustained response on histology and clinically relevant outcomes.

METHODS

The 47 sustained responders (ten with cirrhosis) from two interferon trials involving 235 chronic hepatitis C patients (81 with cirrhosis) were included. Hepatitis C virus (HCV) RNA was assessed every 6 months, liver histological changes from baseline, 6-12 and 48-72 months after treatment discontinuation.

RESULTS

The mean follow-up was 102 +/- 19 months. HCV RNA became undetectable in 36/47 responders. Four responders, who had remained viremic, later relapsed. The histology progressively improved in non-viremic and viremic patients, with a more marked improvement in the former (P = 0.0089), normalizing in 53 vs. 0% (P = 0.0220). No patient progressed to cirrhosis. One non-viremic cirrhotic patient developed a hepatocellular carcinoma. Non-responders from the two original trials had worse histological outcomes and those with cirrhosis had a higher rate of clinically relevant events compared with cirrhotics showing a sustained biochemical response (4.5 vs. 1.2 cases/100 person-years; CI for the difference, 0.3-6.3).

CONCLUSIONS

Most sustained, virological responders without cirrhosis normalize liver histology in the long-term and are cured of the disease. Sustained responders remaining viremic still show histological improvement, albeit to a lesser extent.

Molecular epidemiology of an outbreak of fulminant hepatitis B

A nosocomial outbreak of hepatitis B occurred among the inpatients of a hematology unit. Nine of the 11 infected patients died from fulminant hepatitis. An investigation was conducted to identify the source of infection and the route of transmission. Two clusters of nosocomial hepatitis B were identified. The hepatitis B virus (HBV) genome from serum samples of all case patients, of one HBsAg-positive patient with acute reactivation of the infection, and of eight acutely infected, unrelated cases was identified by PCR amplification of viral DNA and was entirely sequenced. Transmission was probably associated with breaks in infection control practices, which occurred as single events from common sources or through a patient-to-patient route, likely the result of shared medications or supplies. Sequence analysis evidenced close homology among the strains from the case patients and that from the patient with reactivation, who was the likely source of infection. Molecular analysis of viral isolates evidenced an accumulation of mutations in the core promoter/precore region, as well as several nucleotide substitutions throughout the genome. The sequences of all patients were compared with published sequences from fulminant and nonfulminant HBV infections.

The stability of hepatitis C virus RNA after storage at +4 degrees C

One of the major issues in nucleic acid testing is how to store blood samples to obtain reliable results. We therefore studied hepatitis C virus (HCV) RNA concentration in samples after storage at +4 degrees C or freezing and thawing. Six HCV RNA-positive, untreated subjects were studied. Blood samples were collected from these subjects in plasma preparation tubes. The HCV RNA concentration was analysed after storage at +4 degrees C for 168 h or after five freeze-thaw cycles. For HCV RNA quantification we used a qualitative and a quantitative commercial test. After 168 h of storage at +4 degrees C, the HCV RNA concentration was similar to that observed at time-point 0 (5.025 log vs 5.492 log). In one sample we observed a significant fall in HCV RNA concentration. After five freeze-thaw cycles, the HCV RNA concentration was lower than that observed at time-point 0 (4.454 log vs 5.492 log) and in four samples we observed a significant fall in HCV RNA concentration. Our data suggest that HCV RNA is stable in whole blood samples stored at +4 degrees C for 168 h. Based on our results, we conclude that the standard procedures for transport of blood samples (at room temperature for a maximum of 5 h) and storage schedules (+4 degrees C for a maximum of 48 h) can be maintained without compromising the quality of results.

Dominant role of host selective pressure in driving hepatitis C virus evolution in perinatal infection

The dynamics of the genetic diversification of hepatitis C virus (HCV) populations was addressed in perinatal infection. Clonal sequences of hypervariable region 1 of the putative E2 envelope protein of HCV were obtained from four HCV-infected newborns (sequential samples spanning a period of 6 to 13 months after birth) and from their mothers (all samples collected at delivery). The data show that the variants detected between birth and the third month of life in samples from the four newborns were present in the HCV populations of their mothers at delivery. In the newborns, a unique viral variant (or a small group of closely related variants) remained stable for weeks despite active viral replication. Diversification of the intrahost HCV population was observed 6 to 13 months after birth and was substantially higher in two of the four subjects, as documented by the intersample genetic distance (GD) (P = 0.007). Importantly, a significant correlation between increasing GD and high values for the intersample K(a)/K(s) ratio (the ratio between anoffymous and synonymous substitutions; an index of the action of selective forces) was observed, as documented by the increase of both parameters over time (P = 0.01). These data argue for a dominant role of positive selection for amino acid changes in driving the pattern of genetic diversification of HCV populations, indicate that the intrahost evolution of HCV populations is compatible with a Darwinian model system, and may have implications in the designing of future antiviral strategies.

Gastric mucosa as an additional extrahepatic localization of hepatitis C virus: viral detection in gastric low-grade lymphoma associated with autoimmune disease and in chronic gastritis

The hepatitis C virus (HCV) has been linked to B-cell lymphoproliferation and autoimmunity, and has been localized in several tissues. The clinical observation of an HCV-infected patient with Sjögren's syndrome (SS) and Helicobacter pylori (HP) positive gastric low-grade B-cell non-Hodgkin's lymphoma (NHL), which did not regress after HP eradication, led us to investigate the possible localization of HVC in the gastric microenvironment. HCV genome and antigens were searched in gastric biopsy specimens from the previously mentioned case, as well as from 9 additional HCV-infected patients (8 with chronic gastritis and 1 with gastric low-grade B-cell NHL). HCV-specific polymerase chain reaction (PCR) and immunohistochemistry procedures were used. The gastric B-cell NHL from the patient with SS was characterized by molecular analyses of B-cell clonality. HCV RNA was detected in both the gastric low-grade B-cell NHL and in 3 out of 6 gastric samples from the remaining cases. HCV antigens were detected in the residual glandular cells within the gastric B-cell NHL lesions, in glandular cells from 2 of the 3 additional gastric lesions that were HCV positive by PCR, and in 1 additional chronic gastritis sample in which HCV-RNA studies could not be performed. By molecular analyses, of immunoglobulin genes, the B-cell NHL from the patient with SS was confirmed to be a primary gastric lymphoma, subjected to ongoing antigenic stimulation and showing a significant similarity with rheumatoid factor (RF) and anti-HCV- antibody sequences. Our results show that HCV can localize in the gastric mucosa.

Dynamics of hepatitis C viremia after plasma exchange

BACKGROUND/AIMS

The dynamics of hepatitis C viremia after perturbation by plasma exchange was addressed in two infected patients with symptomatic cryoglobulinemia. This approach may offer an alternative to studying patients treated with antivirals in order to understand the dynamics of hepatitis C virion exchange among different compartments in vivo.

METHODS

Plasma exchange sessions were conducted every 24 h for 3 consecutive days; hepatitis C virus RNA copy numbers were evaluated in sequential plasma samples collected before (-24, -12, -8, and 0 h) and at short intervals (at 1, 3, 6, and 12 h) after each session.

RESULTS

After each plasma exchange session viremia dropped by 45.3-93.3% in patient 1, and by 60.5-72.7% in patient 2, paralleling (or, in some cases, exceeding) the amount of fluid exchanged. No mobilization of cell-free hepatitis C virus from extra-vascular sites was documented during the 2-h plasma exchange. The dynamics of hepatitis C viremia after each procedure was also evaluated. Pre-plasma exchange levels were restored within 3-6 h in both patients, and the mean doubling times of residual viremia were 4.6 h and 4.5 h for patients 1 and 2, respectively.

CONCLUSIONS

The results, in agreement with recent evidence indicating that the turnover of hepatitis C virions is a highly dynamic process, extend previous evaluations by documenting that large amounts of newly-produced virions are introduced into the vascular compartment within a few hours of the drop in hepatitis C viremia caused by plasma exchange.

Hepatic stellate cell activation and liver fibrosis are associated with necroinflammatory injury and Th1-like response in chronic hepatitis C

BACKGROUND/AIMS

The involvement of a direct viral cytopathic effect or an immune-mediated mechanism in the progression of hepatic damage in chronic hepatitis C is controversial. The type of immune response is itself a matter of controversy, and histological data are lacking. The aim of this study was to identify the factors associated with the progression of liver injury in 30 HCV/RNA-positive untreated patients with chronic hepatitis.

METHODS

Necroinflammatory and architectural damage were evaluated using Ishak's score. Activated hepatic stellate cells (HSC) were visualized by immunohistochemistry for alpha-smooth muscle actin (alphaSMA) and quantitated by morphometry. Plasma HCV/RNA was evaluated using a competitive RT-PCR method. To study the type of immune response involved in the progression of liver injury, interferon gamma (IFNgamma)-positive cells (as expression of a Th1-like response) were evaluated by immunohistochemistry and quantitated by morphometry.

RESULTS

HSC were mostly detected close to areas of lobular necroinflammation or lining fibrotic septa. The alphaSMA- and Sirius Red-positive parenchyma correlated significantly with necroinflammatory and architectural scores. IFNgamma-positive cells were detected in periportal areas associated with the inflammatory infiltrates and significantly correlated with architectural damage. No relationship was found between the histological features of liver injury and viral load.

CONCLUSIONS

HSC activation and progression of liver injury are unrelated to viral load but associated with a Th1-like response, a plausible target for the treatment of chronic hepatitis C.

Effect of phenolic and chlorine disinfectants on hepatitis C virus binding and infectivity

BACKGROUND

The purpose of this study was to evaluate the inhibitory activity of 2 polyphenolic disinfectants and a chlorine compound (NaDCC) on hepatitis C virus (HCV) binding and infectivity.

METHODS

VERO cells (a continuous cell line derived from cynomolgus kidney cells) suitable for analyzing HCV binding and replication, and the competitive reverse transcription (cRT-PCR) technique for HCV RNA molecules quantitative evaluation have been chosen as a methodologic approach for the antiviral activity testing.

RESULTS

At their recommended use dilutions, polyphenolic disinfectants inhibited HCV binding and replication. The chlorine compound was ineffective, probably a result of its low concentration in the presence of protein substances in VERO cell cultures.

CONCLUSIONS

Inhibition of HCV binding and replication by the tested polyphenolic associations confirm their value in instrument decontamination and environmental disinfection against this clinically important lipid virus.

Comparison of the enzyme-linked immunosorbant assay III, recombinant immunoblot third generation assay, and polymerase chain reaction method in the detection of hepatitis C virus infection in haemodialysis patients

Hepatitis C virus (HCV) serotyping assays have evolved from simple antibody screening tests to complex RNA-based qualitative and quantitative methods. The objective of this study was to compare the HCV screening results from 161 patients in long-term maintenance haemodialysis (HD) as assessed by the recently developed Enzyme Linked ImmunosorbantAssay III (ELISA III), confirmed by the Recombinant Immunoblot 3rd generation assay (RIBA 3rd) and determined by the qualitative HCV reverse transcription polymerase chain reaction (RT-PCR) method. One hundred sixty-one HD patients were tested for the presence of anti-HCV antibodies by the ELISA III and confirmed by the RIBA 3rd. HCV RNA was determined by an HCV RT-PCR method. All reported results that were designated as discrepant, anti-HCV (+) and/or HCV RNA (+) were further investigated by means of a quantitative HCV RT-PCR assay. Reported results obtained from ELISA III and qualitative RT-PCR assays were HCV positive for 16/161 patients (9,93%) and these were designated as anti-HCV (+)/HCV RNA (+). Subsequently, these 16 anti-HCV positive/161 HD patients were confirmed by the RIBA 3rd. Three individuals anti-HCV (-)/RIBA (+)/HCV RNA (-)], the viral load that was reported from the quantitative RT-PCR was less than the assay detection level (< 2,000 viral copies/ml). In view of previous observations, our findings suggest that ELISA III remains still a highly reliable and valuable assay. However, despite the cost, the combination of both ELISA III and qualitative RT-PCR allows a definitive classification on HCV diagnosis.

Hepatitis C virus RNA profiles in chronically infected individuals: do they relate to disease activity?

Fluctuations of hepatitis C virus (HCV)-RNA serum levels were monitored in a multicenter study in 76 chronic HCV carriers who had been followed longitudinally without receiving antiviral therapy to assess their relation with the course of liver disease activity. Forty-four patients had normal transaminases over more than 2 years, while 32 additional patients had fluctuating levels. Viral load was measured in serial serum samples prospectively collected for 10 to 12 months in 54 patients and in sera stored yearly up to 8 years in an additional 22 patients. In patients tested monthly, a lesser extent of fluctuations was detected in cases with constantly normal transaminases as compared with those with fluctuating transaminases. In the former group, the mean difference between maximum and minimum values observed in each individual patient was 0.7 Log, while in the latter group, it was 1.3 Log (P =.0004). Most of these patients experienced, on average, three peaks of viremia over 1 year. The range of variation observed upon yearly testing was between 0.2 and 2.2 Log and did not reach statistical significance between the two groups. In conclusion, a careful viral replication profile can be achieved only by monthly testing, because longer time intervals could miss viremia fluctuations. HCV-RNA levels are more stable in asymptomatic HCV carriers than in patients with biochemical activity of liver disease.

Susceptibility of human and non-human cell lines to HCV infection as determined by the centrifugation-facilitated method

The centrifugation-facilitated inoculation method was used to test 51 human and non-human cell lines for ability to support HCV replication. As determined by nested RT-PCR, one fifth of the cell lines tested were virus positive 15 days post inoculation suggesting that the centrifugation-facilitated inoculation is an efficient method for cell infection with HCV. However, virus production by infected cultures remained of low grade, thus showing that the unknown factors which limit HCV replication in vitro are not overcome by the procedure.

TOFE human-B-cell-line-based adsorption-inhibition assay to detect HCV neutralizing antibodies

We previously demonstrated that the human lymphoblastoid B-cell line (LCL) TOFE, derived from normal human bone marrow, is permissive to HCV infection. In this report we developed an in vitro HCV adsorption-inhibition assay based on TOFE cells, to reveal the presence of neutralizing antibodies in sera from acutely infected patients.

Evolution of hypervariable region 1 of hepatitis C virus in primary infection

The hypervariable region 1 (HVR-1) of the putative envelope encoding E2 region of hepatitis C virus (HCV) RNA was analyzed in sequential samples from three patients with acute type C hepatitis infected from different sources to address (i) the dynamics of intrahost HCV variability during the primary infection and (ii) the role of host selective pressure in driving viral genetic evolution. HVR-1 sequences from 20 clones per each point in time were analyzed after amplification, cloning, and purification of plasmid DNA from single colonies of transformed cells. The intrasample evolutionary analysis (nonsynonymous mutations per nonsynonymous site [Ka], synonymous mutations per synonymous site [Ks], Ka/Ks ratio, and genetic distances [gd]) documented low gd in early samples (ranging from 2. 11 to 7.79%) and a further decrease after seroconversion (from 0 to 4.80%), suggesting that primary HCV infection is an oligoclonal event, and found different levels and dynamics of host pressure in the three cases. The intersample analysis (pairwise comparisons of intrapatient sequences; rKa, rKs, rKa/rKs ratio, and gd) confirmed the individual features of HCV genetic evolution in the three subjects and pointed to the relative contribution of either neutral evolution or selective forces in driving viral variability, documenting that adaptation of HCV for persistence in vivo follows different routes, probably representing the molecular counterpart of the viral fitness for individual environments.

Serum and liver HCV RNA levels in patients with chronic hepatitis C: correlation with clinical and histological features

BACKGROUND

Liver disease in chronic hepatitis C virus (HCV) infection ranges from minimal lesions to liver cirrhosis, eventually evolving to hepatocellular carcinoma. Whether and how HCV determines the different clinical and histological manifestations of the disease is not fully understood.

AIMS

To verify whether the amount of virus in individual patients could be related to the severity of liver injury.

PATIENTS AND METHODS

Levels of HCV RNA were measured in serum in 96 consecutive patients with chronic hepatitis type C using a signal amplification assay. The relation between viraemic values and the corresponding viral load in the liver was assessed in a subgroup of 21 patients in whom HCV RNA was measured in serum samples and liver specimens obtained at the same time.

RESULTS

A positive correlation was observed between the amount of viral nucleic acid in the two compartments, indicating that levels of viraemia reflect the amount of virus present in the liver. Viral load did not correlate with aminotransferase activities nor with histological diagnosis, and serum and liver levels of HCV RNA were not significantly different in patients infected by the various HCV genotypes.

CONCLUSIONS

Measurement of HCV replication in serum is a mirror of viral replication in the liver. The extent of replicative activity of HCV does not seem to play a role in the modulation of the associated hepatic disease.

Comparative study of different standardization concepts in quantitative competitive reverse transcription-PCR assays

Four different standardization approaches based on a competitive reverse transcription (RT)-PCR assay were compared with a noncompetitive assay based on an external standard curve. Criteria for assessment were accuracy in quantitation, correctness of recovery, sensitivity, dynamic range, reproducibility, throughput, and convenience of sample handling. As a model system, we used the 5'-noncoding region of hepatitis C virus (HCV) for amplification in all quantitative RT-PCRs. A computer program that allowed parallel data processing was developed. Surprisingly, all methods were found suitable for accurate quantitation and comparable with respect to the criterion correctness of recovery. All results differed only by a factor of about 2. The reason for this finding might be that all of our mimics, as well as the wild-type genome of HCV, exhibited exactly the same amplification and hybridization efficacy. Moreover, minimal competition occurred in our experiments over a 5-log dynamic range. A further topic of our investigation was the comparison of two different competitive RNA fragments, mimics, with regard to their suitability as internal standards. One was a heterologous mimic, in which only the primer binding sites were identical to the wild type. The second one was a homologous mimic identical to the wild type except for a small region used for differential hybridization, which was replaced by a permutated sequence of the same length. Both the homologous and heterologous internal mimics were found appropriate for an accurate competitive RT-PCR assay, provided that amplification efficacy, as well as capture efficacy, is proven identical for both analyte and mimic.

New quantitative assay of hepatitis B and C viruses by competitive PCR using alternative internal sequences

A competitive PCR was developed for quantitation of hepatitis B virus (HBV) DNA and hepatitis C virus (HCV) RNA, alternatively, using only two constructions containing both priming sites. DNAs corresponding to the HBV-S gene and the HCV-5' non-coding region were introduced into distinct plasmids. HBV plasmid was used as a standard for HBV-DNA quantitation, in competition with the HCV plasmid as internal control. HBV and HCV plasmids also served as template for transcription of HBV-RNA, and HCV-RNA, which was used as internal control and standard, respectively, in competition for HCV-RNA quantitation. The analyzed samples for HBV and HCV quantitation were processed in the same way in competition with the internal controls and to the respective calibration curves obtained by serial dilutions of the mimic standard. This method showed very good specificity and sensitivity, allowing absolute quantitation in a large linear range from 5 viral genomic copies per assay up to 10(6) copies, in sera of chronically HBV and HCV infected patients, as well as in supernatants of cell cultures inoculated with these viruses.

Quantitative liver parameters of HCV infection: relation to HCV genotypes, viremia and response to interferon treatment

BACKGROUND/AIMS

This study aimed to evaluate the relation between the number of hepatocytes positive for HCV antigens and the amount of HCV RNA in the liver and to evaluate the relationship between the above parameters and viremia levels, HCV genotype and response to interferon treatment.

METHODS

This was a retrospective study on 31 consecutive patients with chronic HCV-related liver disease, selected on the basis of the availability of frozen liver tissue for both liver HCV antigens detection and liver HCV RNA quantitation. HCV antigens (immunohistochemistry), liver and plasma HCV RNA (competitive RT-PCR), and HCV genotype (commercial kit) were studied.

RESULTS

A significant correlation (p=0.0005) was found between the amount of liver HCV RNA (log 10 copy/microg of extracted RNA) and the number of HCV-infected hepatocytes (scored from 0 to 3). These parameters were not significantly correlated with viremia levels. The highest liver HCV RNA levels and HCV antigen scores were found in patients infected with genotype 1b. Liver HCV RNA (median 541 x 10(3) vs 118 x 10(3) copy number/microg, p=0.031) and liver HCV antigens (mean score 2.3 vs 1.3, p=0.018) but not plasma HCV RNA (median 14956 x 10(3) vs 2885 [correction of 2.885] x 10(3) copy number/ml, ns) were significantly higher in patients not responding to interferon treatment compared to responders.

CONCLUSIONS

The tissue parameters tested in this study were significantly correlated, shared the same clinical implications and predicted short-term response to interferon treatment better than viremia levels. We suggest that these tests should be included in the study protocol of patients under evaluation for interferon treatment, basing the choice on local facilities.

Comparison of competitive and non-competitive reverse transcription-polymerase chain reaction (RT-PCR) for the quantification of hepatitis C virus (HCV) RNA

A competitive reverse transcription (RT)-nested polymerase chain reaction (PCR) assay for HCV RNA was compared with the Roche Amplicor HCV Monitor assay, based on non-competitive, single step RT-PCR. A total of 83 serum samples were tested in parallel by both assays. All samples could be quantified by competitive RT-PCR (cPCR), whereas seven were negative by the non-competitive assay (ncPCR). The HCV RNA titre of the discordant samples assessed by cPCR was significantly lower than that of the remaining 76 (P < 0.001). Absolute HCV RNA titres were higher by cPCR than by ncPCR (P < 0.001), even if the results of the two methods were statistically correlated (P < 0.001). HCV RNA titre tested by cPCR was not significantly different between samples infected with genotype 1 or 2. However, values obtained by ncPCR were higher in samples with genotype 1 (P < 0.001). Furthermore, all seven discordant samples were infected with genotype 2. When both methods were used to measure serial dilutions of standard HCV RNA, we observed a bias to lower measurements with the ncPCR kit. This study shows a good correlation between the results of two PCR-based methods for the quantification HCV RNA. However, the degree of sensitivity and the absolute HCV RNA titre measured may vary according to the assay used.

Quantitation of hepatitis C virus RNA production in two human bone marrow-derived B-cell lines infected in vitro

The ability of hepatitis C virus (HCV) to replicate in two B-cell lines, CE and TOFE, derived from bone marrow of healthy subjects was compared using qualitative and quantitative molecular methods. The presence of intracellular negative-stranded HCV RNA (replicative intermediate) was investigated by nested polymerase chain reaction (PCR) in the infected cultures at different times after infection. The amounts of positive-stranded HCV RNA (genomic RNA copies) synthesized and released from cells one week after in vitro infection were determined by competitive PCR after reverse transcription of viral RNA for the 5' viral untranslated region. In both cell lines, HCV RNA replication took place, but the TOFE cell line appeared to be a more efficient virus producer than the CE cell line. The TOFE cell line could be a valuable and reliable tool for basic and clinical HCV studies.

Dynamics of viral quasispecies in hepatitis C virus infection

The genomic heterogeneity of hepatitis C virus (HCV) was addressed in the different phases of HCV infection. Viral sequences of the HVR-1 and NS5a regions were obtained by reverse transcription polymerase chain reaction from plasma samples of two patients with acute type-C hepatitis and two patients with chronic infection treated with interferon. The data indicate that in primary infection different degrees of genomic heterogeneity in biologically important viral regions might be associated with different clinical outcomes.

Hepatitis C virus infection of a Vero cell clone displaying efficient virus-cell binding

The susceptibility of Vero cells and derivative cell clones to hepatitis C virus (HCV) infection was assayed by qualitative and quantitative polymerase chain reaction (PCR)-based methods. Cell extracts from Vero cells inoculated with HCV were tested for the presence of both positive and negative strands of HCV RNA; in parallel, cell-free HCV genomes were assayed in culture supernatant fluids. Quantitation of genomic HCV RNA molecules in infected cells by competitive reverse transcription PCR (cRT-PCR) indicated that HCV replication was more efficient in a derivative clone (named clone 10) than in parental Vero cells or other clones under study. Analysis of HCV-binding to cell receptors, performed by cRT-PCR quantitation of viral particles adsorbed to the cell surface, demonstrated a 10-fold higher virus-binding level of clone 10 than that of parental Vero cells. The results shown here indicate that the Vero clone 10 may constitute an efficient model system for analysing early events in HCV infection as well as a source of virus for diagnostic and biotechnological applications.

Detection and identification of ruminant and porcine pestiviruses by nested amplification of 5' untranslated cDNA regions

Based on published gene sequences of bovine viral diarrhoea virus (BVDV) type I and classical swine fever virus (CSFV), genus- and species-specific primers were designed to detect and identify pestivirus cDNA sequences in a nested polymerase chain reaction (PCR). The PCR primers were validated using cDNA synthesized from 146 pestivirus isolates, comprising representatives of all four so far described genotypes (BVDV type I, BVDV type II, CSFV and border disease virus), as well as others of uncertain classification. PCR products of the predicted size were amplified from all viruses with the genus-specific primers. All 53 cattle isolates, including 5 typed antigenically as BVDV type II were amplified by the internal BVDV-specific primers, but not the CSFV-specific primers. The same result was found for other BVDV type I and II viruses isolated from sheep and pigs. Seventy-seven CSF viruses were amplified by their respective internal primers. Available information strongly indicate that 4 CSF viruses also amplified by the BVDV-specific primers had been contaminated with BVDV in cell cultures. Border disease viruses were mostly not detected by the BVDV-specific primers, but were detected weakly by the CSFV-specific primer pair. Using carrier RNA for extraction of viral RNA, the sensitivity of detection of the single and nested PCR was, respectively, 5 and 50 times higher than obtained with a cell culture assay. The RT-PCR also detected BVDV in all of 15 commercial batches of fetal calf serum examined, and verified three earlier diagnoses of CSFV by detecting specific gene sequences in 30 year old frozen archival organ samples.

Development of a quantitative PCR assay for monitoring HCV viraemia levels in patients with chronic hepatitis C

The need to improve the efficacy of anti-viral agents directed against the hepatitis C virus (HCV) has prompted the development of quantitative tests to monitor viraemia levels in relation to therapy. In this respect, we have produced a non-competitive, quantitative PCR assay (Amplicor HCV Monitor) which is based on the single, combined, reverse transcription and amplification of the 5' non-coding region of HCV RNA as well as of an internal standard which serves to assess the overall efficiency of the system. The dynamic range of the assay and its precision allows for an accurate quantification between 1000 and 1,000,000 copies of the viral genome per ml. The results of the first clinical evaluation of the test indicated that determination of viraemia may have predictive value when assessed prior to treatment, as patients with less than 50,000 HCV RNA copies per ml tend to show a long-term response to interferon-alpha (IFN-alpha) treatment. Moreover, a decrease of more than 1.5-2 logarithms occurring at 1 month post-initiation of therapy predicts response in a more timely and accurate fashion than ALT measurement. This may help in a better selection of patients to treat, therapy approaches and schedules and in the optimization of the cost-benefit balance.

Hepatitis C virus infection and mixed cryoglobulinaemia: assessment of HCV RNA copy numbers in supernatant, cryoprecipitate and non-liver cells

The aim of this study was to characterize hepatitis C virus (HCV) infection in patients with mixed cryoglobulinaemia (MC). The HCV RNA copy number was assayed in clinical specimens from 15 consecutive patients with MC and HCV infection. Absolute quantification of HCV RNA molecules was performed using a competitive reverse transcription-polymerase chain reaction (cRT-PCR). Specific HCV RNA sequences were detected and quantified in plasma samples from all patients (mean HCV RNA copy number 4.9 x 10(6) ml-1 plasma). A high concentration of HCV RNA molecules was detected in the cryoprecipitates of eight of the 15 patients, who had a cryoprecipitate/supernatant ratio higher than 3.0 (range 3.60 to 186.80): in the remaining seven patients this ratio was close to or lower than 1.0 (range 0.13 to 1.60). Quantitative analysis of HCV RNA molecules in cells other than hepatocytes (i.e. peripheral blood mononuclear cells (PBMCs) and bone marrow cells (BMCs), in which the HCV replicative intermediate was detected using strand specific RT-PCR, demonstrated that infection is detectable in nearly 60% of these extrahepatic cells. Quantitative analysis of HCV RNA in PBMCs and BMCs revealed low levels of viral nucleic acids.

Low hepatitis C viremia levels in patients with anti-liver/kidney microsomal antibody type 1 positive chronic hepatitis

BACKGROUND/AIMS

The majority of adult patients positive for anti-liver-kidney microsomal antibody are also positive for anti-hepatitis C virus and serum HCV RNA. In these patients the role played by hepatitis C virus infection in the progression of liver damage and its relationship with anti-liver-kidney microsomal antibody are, however, still a matter of debate.

METHODS

To clarify this point we have compared hepatitis C viremia in sera from 31 hepatitis C virus-related chronic hepatitis patients positive for anti-liver-kidney microsomal antibody with that of 31 patients with hepatitis C virus-related chronic hepatitis without autoantibodies using a newly developed competitive reverse transcription-polymerase chain reaction technique. Reverse transcription-polymerase chain reaction was performed using a synthetic competitor of a length similar to that of wild template (71 bp vs 86 bp).

RESULTS

The results obtained have been related to hepatitis C virus genotypes. Anti-liver-kidney microsomal antibody/anti-HCV positive patients show a median value of hepatitis C virus genome molecules (626829/ml, range 9780-25651424), significantly lower than anti-liver-kidney microsomal antibody negative/anti-HCV positive patients (10158314/ml, range 101822-67429974) (p < 0.001). No hepatitis C virus genotype was significantly associated with anti-liver-kidney microsomal antibody, although a predominance of genotype 1 (subtypes a and b) has been observed in these patients.

CONCLUSIONS

Since a low hepatitis C viremia has been observed in anti-liver-kidney microsomal antibody positive patients with disease severity comparable to that of patients without autoantibodies, it is conceivable that in them autoimmune mechanisms may cooperate with viral infection in sustaining disease activity.

Novel, ligation-dependent PCR assay for detection of hepatitis C in serum

A simple, sensitive, and specific ligation-dependent PCR (LD-PCR) method for the detection of hepatitis C virus (HCV) RNA in serum is described. The assay uses two DNA capture probes for RNA isolation and two DNA hemiprobes for subsequent PCR. Each capture probe has a 3' sequence complementary to the conserved 5' untranslated region of HCV RNA and a biotin moiety at the 5' end capable of interacting with streptavidin-coated paramagnetic beads. Each hemiprobe contains a sequence complementary to the 5' untranslated region in juxtaposition to one another and a common sequence for PCR primer binding. In guanidinium thiocyanate solutions, the capture probes and the hemiprobes form a hybrid with their target, and the hybrid can be isolated from serum by the binding of the capture probes to the paramagnetic beads in the presence of a magnetic field. The hemiprobes can then be linked to each other by incubation with T4 DNA ligase to form a full probe that serves as a template for a PCR. When serial 10-fold dilutions of synthetic HCV RNA (10(7) to 10 molecules) were tested, there was a good correlation between the amount of PCR product and the initial number of RNA molecules, with a sensitivity of 100 HCV RNA molecules per reaction. Twenty-four specimens that had been tested by either a branched DNA probe (bDNA) assay (13 specimens) or a reverse transcription PCR (RT-PCR) assay (11 specimens) were also analyzed by LD-PCR. The results showed a good correlation among LD-PCR, RT-PCR, and the bDNA assay. However, both LD-PCR and RT-PCR were more sensitive than the bDNA assay when the HCV titer was low.

Comparison of two quantitative hepatitis C virus reverse transcriptase PCR assays

A quantitative hepatitis C virus reverse transcriptase PCR (HCV RT-PCR) assay established in our laboratory was compared with the Roche Amplicor HCV Monitor test kit for agreement of test results and intra-assay variability. Both assays rely on reverse transcription and amplification of extracted RNA from patients' sera together with an internal RNA standard derived from the 5'-noncoding region of HCV. A panel of clinical serum samples (n = 33) was quantitatively analyzed in parallel by both test systems. The methods demonstrated substantial agreement between 1 x 10(3) and 5 x 10(5) HCV RNA molecules per ml of serum. However, with sera containing more than 5 x 10(5) copies per ml, according to our in-house assay, the results diverged on average in a nonacceptable range of 2 orders of magnitude. Our in-house HCV RT-PCR assay measured up to 5 x 10(7) HCV-RNA molecules per ml in some serum samples. However, the Roche Amplicor HCV Monitor test kit did not detect more than 2 x 10(6) molecules in any of the serum samples tested. After dilution of serum samples prior to testing, an approximately 0.5 order of magnitude more HCV RNA molecules was detected by the Roche HCV test kit in sera containing high copy numbers (> 5 x 10(5) RNA copies according to the in-house assay). The in-house PCR and the Roche Amplicor HCV Monitor test kit revealed coefficients of variation of 6.2 and 7.5%, respectively.

Quantitative molecular methods in virology

During the past few years, significant technical effort was made to develop molecular methods for the absolute quantitation of nucleic acids in biological samples. In virology, semi-quantitative and quantitative techniques of different principle, complexity, and reliability were designed, optimized, and applied in basic and clinical researches. The principal data obtained in successful pilot applications in vivo are reported in this paper and show the real usefulness of these methods to understand more details of the natural history of viral diseases and to monitor specific anti-viral treatments in real time. Theoretical considerations and practical applications indicate that the competitive polymerase chain reaction (cPCR) and competitive reverse-transcription PCR (cRT-PCR) assay systems share several advantages over other quantitative molecular methodologies, thus suggesting that these techniques are the methods of choice for the absolute quantitation of viral nucleic acids present in low amounts in biological samples. Although minor obstacles to a wide use of these quantitative methods in clinical virology still remain, further technical evolution is possible, thus making the quantitative procedures easier and apt to routine applications.

Viral load in samples from hepatitis C virus (HCV)-infected patients with various clinical conditions

Molecular methods for the absolute quantitation of nucleic acids present in biological samples have recently been developed and applied in basic and in medical virology; these studies indicated that competitive polymerase chain reaction (PCR) and competitive reverse transcription PCR (cRT-PCR)-based methodologies are currently the methods of choice for quantifying DNA and RNA species present in clinical samples at low concentration. Recently, quantitative molecular techniques were developed to study the hepatitis C virus (HCV) pathogenic potential, the natural history of HCV-infected patients and the efficiency of antiviral therapies in real time. The pilot study reported here was carried out using a cRT-PCR application for the direct quantitation of HCV RNA molecules in plasma samples of infected individuals which was recently developed in our laboratory. Although sharp individual variability of viral load was documented in this study, the mean HCV RNA copy number detected in samples from untreated HCV-infected patients with various clinical conditions (chronic active hepatitis, cirrhosis, cryoglobulinaemia and chronic hepatitis) was substantially similar, with only one exception: in samples from patients tested positive for anti-liver-kidney microsomal (anti LKM1) auto-antibodies, a significantly lower HCV viraemia level was revealed. Additionally, HCV viraemia was monitored in four patients with sustained biochemical and histological response (at least 12 months) following interferon-alpha discontinuation.