Comparison of plasma virus loads among individuals infected with hepatitis C virus (HCV) genotypes 1, 2, and 3 by quantiplex HCV RNA assay versions 1 and 2, Roche Monitor assay, and an in-house limiting dilution method

Genotyping simplified: rationally designed antisense oligonucleotide-mediated PCR amplification-free colorimetric sensing of viral RNA in HCV genotypes 1 and 3

Molecular diagnosis of viral genotyping devoid of polymerase chain reaction (PCR) amplification in clinical cohorts has hitherto been challenging. Here we present a simplified molecular diagnostic strategy for direct genotyping of hepatitis C virus (HCV) 1 and 3 (prevalent worldwide) using a combination of rationally designed genotype-specific antisense oligonucleotides (ASOs) and plasmonic gold nanoparticles. The ASOs specific to genotypes 1 and 3 have been designed from the nonstructural region 5A (NS5A) of the viral genome using the ClustalW multiple sequence alignment tool. A total of 79 clinical samples including 18 HCV genotype 1, 18 HCV genotype 3, one HIV positive, one HBV positive, and 41 healthy controls have been tested against both the designed ASOs. The study reveals 100% specificity and sensitivity with the employed samples and thereby opens up new avenues for PCR-free direct genotyping of other viruses as well, through the rational design of ASOs.

HCV Detection, Discrimination, and Genotyping Technologies

According to the World Health Organization (WHO), 71 million people were living with Hepatitis C virus (HCV) infection worldwide in 2015. Each year, about 399,000 HCV-infected people succumb to cirrhosis, hepatocellular carcinoma, and liver failure. Therefore, screening of HCV infection with simple, rapid, but highly sensitive and specific methods can help to curb the global burden on HCV healthcare. Apart from the determination of viral load/viral clearance, the identification of specific HCV genotype is also critical for successful treatment of hepatitis C. This critical review focuses on the technologies used for the detection, discrimination, and genotyping of HCV in clinical samples. This article also focuses on advantages and disadvantages of the reported methods used for HCV detection, quantification, and genotyping.

Performance of 6 HCV genotyping 9G test for HCV genotyping in clinical samples

Background

A treatment of HCV infection depends on the genotype and sub-genotype. Therefore, accurate HCV genotyping is critical for selecting the appropriate treatment regimen.

Method

This study included 280 plasma samples to evaluate the performance of 6 HCV Genotyping 9G test. The performance of 6 HCV Genotyping 9G test for accurate detection of HCV 1a, 1b, 2, 3, 4, and 6 genotypes was evaluated by comparing it with LiPA 2.0 assay and sequencing.

Results

6 HCV Genotyping 9G test and LiPA 2.0 assay demonstrated 83.9% (n = 235) agreement. 39/45 samples that showed discrepant results between the two tests were analyzed by sequencing. Sequencing genotyped 39 discrepant samples as 0 (HCV 1a), 24 (HCV 1b), 1 (HCV 6f), 12 (HCV 6i), and 2 (HCV-negative). Results of 6 HCV Genotyping 9G test were very similar to the sequencing as it detected 1, 23, 1, 12, and 2 samples as HCV 1a, 1b, 3 & 6a or 6f, 6i or 6n, and negative, respectively. However, LiPA 2.0 assay showed complete disagreement with sequencing, as it did not detect any of these 39 samples correctly. These results indicate that LiPA 2.0 assay has limitations in identifying HCV genotypes 1b, and 6. The sensitivity, specificity, PPV, and NPV of 6 HCV Genotyping 9G test were 99.5, 98.8, 99.5, and 98.8%, respectively. It is important to note that HCV Genotyping 9G test showed 98.3 and 100% sensitivity for HCV 1b and 6 genotyping, respectively. However, LiPA 2.0 assay demonstrated 57.9 and 71.7% sensitivity for these genotypes.

Conclusions

6 HCV Genotyping 9G test identifies HCV 1a, 1b, 2, 3, and 6 with good agreement with sequencing. Hence, 6 HCV Genotyping 9G test has a high clinical value because it can provide critical information to physicians and assist them to use the correct drug for efficient hepatitis C treatment.

Electronic supplementary material

The online version of this article (10.1186/s12985-018-1017-4) contains supplementary material, which is available to authorized users.

Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays

BACKGROUND

The ability of HIV-1 to integrate into the genomes of quiescent host immune cells, establishing a long-lived latent viral reservoir (LVR), is the primary obstacle to curing these infections. Quantitative viral outgrowth assays (QVOAs) are the gold standard for estimating the size of the replication-competent HIV-1 LVR, measured by the number of infectious units per million (IUPM) cells. QVOAs are time-consuming because they rely on culturing replicate wells to amplify the production of virus antigen or nucleic acid to reproducibly detectable levels. Sequence analysis can reduce the required number of culture wells because the virus genetic diversity within the LVR provides an internal replication and dilution series. Here we develop a Bayesian method to jointly estimate the IUPM and variant frequencies (a measure of clonality) from the sequence diversity of QVOAs.

RESULTS

Using simulation experiments, we find our Bayesian approach confers significantly greater accuracy over current methods to estimate the IUPM, particularly for reduced numbers of QVOA replicates and/or increasing actual IUPM. Furthermore, we determine that the improvement in accuracy is greater with increasing genetic diversity in the sample population. We contrast results of these different methods applied to new HIV-1 sequence data derived from QVOAs from two individuals with suppressed viral loads from the Rakai Health Sciences Program in Uganda.

CONCLUSIONS

Utilizing sequence variation has the additional benefit of providing information on the contribution of clonality of the LVR, where high clonality (the predominance of a single genetic variant) suggests a role for cell division in the long-term persistence of the reservoir. In addition, our Bayesian approach can be adapted to other limiting dilution assays where positive outcomes can be partitioned by their genetic heterogeneity, such as immune cell populations and other viruses.

6 HCV Genotyping 9G test for HCV 1a, 1b, 2, 3, 4 and 6 (6a, 6f, 6i and 6n) with high accuracy

According to EASL guidelines and WHO recommendations, the accurate detection of HCV genotypes such as HCV 1a, HCV1b, HCV 2, HCV 3, HCV 4, and HCV 6 (6a, 6f, 6i, 6n) is crucial for the efficient treatment of hepatitis C. HCV Genotyping 9G test allows simultaneous genotyping of HCV 1a, 1b, 2, 3, 4, and 6 (6a, 6f, 6i, and 6n) in clinical samples in 30min. The performance of the test was evaluated by comparison with sequence analysis. Serum samples (n=152) from HCV-infected patients (n=110) and healthy individuals (n=42) were processed under blinded codes. The k coefficient (kappa) values indicated high agreement between the HCV Genotyping 9G test and sequencing. The sensitivity and specificity of the test were 99.1% and 99.7%, respectively. The results indicate that HCV Genotyping 9G test is rapid, reliable, sensitive, and accurate for screening and genotyping of HCV in the clinical specimens.

6 HCV genotyping 9G test and its comparison with VERSANT HCV genotype 2.0 assay (LiPA) for the hepatitis C virus genotyping

In this article, we describe the 6 HCV Genotyping 9G test and its evaluation by using clinical samples and plasmid DNA standards. In tests with 981 plasmid DNA standards, the 6 HCV Genotyping 9G test showed higher than 92.5% sensitivity and 99.4% specificity. The 6 HCV Genotyping 9G test was compared with the VERSANT HCV Genotype 2.0 assay (LiPA 2.0) for detection and discrimination of HCV genotypes in clinical samples. The results of both tests were verified by genomic sequencing. The 6 HCV Genotyping 9G test demonstrated a 100% agreement with the sequencing results, which was higher than LiPA 2.0. These results indicate that the 6 HCV Genotyping 9G test can be a reliable, sensitive, and accurate diagnostic tool for the correct identification of HCV genotypes in clinical specimens. 6 HCV Genotyping 9G test can genotype six HCV types in 1 PCR in 30min after PCR amplification. The 6 HCV Genotyping 9G test, thus provide critical information to physicians and assist them to apply accurate drug regimen for the effective hepatitis C treatment.

Stability of hepatitis C virus RNA in blood samples by TaqMan real-time PCR

The storage conditions of blood samples for reliable results are very important in hepatitis C virus (HCV) RNA amplification tests used in routine HCV analyses. According to many studies, storage conditions could affect the RNA stability for HCV RNA detection. We have studied HCV RNA stability in blood samples stored at 4 degrees C. Nineteen blood samples containing different HCV RNA levels were stored at 4 degrees C and they were then analyzed by TaqMAN real-time PCR method. HCV RNA levels remained almost stable (100%) at least for five weeks at this storage condition. However, among them, the stability period was up to 11 weeks in two of the samples. As with these findings, there was a slightly significant correlation between the positivity time and the beginning HCV RNA levels (r=0.474, P=0.040). We conclude that, blood samples can be stored at 4 degrees C for five weeks without any significant difference in detected HCV RNA level by using TaqMan real-time PCR.

Development of a low-cost real-time reverse transcriptase-polymerase chain reaction technique for the detection and quantification of hepatitis C viral load

BACKGROUND

It is necessary to develop a highly specific and sensitive assay to quantify the exact amount of hepatitis C virus (HCV) RNA in blood of patients with hepatitis C. For this reason, a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay for quantification of HCV RNA in human plasma was developed.

METHODS

A pair of primers as well as hybridization probes were selected. A real-time RT-PCR was set up and optimized. To establish the sensitivity of the assay, a serial dilution of HCV standards and reference sera, including the six major HCV genotypes, was used. The performance of the assay was evaluated with 191 known HCV-RNA positive and 100 negative samples.

RESULTS

The real-time assay had a sensitivity of 50 IU/mL, with a dynamic range of detection between 10(3) and 10(6) IU/mL. The coefficients of variation of threshold cycle values in intra- and inter-day-runs were <1.77% and 3.40%, respectively. Measurement of HCV-RNA positive samples yielded reproducible data with 100% specificity.

CONCLUSIONS

The high sensitivity, simplicity, reproducibility, wide dynamic range, and low cost of this real-time HCV RNA quantification makes this method especially suitable for monitoring viral load during therapy and tailoring of treatment schedules accordingly.

Hepatitis C virus infection in dialysis patients

Hepatitis C virus (HCV) infection is a global health problem, common worldwide, leading to acute and chronic hepatitis and its consequences of hepatocirrhosis and hepatocellular carcinoma. Patients on hemodialysis belong to the high-risk group of HCV infection. The prevalence of HCV infection in dialysis patients ranges from 4% to more than 70% in some countries. The main reasons for such a high incidence of infections are a high prevalence of HCV infection in the general population, lack of standard infection precautions and effective vaccination, inadequate disinfection procedures of dialysis machines and other medical equipment, as well as spread of infection from patient to patient, especially in dialytic centers with a high percentage of infected patients. The diagnostic procedures useful in the evaluation of HCV infection are detection of anti-HCV antibodies, identification of HCV RNA, counts of virus copies, and identification of its genome. From the 6 major genotypes and multiple subtypes of the HCV, genotypes 1a and 1b are the most common in Europe and Japan, and 1b is responsible for more severe liver disease and aggressive course leading to liver fibrosis. Antiviral therapy of HCV+ dialysis patients with interferon-alpha (INF-alpha) gives slightly better results than in the general population, but is poorly tolerated and associated with side effects. Although ribavirin in not recommended for dialysis patients, the addition of small doses of this compound to pegylated INF is discussed, especially for patients in whom previous infection treatment failed.

A genotype-independent real-time PCR assay for quantification of hepatitis B virus DNA

Accurate quantification of hepatitis B virus (HBV) DNA levels is important for monitoring patients with chronic HBV infection and for assessing their responses to antiviral therapy. This study aimed to develop a real-time PCR assay that is sensitive and can accurately quantify a wide range of HBV DNA levels across the known HBV genotypes. An "in-house" real-time PCR assay using primers and a TaqMan probe in a highly conserved region of the HBV surface gene was designed. The assay was standardized against a WHO standard and validated against plasmids of HBV genotypes A through H. The linear quantification range was approximately 5 x 10(0) to 2.0 x 10(9) IU/ml. Results of samples from patients infected with HBV genotypes A through H tested using our real-time "in-house" PCR assay showed an excellent correlation with those of the Cobas Amplicor HBV Monitor (R2=0.9435) and the Cobas TaqMan HBV (R2=0.9873) tests. We have established a real-time PCR assay that is genotype independent and can accurately quantify a wide range of HBV DNA levels. Further studies of additional samples are ongoing to validate the genotype independence of our assay.

Clinical Applications of the Polymerase Chain Reaction: An Update

The development, in the past decade, of nucleic acid amplification and detection methods is useful in the study of the etiopathogenesis, diagnosis, and management of a variety of clinical (including rheumatologic) disorders. An association between infectious agents and rheumatic disorders has been established through such methods as polymerase chain reaction. This article describes the principles behind polymerase chain reaction-based diagnosis and updates its clinical applications. It is beyond the scope of this article, however, to describe other nucleic acid amplification methods or to include a complete list of all polymerase chain reaction assays that have been developed. Other recent reviews offer additional details.

Design, development and evaluation of a competitive RT-PCR for quantitation of GBV-C RNA

Although GB virus C (GBV-C) hepatocyte pathogenicity is still controversial, it appears that at least some strains of this virus are lymphotropic. During the past few years, several reports have documented an apparently beneficial role played by GBV-C in the course of HIV-1 infection. At present, a commercial kit for GBV-C RNA quantitation is not available. In this study, a competitive RT-PCR method for GBV-C in serum samples is described. The sensitivity of the assay proved to be 10(4) and 10(3) genomic equivalents for positive and negative sense RNAs, respectively. This method will discriminate specifically between positive and negative strand RNAs with a discrimination index of at least five log10. Out of 60 samples from different hematological disorders (n = 49), HIV-1 positive patients (n = 7), and blood donors (n = 4), 10 proved to be GBV-C RNA positive. Viral load ranged from 1.1 x 10(7) to 2.34 x 10(8) genomic equivalents/ml. Such values correlated linearly (r = 0.986) with those obtained by a 10-fold serial dilution method. In studies exploring the GBV-C pathogenicity, the measurement of viral load may contribute to understand the possible mechanisms involved.

Analytical and biological variables influencing quantitative hepatitis C virus (HCV) measurement in HIV-HCV coinfection

The present review considers issues pertaining to the precision and variability of quantitative hepatitis C virus (HCV) measurement in general, outlines the characteristics of HCV RNA in HIV-HCV coinfection and evaluates those factors which may affect this measure. The clinical relevance of accurate HCV measurement in HIV-HCV coinfection is discussed.

Chronic hepatitis C virus infection: genotyping and its clinical role

Chronic hepatitis C virus (HCV) infection is a worldwide public health problem with a global prevalence of 2%. A high proportion of those infected are at risk of developing cirrhosis and hepatocellular carcinoma and modeling data predicts that the burden of disease could soon increase substantially. The liver disease associated with chronic infection has led investigators to look for correlates between viral properties and disease progression, severity of disease and the response to antiviral therapy. HCV has been classified into six genotypes but genotype does not appear to influence disease presentation or severity of disease. However, genotype has been identified as a major predictor of response to interferon-based antiviral therapy. Antiviral regimens have been optimized for infections with HCV genotypes 1-4, although treatment strategies for genotypes 5 and 6 have yet to be developed. The molecular basis for the differences in response of HCV genotypes has yet to be determined.

A refined long RT-PCR technique to amplify complete viral RNA genome sequences from clinical samples: application to a novel hepatitis C virus variant of genotype 6

The goal of this study was to adapt a long RT-PCR technique to amplify large PCR fragments from the genome of hepatitis C virus (HCV) isolates using clinical samples. This was done by using a reverse transcriptase devoid of RNase H activity and a mixture of two antibody-bound thermostable polymerases to combine the high processivity of Taq and the high fidelity of Pwo with its 3'-->5' exonuclease activity. Other modifications included gentle handling during RNA extraction, the absence of tRNA and random primers, a two-step reverse transcription procedure to optimize cDNA synthesis, and increasing the annealing temperature for primers. With this approach, the HCV-1 genome (nucleotides 35-9282) was amplified consistently as two overlapping fragments of 5344 and 4675 bp from a pooled chimpanzee plasma sample containing approximately 10(6) genome copies of HCV RNA/ml. Using the conditions that we identified, 96% of the complete genomic sequence of a distinct HCV genotype 6 variant (km45) was determined from less than 300 microl of serum. This method should prove useful for molecular, epidemiological and clinical studies of hepatitis C where samples are limited but complete virus sequence is required, for example, identifying mutational hot spots of HCV under specific clinical conditions.

Longitudinal study in HIV/HCV-coinfected HAART-naive patients and role of HCV genotype

To evaluate the impact of highly active antiretroviral therapy (HAART) on the course of hepatitis C (HCV) infection, we studied the biological and virological characteristics of 23 HCV/HIV-coinfected HAART-naive patients. The HCV genotype, HCV and HIV viral loads, serum alanine aminotransferase, CD4+ and CD8+ cell/mm3 were determined at baseline, 1 month, 6 months and 12 months after initiation of HAART. Results were analyzed both in terms of total population and of HCV genotype. The study of the total population suggests that this therapy did not determine a significant alteration of HCV viremia and levels of ALT, while a significant decrease in HIV viremia (-1.7log10 at one year from the start of HAART) and increase in CD4+ counts was observed (P < 0.005). The biological and virological parameters of HCV/HIV coinfection differed according to the HCV genotype. In particular, only genotype 4 showed a significant inverse correlation between HCV and HIV viral loads.

Usefulness of a new immuno-radiometric assay to detect hepatitis C core antigen in a community-based population

A new immuno-radiometric assay (IRMA) to detect hepatitis C virus (HCV) core antigen (HCVcAg) has been developed. The aim of the present study was to investigate the sensitivity and specificity of this IRMA to measure HCV antigenemia, based on the detection of HCV RNA as the gold standard, and to assess the utility of the IRMA in a community-based population. Anti-HCV positive residents in a hyperendemic area of HCV infection in Japan were studied. Serum levels of HCVcAg were measured using IRMA, and the presence of HCV RNA was determined by a qualitative reverse transcription-polymerase chain reaction (RT-PCR) assay. The sensitivity and the specificity of the IRMA were 96.4 and 100%, respectively. The sensitivity of the IRMA was similar between serological HCV group I (HCV genotypes 1a and 1b) (97.6%) and group II (HCV genotypes 2a and 2b) (94.0%). There was a strong correlation between serum HCVcAg level and HCV-RNA measured by a quantitative RT-PCR (r = 0.832, P < 0.0001). There also was a very strong correlation of HCVcAg level between IRMA measurements performed on serum and those performed on plasma (r = 0.984, P < 0.0001). In conclusion, this new IRMA is useful for the detection of HCV core antigen in a community-based population.

The use of class-I HLA tetramers for the detection of hepatitis C virus NS3-specific CD8(+) T cells in patients with chronic infection

BACKGROUND/AIMS

New methods to detect virus-specific T-cell responses have recently been developed. Several human leukocyte antigen (HLA)-peptide tetramers for the detection of hepatitis C virus (HCV)-specific CD8(+) T cells are under evaluation.

METHODS

Evaluation of one HLA class I-tetramer (HCVNS3-2) for the detection of HCV NS3-specific CD8(+) T cells in a series of 38 HLA-A2(+) chronically infected patients.

RESULTS

Almost half (42%) of the patients had detectable NS3-specific CD8(+) T cells. The frequencies of such cells ranged from 0.01% to 0.22% of total CD8(+) T cells. No significant differences in clinical features or mean viral load were detected between patients with or without tetramer + CD8(+) T cells.

CONCLUSIONS

The tetramer HCVNS3-2 may be very useful for the study of the HCV-specific CD8(+) immune response. Combination of this reagent with other tetramers based on other HCV peptides may help in the understanding of the immune response to the virus. However, a panel of tetramers based on several parts of the HCV polyprotein may be a mandatory requirement to explore the whole breadth of the CD8(+) T-cell response against HCV and to detect that response in the majority of patients with chronic infection.

Development and evaluation of a quantitative competitive reverse transcription polymerase chain reaction (RT-PCR) for hepatitis C virus RNA in serum using transcribed thio-RNA as internal control

A method for quantitation of hepatitis C virus (HCV) RNA was developed based on competitive reverse transcription polymerase chain reaction (RT-PCR) using in vitro transcribed mutated thio-RNA as a competitor template. The thio-RNA is more resistant to RNAse and is stable over a year. This assay was compared with the commercially available Roche Amplicor HCV Monitor assay V 2.0 and real time PCR using SYBR green 1 dye method. A total of 18 pre-therapy serum samples from chronic hepatitis C cases were tested in parallel by the three assays. All samples could be quantitated using the in-house competitive RT-PCR and real time PCR and there was a significant correlation in the virus titer (P<0.05). However, 8 (44%) samples could not be quantified by Amplicor HCV Monitor assay, which has a lower detection range (10(2) to 10(5.5) copies/ml). The in-house method of competitive RT-PCR showed a detection range of 10(3) to 10(10) copies/ml. In the patients the mean viral titer was found to be (9.66+/-9.3)x10(6) copies/ml. Ten (55%) of the samples, assessed by the Amplicor HCV Monitor assay showed a mean viral titre of (1.13+/-0.75)x10(6) copies/ml, which was lower than the other two tests. The competitive PCR method and real time PCR could amplify all prevalent genotypes. This in-house quantitative competitive RT-PCR method is simple, cheap, reproducible and useful for estimation of HCV RNA load.

Clinical evaluation of an HIV-1 and HCV assay and demonstration of significant reduction of the HCV detection window before seroconversion

BACKGROUND

One HIV-1 and HCV assay simultaneously detects HIV-1 and HCV RNA (Procleix, Chiron Corp.). The main intended use of the assay is the testing of blood and blood products in blood banking.

STUDY DESIGN AND METHODS

To evaluate the clinical sensitivity of the assay, 164 anti-HIV-1+ and 160 anti-HCV+ patients of different viral load were tested. The assay specificity was determined in 1000 HIV-1- and HCV-seronegative blood donors. The ability of the assay to detect different HCV genotypes was investigated in a total of 40 patients of different genotypes (1-4). Furthermore, to investigate the reduction of the HCV window phase before seroconversion, serial samples of 25 hemodialysis patients who seroconverted to anti-HCV were also tested.

RESULTS

The assay detected all 60 HIV-1-infected patients with a viral load of greater than 50 copies per mL and 48 of 104 patients with a viral load of less than 50 copies per mL. Moreover, all 60 patients with an HCV RNA load of greater than 521 IU per mL and 7 of 100 patients with a viral load of less than 50 IU per mL tested positive. The assay specificity was found to be 100 percent. In addition, all 40 patients of different HCV genotypes were successfully detected. Finally, the median time that the assay detected HCV infection before second- and third-generation anti-HCV assay was found to be 183 and 91 days, respectively.

CONCLUSION

The assay sensitivity and specificity, its ability to detect different HCV genotypes, and the significant reduction of window period of HCV infection further support its use for improving the safety of blood and blood products.

Comparison of different HCV viral load and genotyping assays

BACKGROUND

We report an interlaboratory comparison of methods for the determination of hepatitis C virus (HCV) serum load and genotype between a recently, established molecular laboratory at the Alaska Native Medical Center (ANMC) and two independent laboratories using different assays. At ANMC, a Real-time quantitative RT-PCR amplification methodology (QPCR) has been developed in which HCV viral loads are determined by interpolation of QPCR results to those of standards calibrated to the World Health Organization (WHO) First International Standard for HCV. HCV genotype is subsequently determined by direct sequencing of the DNA fragment generated from the QPCR assay.

OBJECTIVES AND STUDY DESIGN

The above methods were statistically compared to results obtained for the same patient sera by two independent laboratories using different commercially available viral load assays; Quantiplex HCV RNA (Bayer Diagnostics) and Amplicor HCV Monitor (v 2.0) (Roche Molecular Systems), as well as two different genotyping assays; restriction fragment length polymorphism (RFLP) and INNO-LiPA HCV II (Innogenetics).

RESULTS

ANMC's Real-time QPCR HCV viral load results compared moderately well with those obtained by the Quantiplex HCV RNA method (R2=0.3813), and compared quite well with recent lot numbers of Amplicor HCV Monitor in which viral loads are derived in IU/ml (R2=0.6408), but compared poorly with earlier lot numbers of Amplicor HCV Monitor in which viral loads were derived in copies/ml (R2=0.0913). The ANMC direct sequencing method for genotype determination compared moderately to very well with both the RFLP (84-86%) and INNO-LiPA (85-97.5%) methods.

CONCLUSIONS

These viral load comparisons highlight the discrepancies that may occur when patient HCV viral loads are monitored using different types of assays. Comparison of HCV genotype by different methods is more reliable statistically and important clinically for predicting probability of response to antiviral therapy. However, viral loads are important for monitoring response once therapy has begun.

Frequent recovery and broad genotype 2 diversity characterize hepatitis C virus infection in Ghana, West Africa

Hepatitis C virus (HCV) infection is thought to mostly become chronic and rarely resolves. HCV infection was serologically screened in 4,984 samples from Ghanaian blood donors, and 1.3% prevalence was found. At least 53% of confirmed anti-HCV carriers had no detectable viral RNA and were considered to have cleared the virus and recovered from the infection. Confirmation was authenticated by the presence of antibodies specific to at least two viral antigens, mostly NS3 and E2. Reactivity to HCV core antigens was lower in Ghanaian than United Kingdom blood donors. The minority of chronically infected donors carried a viral load significantly lower than an unselected comparative group of United Kingdom blood donors (2.5 x 10(5) versus 2.9 x 10(6) IU/ml; P = 0.004). HCV genotype 2 was largely predominant (87%). Sequence clustering was similarly broad in the E1/E2 and NS5 regions. The phylogenetic diversity and the incapacity to distinguish subtypes within genotype 2 in our and others' West African strains suggested that West Africa may be the origin of HCV genotype 2. The genetic diversity extended to the identification of strains clearly separated from known subtypes of genotype 2 and genotype 1. One strain appears to be part of a new HCV genotype. HCV infection in Ghana is characterized by a high rate of recovery and the predominance of broadly divergent genotype 2 strains.

In vitro detection of dissimilar amounts of hepatitis C virus (HCV) subtype-specific RNA genomes in mixes prepared from sera of persons infected with a single HCV genotype

The level of in vitro detection of viral genomes in mixes with two different hepatitis C virus (HCV) subtypes was investigated by artificially mixing previously measured subtype-specific HCV RNA genomes. The RNAs in these mixtures were reverse transcribed and then PCR amplified by using two sets of primers corresponding to the 5' untranslated region and digested with endonucleases to analyze the restriction fragment length polymorphism patterns. This approach facilitated detection of a wider range of type-specific HCV genomes than originally described, beyond equimolar concentrations of contributing HCV subtypes. Moreover, by using computerized image analysis, this study also demonstrated that the true contribution of each virus type-and consequently of mixed infections-may be underestimated when only visual observation is carried out. These results may be useful for comparing data obtained from this and other currently used methodologies.

Comparison of three commercially available assays for HCV RNA using the international unit standard: implications for management of patients with chronic hepatitis C virus infection in clinical practice

OBJECTIVES

The present study was performed to evaluate the impact of the international unit standard for measuring HCV RNA in the management of patients with chronic hepatitis C virus (HCV) infection.

METHODS

The three assays used were Amplicor Monitor PCR, the National Genetics Institute PCR assay, and branched chain DNA. HCV RNA was measured at four time points (baseline, 3 months after the start of therapy, at the end of treatment, and 6 months after discontinuation of therapy) in 106 consecutive patients who received interferon and ribavirin for chronic HCV.

RESULTS

The mean age of the patients was 44 yr. Of the patients, 62% were male, 24% were African American, 38% had bridging fibrosis or cirrhosis, and 75% were HCV genotype 1. Of the 424 samples analyzed, 82-89% of values were within 1 log unit and 85-92% were within 2 log units by the various assays. This variability was not dependent upon HCV genotype. HCV RNA was undetectable in 1.4-6.8% of samples when virus was detected by another assay. The mean HCV RNA in these discordant samples was 1.47-6.33 log IU/ml (30-2,100,000 IU/ml).

CONCLUSIONS

These data demonstrate that approximately 90% of serum values for HCV RNA were within 1 log unit by the international unit standard regardless of which virological assay was used. However, false positive and false negative results as well as variations in the HCV RNA level of more than 1 to 2 log units can occur with any of the assays, and these results may have an impact upon the management of patients receiving interferon therapy. It is therefore unwise in clinical practice to base important treatment decisions upon a single HCV RNA determination.

Prediction of treatment outcome in patients with chronic hepatitis C: significance of baseline parameters and viral dynamics during therapy

In patients with chronic hepatitis C virus (HCV) infection scheduled for a 48-week treatment period, premature discontinuation of treatment was previously recommended if HCV-RNA levels remained detectable at week 24 of therapy. Considering the number of side effects and treatment costs, measurement of initial viral decline during therapy may identify virologic nonresponse earlier than 24 weeks. We retrospectively analyzed 260 European patients treated with standard or pegylated interferon alfa (IFN-alpha) and ribavirin for 24 to 48 weeks. Early prediction of virologic response by HCV-RNA decline at weeks 4 and 12 (Versant Quantitative [branched DNA (bDNA) 3.0]; Bayer Diagnostics, Emeryville, CA; and Qualitative [transcription-mediated amplification (TMA)] HCV RNA assay; Bayer Diagnostics) as well as clinical, biochemical, virologic, and histologic baseline parameters were analyzed by logistic regression and receiver operating characteristic (ROC) curves. A viral load at treatment week 4 above 450,000 IU/mL and at week 12 above 30,000 IU/mL was 100% predictive for virologic nonresponse in all patients. From multivariate logistic regression analysis of all patients, independent predictors for sustained virologic response were: genotypes 2 and 3 (P <.0001), a low baseline gamma-glutamyltransferase (GGT) level (P <.0001), a high baseline alanine aminotransferase level (P =.002), and a low baseline viral load (P =.04). None of the latter 3 factors were predictive for sustained virologic response when analysis was restricted to the subgroup of genotypes 2- and 3-infected patients. In conclusion, virologic nonresponse can be predicted early at week 12 of treatment independent from the applied therapeutic regimen based on a cutoff level for HCV RNA of 30,000 IU/mL. This algorithm recognizes 53.7% of nonresponders previously identified at week 24 of treatment.

Applications of polymerase chain reaction in rheumatology

Polymerase chain reaction (PCR) is a highly sensitive and specific method for detection and quantification of specific nucleic acids from a clinical sample. With its use, genetic, infectious, neoplastic, and autoimmune diseases can be diagnosed and managed with a high level of sensitivity, accuracy, and rapidity. This technique exactly reproduces unlimited copies of DNA, even if only a small amount are present initially. PCR assays can detect presence of fastidious and slow-growing microorganisms, such as chlamydia, mycoplasmas, mycobacterias, and viruses directly from clinical specimens and also can detect antimicrobial resistance. The value of viral load measurement by nucleic acid amplification in the management of patients with HIV infection or hepatitis C has also been well established. From the point of view of a clinician, the applications of PCR are focused mainly in the amplification and detection of diagnostic DNA segments from the genomes of both pathogens and patients.

Hepatitis C virus genetic variability: pathogenic and clinical implications

HCV is variable because of the properties of the viral RdRp, high levels of replication, and large population sizes. The Darwinian evolution of HCV has been characterized by the emergence of the HCV genotypes, including six main types and a large number of subtypes. The study of HCV genotype epidemiology provides useful information on the worldwide HCV epidemics. The HCV genotype is an important predictor of the response to IFN-alpha-based antiviral therapy, and genotype determination is currently used to tailor treatment indications. In addition, HCV circulates and behaves in infected individuals as mixtures of closely related but distinct viral populations referred to as quasispecies. This particular nature of the virus influences its transmission, the pathogenesis of liver disease and extra-hepatic manifestations, and the outcome during and after antiviral therapy or after transplantation for HCV-related end-stage liver disease. Further studies are needed to understand better the implications of HCV quasispecies diversity in the pathophysiology of HCV infection.

Collaborative study to calibrate hepatitis C virus genotypes 2-6 against the HCV International Standard, 96/790 (genotype 1)

BACKGROUND AND OBJECTIVES

A major requirement of a hepatitis C virus (HCV) RNA nucleic acid amplification technology (NAT) assay validation is the ability of the assay to detect the six major genotypes of HCV with equivalent sensitivities. The aim of this study was to characterize and calibrate an HCV genotype panel for use in such studies.

MATERIALS AND METHODS

Panels consisting of the first International Standard (IS) for HCV RNA NAT assays (96/790; HCV genotype 1a) and isolates of genotypes 2-6 were sent to 17 laboratories worldwide which use a variety of NAT tests, both qualitative and quantitative. The HCV RNA content of each panel member was determined and the mean titre calculated in International Units/ml (IU/ml).

RESULTS

The calculated mean titres (calibrated against the HCV International Standard), in log10 IU/ml, of the genotype 2-6 samples were 3.99, 3.81, 4.14, 4.18 and 4.61, respectively.

CONCLUSIONS

An HCV genotype panel, calibrated in IU/ml, has been established and should be valuable for assay validation. All the genotypes were detected by all the assays used, but it was not possible to demonstrate that the genotypes were detected with equal efficiencies.

Evaluation of the clinical usefulness of COBAS AMPLICOR HCV MONITOR assay (ver2.0): Comparison with AMPLICOR HCV MONITOR assay (ver1.0) and HCV core protein level

The quantitation of serum levels of hepatitis C virus (HCV) RNA in chronic hepatitis C has been regarded as one of the most important indicators for the outcome of interferon (IFN) therapy. The AMPLICOR HCV MONITOR version 1.0 (AMPLICOR v1.0) assay is widely used for the evaluation of the HCV level. A new generation assay called the COBAS AMPLICOR HCV MONITOR version 2.0 (COBAS v2.0) assay, which is semiautomated and modified to amplify all genotypes equally, has been developed. The aim of this study was to evaluate the clinical relevance of the COBAS v2.0 assay in comparison with the AMPLICOR v1.0 assay and HCV core protein assay in patients with chronic hepatitis C before IFN therapy. HCV RNA was detectable in 230 cases (97.5%) and undetectable in 6 cases (2.5%) by the COBAS v2.0 assay. The RNA levels measured by the AMPLICOR v1.0 assay correlated significantly with those measured by the COBAS v2.0 assay, and the sensitivity of the new version 2.0 assay was better than that of version 1.0, especially in serotype 2. In relation to the outcome of IFN therapy, HCV RNA levels from virologically sustained responders by the AMPLICOR v1.0 assay were 82.3 +/- 22.9 kcopies/ml in serotype 1 and 36.9 +/- 13.4 kcopies/ml in serotype 2, and those from virologically nonsustained responders were 525.2 +/- 48.6 kcopies/ml in serotype 1 and 76.7 +/- 19.5 kcopies/ml in serotype 2. The rates of sustained response to <100 kcopies/ml were 34/63 (54.0%) in serotype 1 and 24/48 (50.0%) in serotype 2. A statistically significant virological response was seen in serotype 1 (P < 0.0001), but not in serotype 2. In contrast, the levels in virologically sustained responders by the COBAS v2.0 assay were 88.2 +/- 20.5 KIU/ml in serotype 1 and 136.8 +/- 40.1 KIU/ml in serotype 2, and those in virologically nonsustained responders were 608.8 +/- 48.4 KIU/ml in serotype 1 and 328.3 +/- 62.8 KIU/ml in serotype 2. The rates of sustained response to <100 KIU/ml were 33/60 (55.0%) in serotype 1 and 21/35 (60.0%) in serotype 2. Statistical significance in virological response was seen in both serotype 1 (P < 0.0001) and serotype 2 (P < 0.05). Although the sensitivity of the HCV core protein assay was lower than that with the COBAS v2.0 assay, the HCV core protein levels also correlated well with the results of the COBAS v2.0 assay. The HCV core protein levels of virologically sustained responders were 37.6 +/- 12.0 pg/ml in serotype 1, 81.3 +/- 37.0 pg/ml in serotype 2, and those of virologically nonsustained responders were 289.9 +/- 23.5 pg/ml in serotype 1, 191.4 +/- 32.1 pg/ml in serotype 2. This assay could predict the outcome of IFN therapy in both serotype 1 (P < 0.0001) and serotype 2 (P < 0.05). Thus, both the COBAS v2.0 assay and the HCV core protein assay showed that the viral load was an indicator of virologically sustained response in serotype 2 and in serotype 1.

Variation of hepatitis C virus load, hypervariable region 1 quasispecies and CD81 hepatocyte expression in hepatocellular carcinoma and adjacent non-cancerous liver

Hepatitis C virus (HCV) infection is etiologically associated with the development of hepatocellular carcinoma (HCC) worldwide. HCV has been reported to exist and replicate in both HCC and adjacent non-cancerous liver tissue, but limited information was available on HCV viral load and quasispecies composition in HCC relative to adjacent non-cancerous hepatocytes. Previous study has also suggested CD81, a surface hepatocyte protein, as a receptor for HCV. To clarify the above, HCV-RNA and CD81-RNA titers in 20 paired hepatectomized liver and serum were quantitatively measured by chemiluminescent RT-cPCR. Hypervariable region 1 (HVR-1) variations of parallel specimens were analyzed after subcloning in 6 patients. HCV-RNA levels in serum and non-cancerous liver were markedly higher for HCV genotype 1 than genotype non-1. HCV levels were markedly higher in non-cancerous liver than in HCC (P = 0.001) in a genotype-independent manner, with a mean ratio of 56:1 for non-cancerous tissue to HCC. Both non-cancerous and HCC tissues had the same level of CD81-RNA expression, which was not linked to HCV load. HCV-RNA quantity in both HCC and non-cancerous liver correlated with the number of HVR-1 quasispecies in the tissue, and distinct HVR-1 subclones existed.

Review of the effect of highly active antiretroviral therapy on hepatitis C virus (HCV) RNA levels in human immunodeficiency virus and HCV coinfection

The effect of anti-human immunodeficiency virus (HIV) treatment on hepatitis C virus (HCV) RNA levels in HIV-HCV-coinfected persons is uncertain. Although it is commonly believed that, with the initiation of HIV treatment, there may be an initial increase followed by a gradual decrease of HCV RNA levels to lower than those at pretreatment, the published studies evaluating this are of small and heterogeneous populations, are limited in follow-up, and have conflicting results. A prospective clinical trial of sufficient size and duration may help clarify this issue. This may be clinically relevant, because lower HCV RNA levels are a predictive factor for favorable response to HCV antiviral therapy.

Sensitive detection of genetic variants of HIV-1 and HCV with an HIV-1/HCV assay based on transcription-mediated amplification

This paper describes a comprehensive study of hepatitis C virus (HCV) and human immunodeficiency virus type 1 (HIV-1) genotype sensitivity of the transcription-mediated amplification (TMA)-based HIV-1/HCV assay, developed and manufactured by Gen-Probe Incorporated (San Diego, CA) for screening human plasma specimens in blood bank settings. The TMA HIV-1/HCV assay is a qualitative, in vitro nucleic acid testing system used for initial screening. HIV-1 and HCV discriminatory assays are used to distinguish between HIV-1 and HCV infection or co-infection. In this study, multiple unique specimens representing HCV genotypes 1-6 were tested at various dilutions. The results show that the TMA HIV-1/HCV assay and the TMA HCV discriminatory assay have similar HCV genotype sensitivity, as both assays detected all six genotypes at 100 copies/ml and nearly all replicates tested at 30 copies/ml. Similarly, numerous unique specimens representing HIV-1 group M subtypes (A-G), HIV-1 group N, and group O specimens were tested at various dilutions. The TMA HIV-1/HCV assay and the TMA HIV-1 discriminatory assay were found to have similar HIV-1 subtype sensitivity; all variants at 100 copies/ml and nearly all at 30 copies/ml were detected. These results indicate that the TMA assays meet the sensitivity requirements for blood screening in blood banks worldwide.

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.

Hepatitis C virus (HCV) RNA level determined by second-generation branched-DNA probe assay as predictor of response to interferon treatment in patients with chronic HCV viremia

Using first- and second-generation branched-DNA probe assays (1st- and 2nd-bDNA), we investigated the predictors of favorable clinical response to interferon (IFN) treatment in patients with chronic HCV viremia. A total of 122 patients (85 genotype lb and 37 genotype 2a) with chronic HCV viremia received 24-week IFN-alpha treatment. Patients with sustained clearance of serum HCV RNA by polymerase chain reaction at six months after IFN treatment were defined as having a sustained response (SR). HCV RNA level was determined by 1st- and 2nd-bDNA assays prior to treatment. Mean HCV RNA level by 1st-bDNA was significantly higher in genotype lb patients [5.4 x 10(6) HCV genome equivalent (Meq)/ ml] than in genotype 2a patients (0.9 Meq/ml) (P < 0.05). There was no significant difference between patients with these genotypes in the level by 2nd-bDNA (1b: 5.2 Meq/ml and 2a: 3.1 Meq/ml). SR was achieved by 43 (35.2%) of 122 patients. Mean HCV RNA levels by both the 1st- and 2nd-bDNA of SR patients (1.0 and 1.9 Meq/ml) were significantly lower than those of non-SR patients (5.3 and 6.0 Meq/ml) (both P < 0.05). The SR rate in genotype 2a patients (59.5%) was significant higher than in genotype lb patients (24.7%) (P < 0.05). Stepwise logistic regression analysis showed that HCV RNA level < or = 1.0 Meq/ml by 2nd-bDNA (odds ratio = 7.6, compared to level > 1.0 Meq/ml, P < 0.05) was a significant predictive cutoff for SR. Using 2nd-bDNA, a significantly higher rate of SR was found in genotype lb patients with level < or = 1.0 Meq/ml (57.6%) than in those with level > 1.0 Meq/ml (3.8%) (P < 0.05). The SR rate of genotype 2a patients with level >1.0 Meq/ml (68.6%) was somewhat higher than for those with level < or = 1.0 Meq/ml (52.4%). These findings suggested that, using 2nd-bDNA, a low HCV RNA level of < or = 1.0 Meq/ml was the most favorable marker of successful IFN treatment and that patients with genotype 2a, even those with level >1.0 Meq/ml, had a high rate of SR to IFN treatment.

Quantitation of hepatitis C virus RNA by third generation branched DNA-based signal amplification assay

Quantitation of hepatitis C virus (HCV) RNA has become an important tool in different clinical settings and is used extensively for pretreatment evaluation of patients infected chronically with HCV. In this study, the performance characteristics of the third generation branched DNA-based signal amplification assay (bDNA 3.0) for HCV RNA quantitation were established. The new assay version showed an analytical specificity of 98%. Mean intra- and between-run imprecisions were 6.8 and 11.2%, respectively. The assay was linear over its entire dynamic range. Quantitation appeared to be unaffected by the genotypic variability of HCV. A comparison of bDNA 3.0 with the second generation bDNA assay calibrated against the international WHO HCV RNA standard, and the PCR-based Cobas Amplicor HCV Monitor 2.0 revealed a fairly good correlation among the assays. Twenty-nine and 11% of the paired quantitative results differed by more than log(10)0.5 (i.e. three-fold). All three assays after calibration against the WHO standard also yielded clinically comparable results with regard to the tailoring of interferon alpha/ribavirin treatment duration in patients infected by HCV genotypes 1, 4, and 5.

Comparative evaluation of the VERSANT HCV RNA 3.0, QUANTIPLEX HCV RNA 2.0, and COBAS AMPLICOR HCV MONITOR version 2.0 Assays for quantification of hepatitis C virus RNA in serum

A comparison of quantitative results expressed in hepatitis C virus (HCV) international units per milliliter, obtained from the VERSANT HCV RNA 3.0 (bDNA-3.0) assay, the QUANTIPLEX HCV RNA 2.0 (bDNA-2.0) assay, and the COBAS AMPLICOR HCV MONITOR version 2.0 (HCM-2.0) test was performed. A total of 168 patient specimens submitted to the Mayo Clinic Molecular Microbiology Laboratory for HCV quantification or HCV genotyping were studied. Of the specimens tested, 97, 88, and 79% yielded quantitative results within the dynamic range of the bDNA-3.0, bDNA-2.0, and HCM-2.0 assays, respectively. Overall, there was substantial agreement between the results generated by all three assays. A total of 15 out of 29 (52%) of the specimens determined to contain viral loads of <31,746 IU/ml by the bDNA-3.0 assay were categorized as containing viral loads within the range of 31,746 to 500,000 IU/ml by the bDNA-2.0 assay. Although substantial agreement was noted between the results generated by the bDNA-2.0 and bDNA-3.0 assays, a bias toward higher viral titer by the bDNA-2.0 assay was noted (P = 0.001). Likewise, although substantial agreement was noted between the results generated by the HCM-2.0 and bDNA-3.0 assays, a bias toward higher viral titer by the bDNA-3.0 assay was noted (P < or = 0.001). The discrepancy between the HCM-2.0 and bDNA-3.0 results was more pronounced when viral loads were >500,000 IU/ml and resulted in statistically significant differences (P < or = 0.001) in determining whether viral loads were above or below 800,000 IU/ml of HCV RNA, the proposed threshold value for tailoring the duration of combination therapy. The expression of quantitative values in HCV international units per milliliter was a strength of both the bDNA-3.0 and HCM-2.0 assays.

Fluctuation of serum HCV-RNA levels in untreated blood donors with chronic hepatitis C virus infection

The hepatitis C virus (HCV)-RNA levels were measured in 281 serum samples from 32 untreated volunteer blood donors prospectively collected over a period of 14-73 months. The HCV-RNA levels were tested by the branched DNA signal amplification assay. The mean HCV-RNA levels of each donor ranged from 4.92 log10-6.36 log10 gene equivalents/mL (25%, median, 75% percentile; 5.51, 5.79, 6.12 log10 gene equivalents/mL). The fluctuations of HCV-RNA levels in individuals, represented by the ratio of the maximum value divided by the minimum value, ranged from a 1.7- to a 141-fold change. Fluctuations with more than a 10-fold change were observed in five subjects: 11-, 15-, 17-, 96- and 141-fold changes. Eleven subjects were followed for at least 5 years; all subjects had fluctuations of HCV-RNA levels greater than 3-fold during the observation period. No blood donor was observed whose HCV levels changed from a high-level phase to a low-level phase or from low to high. No subjects cleared HCV during follow-up, although two had undetectable HCV-RNA levels transiently. These findings reveal that changes in HCV-RNA levels occur which are unrelated to treatment with interferon and ribavirin.

Advances in the molecular diagnosis of hepatitis C and their clinical implications

Serologic assays for diagnosis of hepatitis C infection may yield indeterminate results despite improvements in sensitivity and specificity through second- and third-generation assays. Direct detection of hepatitis C virus (HCV) RNA based on qualitative reverse transcription-polymerase chain reaction or transcription-mediated amplification allows diagnosis in the early stages of acute infection and in patients unable to mount an antibody response. Quantitative HCV RNA assays are useful for selecting appropriate antiviral therapies, but until recently they have lacked comparability between tests. More sensitive qualitative assays should be used for determining duration of treatment or recognizing a sustained virologic response to therapy. Hepatitis C virus genotyping can be performed from a limited sequence analysis of the viral genome by using various techniques. Although newer genotyping methods are relatively practicable and are satisfactory for the discrimination of the majority of genotypes, discrimination between subtypes can be challenging. Serologic typing of HCV lacks sensitivity and specificity compared with molecular-based techniques. Recent advances in serologic assays and nucleic acid detection techniques allow physicians to make accurate diagnoses, and these assays serve as important tools in treatment planning.

Laboratory diagnosis of viral hepatitis

Both serologic and molecular assays are useful in the diagnosis of viral hepatitis. They may detect early infections before other signs of disease appear, differentiate acute from chronic infections, and detect persistence of viremia or verify development of immunity. Molecular assays may also be used to monitor responses to antiviral therapy, and in the future, be a primary method to screen blood and organ donors (NAT). EIA serologies are used to diagnose acute HAV infections or establish immune status. Similar immunoassays are used to detect HBV infections, verify persistence of antigenemia and degree of infectivity, and indicate immunity (including the response to vaccination). HBV molecular assays can shorten the diagnostic window period, verify persistence of viremia, including monitoring response to antiviral therapy, and be useful in NAT screening of donors. Molecular assays play a major role in HCV diagnosis where serologic tests can document past or present infection but cannot differentiate one from the other. A variety of molecular tests can be used as sensitive (and early) detectors of viremia (and serve as confirmatory tests for positive serologies and as donor NAT methods), document its persistence as an indicator of chronic infection, and monitor responses to antiviral therapy. Both qualitative and quantitative molecular assays are available, and their efficient use requires familiarity with the sensitivity and dynamic ranges of each method.

Performance characteristics of a transcription-mediated nucleic acid amplification assay for qualitative detection of hepatitis C virus RNA

The detection of hepatitis C virus (HCV) RNA by nucleic acid amplification techniques is the method of choice to differentiate between ongoing and past infection, and can be used to monitor the course of HCV infection. In this study, we evaluated the performance characteristics of a newly developed transcription-mediated amplification (TMA)-based assay, the VERSANT HCV RNA qualitative assay, which was designed to qualitatively detect HCV RNA. Samples tested by the TMA assay included 100 HCV antibody negative sera; serial dilutions of an HCV genotype 1a panel; the WHO HCV RNA standard 76/790; an HCV genotyping panel; and 150 clinical specimens, including sera from patients who had received alpha interferon (IFN) treatment or liver transplants. TMA test results were compared with the Cobas Amplicor HCV polymerase chain reaction (PCR) assay. The analytical specificity of the HCV TMA assay was > 98%. No carry-over contaminations were observed. The assay demonstrated an analytical sensitivity of 100% at 41 HCV RNA copies/mL (genotype 1a panel) and 5 IU/mL (WHO standard), respectively. HCV genotypes and subtypes did not affect the results. Qualitative RNA detection by diagnostic Amplicor PCR and TMA was in agreement in > 97% of all 150 clinical samples tested. In our study, the TMA-based assay proved to be a specific and sensitive method for qualitative HCV RNA detection. The test may turn out to be an attractive alternative to already established techniques for HCV RNA amplification in routine clinical laboratories.

Evaluation of disinfectant efficacy against hepatitis C virus using a RT-PCR-based method

The methods traditionally used to evaluate the antiviral activity of antiseptics and disinfectants are based on cell cultures. However, such methods are not applicable to non-cultivable viruses such as hepatitis C (HCV). Therefore, in this case, virucidal activity is normally tested using surrogate viruses able to grow in cell culture. This paper describes a RT-PCR method for testing antiseptic/disinfectant activity against HCV, as a model for non-cultivable viruses. A chlorine-based agent used for skin and tissues, and a 2% glutaraldehyde solution used for endoscope disinfection, were the test materials. The results are discussed in the light of the use of these agents. The method is simple, fast and inexpensive, and could be used for tests on other viruses with minor modification.

Advances in the molecular diagnosis of hepatitis C and their clinical implications

Serologic assays for diagnosis of hepatitis C infection may yield indeterminate results despite improvements in sensitivity and specificity through second- and third-generation assays. Direct detection of hepatitis C virus (HCV) RNA based on qualitative reverse transcription-polymerase chain reaction or transcription-mediated amplification allows diagnosis in the early stages of acute infection and in patients unable to mount an antibody response. Quantitative HCV RNA assays are useful for selecting appropriate antiviral therapies, but until recently they have lacked comparability between tests. More sensitive qualitative assays should be used for determining duration of treatment or recognizing a sustained virologic response to therapy. Hepatitis C virus genotyping can be performed from a limited sequence analysis of the viral genome by using various techniques. Although newer genotyping methods are relatively practicable and are satisfactory for the discrimination of the majority of genotypes, discrimination between subtypes can be challenging. Serologic typing of HCV lacks sensitivity and specificity compared with molecular-based techniques. Recent advances in serologic assays and nucleic acid detection techniques allow physicians to make accurate diagnoses, and these assays serve as important tools in treatment planning.

Quantitation of HCV RNA using real-time PCR and fluorimetry

Real-time PCR technology may provide an accurate and sensitive method to quantify hepatitis C virus (HCV) RNA. So far, studies have been carried out using the Taqman technology with the ABI Prism 7700 sequence detector. An alternative and simple real-time PCR assay is described with no probe requirement, based on the SYBR Green I dye and LightCycler fluorimeter. Amplicon synthesis was monitored continuously by SYBR Green I dye binding to double stranded DNA during PCR of the 5' HCV non-coding (NC) region. Specificity was verified by amplicon melting temperatures. An external standard curve was constructed with serial 10 fold dilutions of a modified synthetic HCV 5' NC RNA. A wide range linear relationship (up to 3.7x10(9) copies/ml) was observed between number of PCR cycle needed to detect a fluorescent signal and number of RNA copy. Intra- and inter-assay coefficients of variation were 0.7 to 2.1 and 3.7% respectively, indicating good reproducibility of the method. Thirty-three HCV positive sera of different genotypes were quantified by this method and gave similar but more sensitive results compared to the branched DNA (bDNA) technology.

Hepatitis C virus RNA assays: a comparison of SuperQuant and Monitor

Hepatitis C RNA testing has been used extensively to assess the efficacy of antiviral therapy and has increasingly become an integral part of clinical management of patients with chronic hepatitis C. A variety of commercially available hepatitis C virus (HCV) RNA tests are used to detect HCV RNA qualitatively or quantitatively. These commercial tests have fundamental differences that are reflected on the values they generate. We compared two widely used assays, HCV SuperQuant (SQ) and Amplicor HCV Monitor (M1 and M2), in sera of patients with chronic hepatitis C. A total of 506 sera from 79 patients were tested with both assays. The data were logarithmically transformed and analyzed by linear regression and measurement of agreement. Two hundred thirty-eight sera had HCV RNA values within the dynamic range of both assays. The correlation between the assays was fair, with a correlation coefficient (r) of 0.699. Overall, SQ generated higher values than M1 with a mean difference of 0.558 log (SD = 0.624). One hundred ninety-four (38%) and 121 (24%) of the sera were below the dynamic range of M1 and SQ, respectively. Seventy-three sera, undetectable by M1, were positive by SQ. The Amplicor HCV Monitor 2.0 (M2) was performed in 66 sera. All were positive by SQ and M2, but only 38 were within the dynamic range of M1. The correlations between these tests were good (r = 0.68-0.78), but the agreement was rather poor. In conclusion, this study confirms that both SQ and M2 are more sensitive than M1. Additionally, our results show rather poor agreements between these assays. The recent attempts in standardizing the reporting of these assays should make their results more easily interchangeable.

A case of autoimmune hepatitis with a high titer of antimitochondrial antibody and normal gamma-globulinemia

We report here a patient with chronic active hepatitis who had no markers for hepatitis viruses and no hyper-gamma-globulinemia, but had high titers of antimitochondrial antibody. Serum levels of alkaline phosphatase were normal, and antinuclear antibody, antismooth muscle antibody, and antiliver kidney microsome antibody tested negative. The titers of antimitochondrial antibody exceeded 1:640, and the positivity for anti-M2 was ascertained by using both ELISA and immunoblot with beef-heart mitochondria and a recombinant pyruvate dehydrogenase E2 subunit as antigens. This patient responded to ursodeoxycholic acid (UDCA) therapy in the beginning, but her hepatitis flared up during UDCA therapy. In contrast, she responded completely to corticosteroid therapy. The clinical course and histological findings of this patient strongly suggest that this patient has autoimmune hepatitis.

Evaluation of quantitative measurements of hepatitis C virus RNA to predict sustained response to interferon by genotype

Hepatitis C virus (HCV) virus load is one of the most important predictive factors for the outcome of interferon (IFN) therapy. Recent technological advances have allowed a more precise measurement of HCV load. However, the exact cutoff values that could be used to predict the outcome of IFN have not been established for each assay. Five recent quantitative assays were evaluated for the measurement of HCV (Amplicor monitor ver 1.0, Amplicor monitor ver 2.0 (GT), Amplicor monitor ver 2.0 (Cobas), Quantiplex branched DNA amplification (bDNA) ver 2.0 and HCV core protein level by enzyme immunosorbent assay) in 209 consecutive patients with chronic hepatitis C, who received IFN therapy. The results of the two second generation Amplicor monitor tests (GT and Cobas) showed the best correlation (r = 0.930), but the other tests also showed relatively good correlations (r = 0.646-0.925). Each method predicted the effect of IFN with comparable predictive efficacy, ranging from 77.0 to 80.8%. Receiver operating characteristic (ROC) curve analysis showed that Amplicor monitor ver 2.0 and bDNA ver 2.0 are superior in predicting the response in genotype 2a. The best cutoff value for predicting the response to IFN was different by genotype, which should be considered in selecting candidates for IFN treatment.

Strategy for the maximization of clinically relevant information from hepatitis C virus, RT-PCR quantification

BACKGROUND

The increasing clinical application of viral load assays for monitoring viral infections has been an incentive for the development of standardized tests for the hepatitis C virus.

OBJECTIVE

To develop a simple model for the prediction of baseline viral load in individuals infected with the hepatitis C virus.

METHODOLOGY

Viral load quantification of each patient's first sample was assessed by RT-PCR-ELISA using the Roche MONITOR assay in triplicate. Genotype of the infecting virus was identified by reverse line probe hybridization, using amplicons resulting from the qualitative HCV Roche AMPLICOR assay.

RESULTS

Retrospective evaluation of first quantitative values suggested that 82.4% (n=168/204) of individuals had a viral load between 4.3 and 6.7 log(10) viral copies per ml. A few patients (3.4%; n=7/204) have a serum viremia less than the lower limit of the linear range of the RT-PCR assay. Subsequent, prospective evaluation of hepatitis C viral load of all new patients using a model based on the dynamic range of viral load in the retrospective group correctly predicted the dynamic range in 75.9% (n=33/54).

CONCLUSION

The dynamic range of hepatitis C viremia extends beyond the linear range of the Roche MONITOR assay. Accurate determination of serum viremia is substantially improved by dilution of specimens prior to quantification.