Multicenter evaluation of the VERSANT hepatitis B virus DNA 3.0 assay

Establishment of a fluorescent in situ hybridization assay for imaging hepatitis B virus nucleic acids in cell culture models

While chronic hepatitis B remains a global public health problem, the detailed spatiotemporal dynamics of the key molecular events leading to the multiplication and egress of hepatitis B virus (HBV) are still largely unclear. Previously, we developed a chromogenic in situ hybridization assay for detection of HBV RNA, DNA and covalently closed circular DNA in clinical liver biopsies. Here, we report the establishment of a fluorescent in situ hybridization method for the visualization of HBV RNA, HBV core particle DNA and intranuclear DNA in a tetracycline-inducible HBV replication system (HepAD38) and a de novo infection system (HepG2-NTCP). Using 3D-STORM (three-dimensional stochastic optical reconstruction microscopy), we were able to obtain images of HBV RNA and DNA with improved spatial resolution allowing in-depth analyses of key virological events within complex subcellular compartments. Taken together, these techniques should facilitate a deeper understanding of the molecular events of the HBV life cycle and shed new light on the intricate mechanisms of virus-host interactions.

Update on hepatitis B and C virus diagnosis

Viral hepatitis B and C virus (HBV and HCV) are responsible for the most of chronic liver disease worldwide and are transmitted by parenteral route, sexual and vertical transmission. One important measure to reduce the burden of these infections is the diagnosis of acute and chronic cases of HBV and HCV. In order to provide an effective diagnosis and monitoring of antiviral treatment, it is important to choose sensitive, rapid, inexpensive, and robust analytical methods. Primary diagnosis of HBV and HCV infection is made by using serological tests for detecting antigens and antibodies against these viruses. In order to confirm primary diagnosis, to quantify viral load, to determine genotypes and resistance mutants for antiviral treatment, qualitative and quantitative molecular tests are used. In this manuscript, we review the current serological and molecular methods for the diagnosis of hepatitis B and C.

Usefulness of in-house PCR methods for hepatitis B virus DNA detection

The aim of the present study was to evaluate the performance of three in-house PCR techniques for HBV DNA detection and compare it with commercial quantitative methods to evaluate the usefulness of in-house methods for HBV diagnosis. Three panels of HBsAg reactive sera samples were evaluated: (i) 50 samples were examined using three methods for in-house qualitative PCR and the Cobas Amplicor HBV Monitor Assay; (ii) 87 samples were assayed using in-house semi-nested PCR and the Cobas TaqMan HBV test; (iii) 11 serial samples obtained from 2 HBV-infected individuals were assayed using the Cobas Amplicor HBV test and semi-nested PCR. In panel I, HBV DNA was detected in 44 samples using the Cobas Amplicor HBV test, 42 samples using semi-nested PCR (90% concordance with Cobas Amplicor), 22 samples using PCR for the core gene (63.6% concordance) and 29 samples using single-round PCR for the pre-S/S gene (75% concordance). In panel II, HBV DNA was quantified in 78 of the 87 HBsAg reactive samples using Cobas TaqMan but 52 samples using semi-nested PCR (67.8% concordance). HBV DNA was detected in serial samples until the 17th and 26th week after first donation using in-house semi-nested PCR and the Cobas Amplicor HBV test, respectively. In-house semi-nested PCR presented adequate concordance with commercial methods as an alternative method for HBV molecular diagnosis in low-resource settings.

Methods for quantifying gene expression in ecoimmunology: from qPCR to RNA-Seq

Historically, the use of cutting-edge molecular techniques to study immunological gene expression and related cellular pathways has been largely limited to model organisms. Few studies have been performed that quantify the molecular immunological responses of non-model species, especially in response to environmental factors, life-history events, or exposure to parasites. This dearth of information has largely occurred due to the lack of available non-model species-specific gene sequences and immunological reagents and also due to prohibitively expensive technology. However, with the rapid development of various sequencing and transcriptomic technologies, profiling the gene expression of non-model organisms has become possible. Technologies and concepts explored here include an overview of current technologies for quantifying gene expression, including: qPCR, multiplex branched DNA assays, microarrays, and profiling gene expression (RNA sequencing [RNA-Seq]) based on next-generation sequencing. Examples of the advancement of these technologies in non-model systems are discussed. Additionally, applications, limitations, and feasibility of the use of these methodologies in non-model systems to address questions in ecological immunology and disease-ecology are specifically addressed.

Comparison of currently available assays for detection of hepatitis B virus DNA in the routine diagnostic laboratory

Infection with the hepatitis B virus (HBV) continues to present diagnostic and therapeutic challenges worldwide. Today, many routine diagnostic laboratories have implemented assays based on molecular techniques for the detection of HBV DNA. However, the standard algorithm for specific diagnosis of HBV infection still relies on serologic testing. Molecular assays are employed for pretreatment evaluation, clinical staging and monitoring of antiviral therapy. Furthermore, molecular methods are essential for identification of mutations in the HBV genome. Although a continuous improvement of assay performance has been observed during recent years, lack of comparability of different molecular assays remains a problem to be resolved in the future. The limited range of linearity when employing conventional PCR will be overcome by using real-time assays.

Significance of expression of ITGA5 and its splice variants in acute myeloid leukemia: a report from the Children's Oncology Group

Acute myeloid leukemia (AML) encompasses a heterogeneous group of diseases, and novel biomarkers for risk refinement and stratification are needed to optimize patient care. To identify novel risk factors, we performed transcriptome sequencing on 68 diagnostic AML samples and identified 2 transcript variants (-E2 and -E2/3) of the α-subunit (ITGA5) of the very late antigen-5 integrin. We then quantified expression of ITGA5 and these splice variants in specimens from participants of the AAML03P1 trial. We found no association between ITGA5 expression and clinical outcome. In contrast, patients with the highest relative expression (Q4) of the -E2/3 ITGA5 splice variant less likely had low-risk disease than Q1-3 patients (21% vs. 38%, P = 0.027). Q4 patients had worse response to chemotherapy with a higher proportion having persistent minimal residual disease (50% vs. 23%, P = 0.003) and inferior overall survival (at 5 years: 48% vs. 67%, P = 0.015); the latter association was limited to low-risk patients (Q4 vs. Q1-3: 56% vs. 85%, P = 0.043) and was not seen in standard-risk (51% vs. 60%, P = 0.340) or high-risk (33% vs. 38%, P = 0.952) patients. Our exploratory studies indicate that transcriptome sequencing is useful for biomarker discovery, as exemplified by the identification of ITGA5 -E2/3 splice variant as potential novel adverse prognostic marker for low-risk AML that, if confirmed, could serve to further risk-stratify this patient subset.

Detection of infections with hepatitis B virus, hepatitis C virus, and human immunodeficiency virus by analyses of dried blood spots--performance characteristics of the ARCHITECT system and two commercial assays for nucleic acid amplification

BACKGROUND

Nowadays, dried blood spots (DBS) are primarily used to obtain diagnostic access to risk collectives such as intravenous drug users, who are prone to infections with hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV). Before DBS analyses can be used in this diagnostic context, however, a comprehensive evaluation of its performance characteristics must be conducted. To the best of our knowledge, the current study presents for the first time such essential data for the Abbott ARCHITECT system, which is currently the worldwide leading platform in this field of infection diagnostics.

METHODS

The investigation comprised 1,762 paired serum/DBS samples and a total of 3,524 determinations with the Abbott ARCHITECT HBsAg, anti-HBc, anti-HBs, anti-HCV and HIV-1-p24-antigen/anti-HIV 1/2 assays as well as with the artus HBV LC PCR and VERSANT HCV RNA qualitative (TMA) tests.

RESULTS

In the context of DBS testing, a specificity of 100% was recorded for the seven serological and molecular biological assays. The analytical sensitivity of HBsAg, anti-HBc, anti-HBs, anti-HCV, HIV-1-p24-antigen/anti-HIV 1/2, HBV DNA, and HCV RNA detections in DBS eluates was 98.6%, 97.1%, 97.5%, 97.8%, 100%, 93%, and 100%, respectively.

DISCUSSION/CONCLUSIONS

The results obtained indicate that it is today possible to reliably detect HBsAg, anti-HBc, anti-HBs, anti-HCV and HIV-1-p24 antigen/anti-HIV 1/2 with state-of-the-art analytical systems such as the Abbott ARCHITECT in DBS eluates even when a comparatively high elution volume of 1,000 μl is used. They also provide evidence for the inherent analytical limits of DBS testing, which primarily concern the anti-HBc/anti-HBs system for individuals with HIV infections and nucleic acid tests with relatively low analytical sensitivity.

Detection of infections with hepatitis B virus, hepatitis C virus, and human immunodeficiency virus by analyses of dried blood spots--performance characteristics of the ARCHITECT system and two commercial assays for nucleic acid amplification

BACKGROUND

Nowadays, dried blood spots (DBS) are primarily used to obtain diagnostic access to risk collectives such as intravenous drug users, who are prone to infections with hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV). Before DBS analyses can be used in this diagnostic context, however, a comprehensive evaluation of its performance characteristics must be conducted. To the best of our knowledge, the current study presents for the first time such essential data for the Abbott ARCHITECT system, which is currently the worldwide leading platform in this field of infection diagnostics.

METHODS

The investigation comprised 1,762 paired serum/DBS samples and a total of 3,524 determinations with the Abbott ARCHITECT HBsAg, anti-HBc, anti-HBs, anti-HCV and HIV-1-p24-antigen/anti-HIV 1/2 assays as well as with the artus HBV LC PCR and VERSANT HCV RNA qualitative (TMA) tests.

RESULTS

In the context of DBS testing, a specificity of 100% was recorded for the seven serological and molecular biological assays. The analytical sensitivity of HBsAg, anti-HBc, anti-HBs, anti-HCV, HIV-1-p24-antigen/anti-HIV 1/2, HBV DNA, and HCV RNA detections in DBS eluates was 98.6%, 97.1%, 97.5%, 97.8%, 100%, 93%, and 100%, respectively.

DISCUSSION/CONCLUSIONS

The results obtained indicate that it is today possible to reliably detect HBsAg, anti-HBc, anti-HBs, anti-HCV and HIV-1-p24 antigen/anti-HIV 1/2 with state-of-the-art analytical systems such as the Abbott ARCHITECT in DBS eluates even when a comparatively high elution volume of 1,000 μl is used. They also provide evidence for the inherent analytical limits of DBS testing, which primarily concern the anti-HBc/anti-HBs system for individuals with HIV infections and nucleic acid tests with relatively low analytical sensitivity.

Introduction of an automated system for the diagnosis and quantification of hepatitis B and hepatitis C viruses

Hepatitis B virus (HBV) and Hepatitis C virus (HCV) infections pose major public health problems because of their prevalence worldwide. Consequently, screening for these infections is an important part of routine laboratory activity. Serological and molecular markers are key elements in diagnosis, prognosis and treatment monitoring for HBV and HCV infections. Today, automated chemiluminescence immunoassay (CLIA) analyzers are widely used for virological diagnosis, particularly in high-volume clinical laboratories. Molecular biology techniques are routinely used to detect and quantify viral genomes as well as to analyze their sequence; in order to determine their genotype and detect resistance to antiviral drugs. Real-time PCR, which provides high sensitivity and a broad dynamic range, has gradually replaced other signal and target amplification technologies for the quantification and detection of nucleic acid. The next-generation DNA sequencing techniques are still restricted to research laboratories.The serological and molecular marker methods available for HBV and HCV are discussed in this article, along with their utility and limitations for use in Chronic Hepatitis B (CHB) diagnosis and monitoring.

Gene expression analysis of leprosy by using a multiplex branched DNA assay

Leprosy is caused by Mycobacterium leprae, and the global registered prevalence of leprosy at the beginning of 2009 stood at 213,036 cases. It has long been thought that leprosy has a strong genetic risk. Recently, we have identified significant associations (P < 1.00 × 10(-10)) between SNPs in the genes CCDC122, C13orf31, NOD2, TNFSF15, HLA-DR and RIPK2 and a trend towards an association (P = 5.10 × 10(-5)) with a SNP in LRRK2. Here, we investigated the expression of these seven genes in formalin-fixed, paraffin-embedded skin tissues of leprosy and matched normal tissues using branched DNA technology. This technology allows for direct measurement of targeted mRNA within cellular lysate using a 96-well plate format in a time frame compared to a reporter gene assay. The clear upregulation of all seven genes was found in leprosy tissues compared to normal tissues, which further supports our genome-wide association study results.

Measurement of ER and PR status in breast cancer using the QuantiGene2.0 assay

AIM

The QuantiGene2.0 assay has low interlaboratory variability and can directly measure RNA levels without a reverse transcription step or a polymerase chain reaction process. To evaluate the utility of the QuantiGene2.0 assay for the assessment of oestrogen receptor (ER) and progesterone receptor (PR) status as an alternative to immunohistochemistry (IHC), we compared disease-free survival according to quantitative ER and PR measurements when using IHC and the QuantiGene2.0 assay.

METHODS

Samples were collected from 171 patients who underwent breast cancer surgery between January 2003 and December 2006. Cox proportional hazard analysis was performed and concordance between IHC and the QuantiGene2.0 assay for the assessment of ER and PR status was evaluated.

RESULTS

ER and PR assessments were well correlated between IHC and the QuantiGene2.0 assay. The difference in disease-free survival was statistically significant according to expression of PR, but not ER, between the two groups.

CONCLUSIONS

The QuantiGene2.0 assay showed results similar to those of IHC for the assessment of ER and PR in response to treatment. Therefore, our data suggest that the QuantiGene2.0 assay can be used to determine ER and PR status and corroborate IHC findings, which at present are considered as the standard for the evaluation of ER and PR status.

Stability of hepatitis C virus, HIV, and hepatitis B virus nucleic acids in plasma samples after long-term storage at -20°C and -70°C

The storage of biological samples may affect detection of viral nucleic acid, yet the stability of viral nucleic acid at standard laboratory storage temperatures (-70°C and -20°C) has not been comprehensively assessed. Deterioration of viral RNA and DNA during storage may affect the detection of viruses, thus leading to an increased likelihood of false-negative results on diagnostic testing. The viral loads of 99 hepatitis C virus (HCV), 41 HIV, and 101 hepatitis B virus (HBV) patient samples were measured before and after storage at -20°C and -70°C for up to 9.1 years using Versant branched DNA assays, Cobas Monitor assays, and/or AmpliPrep/AmpliScreen assays. Clinical samples stored at -20°C for up to 1.2 years and at -70°C for up to 9 years showed a statistically significant difference from baseline with respect to HCV RNA titer, although this difference was not greater than 0.5 log(10) unit. The concentration of HIV RNA in clinical samples stored at -20°C for 2.3 years and at -70°C for up to 9.1 years did not differ significantly from the baseline viral load. HBV DNA-positive clinical samples stored at -20°C for up to 5 years and at -70°C for up to 4 years differed significantly in viral load. In all studies, however, the loss of viral load of HCV, HIV, or HBV in clinical samples tested after storage at -20°C and -70°C for up to 9 years ranged from 0.01 to 0.35 log(10) IU/ml and did not exceed 0.5 log(10), which is the estimated intra-assay variation for molecular tests. Hence, the loss was considered of minimal clinical impact and adequate for the detection of HCV, HIV-1, and HBV nucleic acids using nucleic acid assays for the assessment of the infectious risk of cell, blood, and tissue donors.

Molecular methods in the diagnosis and management of chronic hepatitis B

Chronic hepatitis B (CHB) infection remains a major global problem but the recent advances in molecular methods have revolutionized the diagnosis and management of CHB. Hepatitis B virus (HBV) DNA quantitation is the most useful molecular marker for the diagnosis and management of CHB. There is increasing evidence that the clinical outcome and efficacy of antiviral therapy for CHB could vary with the infecting HBV genotype, core promoter and precore mutations. Early identification of drug resistance is imperative in the management of CHB. The molecular methods for HBV DNA quantitation, HBV genotyping, the identification of mutants, genotypic and phenotypic methods for monitoring drug resistance and their utility and limitations for use in the diagnosis and monitoring of CHB are discussed in this article.

A real-time quantitative assay for hepatitis B DNA virus (HBV) developed to detect all HBV genotypes

Hepatitis B virus (HBV) is a major cause of chronic liver disease worldwide. Besides genotype, quantitative analysis of HBV infection is extensively used for monitoring disease progression and treatment. Affordable viral load monitoring is desirable in resource-limited settings and it has been already shown to be useful in developing countries for other viruses such as Hepatitis C virus (HCV) and HIV. In this paper, we describe the validation of a real-time PCR assay for HBV DNA quantification with TaqMan chemistry and MGB probes. Primers and probes were designed using an alignment of sequences from all HBV genotypes in order to equally amplify all of them. The assay is internally controlled and was standardized with an international HBV panel. Its efficacy was evaluated comparing the results with two other methods: Versant HBV DNA Assay 3.0 (bDNA, Siemens, NY, USA) and another real-time PCR from a reference laboratory. Intra-assay and inter-assay reproducibilities were determined and the mean of CV values obtained were 0.12 and 0.09, respectively. The assay was validated with a broad dynamic range and is efficient for amplifying all HBV genotypes, providing a good option to quantify HBV DNA as a routine procedure, with a cheap and reliable protocol.

Performance of version 2.0 of the Cobas AmpliPrep/Cobas TaqMan real-time PCR assay for hepatitis B virus DNA quantification

The detection and quantification of hepatitis B virus (HBV) DNA are essential for the diagnosis and treatment of chronic HBV infection. The use of real-time PCR assays for HBV DNA quantification is strongly recommended. The goal of this study was to evaluate the intrinsic characteristics and clinical performance of version 2.0 (v2.0) of the Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) assay, a fully automated platform for HBV DNA quantification in serum or in plasma with a claimed lower limit of detection of 20 IU/ml and a claimed upper limit of quantification of 1.7 × 10(8) IU/ml. The specificity of the assay was 99% (95% confidence interval, 94.7 to 100%). Intra-assay and interassay coefficients of variation ranged from 0.21% to 2.67% and from 0.65% to 2.25%, respectively. The calibration of the assay was found to be satisfactory. Study of blood specimens from patients infected with HBV genotypes A to F showed good correspondence between HBV DNA levels measured by the CAP/CTM v2.0 assay, version 1.0 of the same assay, and the third-generation "branched DNA" assay. The CAP/CTM v2.0 assay quantified HBV DNA levels in serum or plasma from the same patients equally. In conclusion, the new version of the CAP/CTM assay is sensitive, specific, and reproducible. It accurately quantifies HBV DNA levels in patients chronically infected with HBV genotypes A to F. Improvements made to ensure equal quantification of HBV DNA in serum and plasma have been successful. Overall, the CAP/CTM assay, version 2.0, is well suited to monitoring clinical HBV DNA levels according to current clinical practice guidelines.

Effect of HIV co-infection on mutation patterns of HBV in patients with lamivudine-resistant chronic hepatitis B

A retrospective review was performed comparing lamivudine-resistance mutation patterns between patients infected with hepatitis B virus (HBV) with or without human immunodeficiency virus (HIV) co-infection. Medical records that included a genotypic test of patients infected with HBV and treated with lamivudine as the only anti-HBV drug were reviewed. Pol gene mutations were assessed by direct sequencing of the reverse transcriptase fragment 125-213 aa. Eighty-nine patients infected with HBV (29 co-infected with HIV) with rtM204V or rtM204I mutations were included. Multiple mutations associated with the YMDD motif were observed in 33 (55%) of 60 patients infected with HBV only and in 28 (96.6%) of patients co-infected with HIV/HBV. In this latter group, the prevalence of the rtV173L + rtL180M + rtM204V triple mutation was 31% versus a prevalence of 3.4% observed among patients infected with HBV only. All patients with the triple mutational pattern showed sE164D + sI195M changes in the envelope gene. Multivariate analysis demonstrated that HIV co-infection (adjusted OR 11.2, 95% CI 2.0-61.0) and HBV genotype A (adjusted OR 7.2, 95% CI 1.5-34.8) were the only independent variables associated with the chance of harboring rtM204V. Patients with HBV genotype A or HIV co-infection were more likely to harbor the rtM204V mutation. Patients co-infected with HIV showed multiple mutations more frequently, including the triple mutation that may elicit a vaccine escape phenotype. Among patients co-infected with HIV/HBV, strict HBV DNA monitoring is essential to detect treatment failure and adapt therapy to avoid limitations of future therapeutic options or the emergence of a public health threat.

Performance of the Cobas AmpliPrep/Cobas TaqMan real-time PCR assay for hepatitis B virus DNA quantification

Hepatitis B virus (HBV) DNA quantification is used to establish the prognosis of chronic HBV-related liver disease, to identify those patients who need to be treated, and to monitor the virologic response and resistance to antiviral therapies. Real-time PCR-based assays are gradually replacing other technologies for routine quantification of HBV DNA in clinical practice. The goal of this study was to evaluate the intrinsic characteristics and clinical performance of the real-time PCR Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) platform for HBV DNA quantification. Specificity was satisfactory (95% confidence interval, 98.1 to 100%). Intra-assay coefficients of variation ranged from 0.22% to 2.68%, and interassay coefficients of variation ranged from 1.31% to 4.13%. Quantification was linear over the full dynamic range of quantification of the assay (1.7 to 8.0 log(10) IU/ml) and was not affected by dilution. The assay was accurate regardless of the HBV genotype. Samples containing HBV DNA levels above 4.5 log(10) IU/ml were slightly underestimated relative to another accurate assay based on branched-DNA technology, but this is unlikely to have noteworthy clinical implications. Thus, the CAP/CTM HBV DNA assay is sensitive, specific, and reproducible, and it accurately quantifies HBV DNA levels in patients chronically infected by HBV genotypes A to F. Samples with HBV DNA concentrations above the upper limit of quantification need to be diluted and then retested. Broad use of fully automated real-time PCR assays should improve the management of patients with chronic HBV infection.

Comparison of real-time polymerase chain reaction with the COBAS Amplicor test for quantitation of hepatitis B virus DNA in serum samples

AIM: To compare the clinical performance of a real-time PCR assay with the COBAS Amplicor Hepatitis B Virus (HBV) Monitor test for quantitation of HBV DNA in serum samples.

METHODS: The reference sera of the Chinese National Institute for the Control of Pharmaceutical and Biological Products and the National Center for Clinical Laboratories of China, and 158 clinical serum samples were used in this study. The linearity, accuracy, reproducibility, assay time, and costs of the real-time PCR were evaluated and compared with those of the Cobas Amplicor test.

RESULTS: The intra-assay and inter-assay variations of the real-time PCR ranged from 0.3% to 3.8% and 1.4% to 8.1%, respectively. The HBV DNA levels measured by the real-time PCR correlated very well with those obtained with the COBAS Amplicor test (r = 0.948). The real-time PCR HBV DNA kit was much cheaper and had a wider dynamic range.

CONCLUSION: The real-time PCR assay is an excellent tool for monitoring of HBV DNA levels in patients with chronic hepatitis B.

Comparison of VERSANT Hepatitis B virus DNA 3.0 Assay with Digene Hybrid Capture II Hepatitis B virus DNA test in relation to clinical status of Hepatitis B virus

BACKGROUND

Some differences exist among various Hepatitis B virus (HBV) DNA quantification assays due to lack of standardization and besides clinical usefulness has not been firmly elucidated in Korean HBV patients.

METHODS

We compared Bayer VERSANT HBV DNA 3.0 Assay (VERSANT 3.0) with Digene Hybrid Capture II HBV DNA Test (HC-II) according to HBeAg status and ALT levels in 232 HBV-infected Korean patients. One hundred and seventeen sera with undetectable DNA levels by HC-II were further analyzed by Real-Q HBV quantification assay (BioSewoom).

RESULTS

Although VERSANT 3.0 and HC-II showed an excellent correlation (r=0.9739), the results (copies/mL) by VERSANT 3.0 were 0.45 log(10) higher than those by HC-II. HBV DNA levels were higher in HBeAg-positive group than in HBeAg-negative group (P=0.002), and in abnormal ALT group than in normal ALT group (P<0.0001). The detection rate of HBV DNA by VERSANT 3.0 was lower in HBeAg-negative and normal ALT group (n=68) than in HBeAg-positive or abnormal ALT group (n=164) (35.3% vs 89.6%, P<0.0001). Fifty two sera out of 61 sera with undetectable DNA by VERSANT 3.0 were measurable by Real-Q with mean value of 3.26 log(10) copies/mL.

CONCLUSIONS

VERSANT 3.0 and HC-II showed an excellent correlation, but a little difference (0.45 log10) existed. VERSANT 3.0 effectively measured clinically relevant HBV DNA levels in most HBV-infected patients in Korea. However, more sensitive assays are needed for patients with negative HBeAg and normal ALT to see the low copies of HBV DNA levels.

Characterization of a new sensitive PCR assay for quantification of viral DNA isolated from patients with hepatitis B virus infections

Sensitive and accurate quantification of hepatitis B virus (HBV) DNA is necessary for monitoring patients with chronic hepatitis receiving antiviral therapy in order to determine treatment response and to adapt therapy in case of inadequate virologic control. The development of quantitative PCR assays has been crucial in meeting these needs. The objective of this study was to compare the performance of a new real-time PCR assay (Abbott RealTime) for HBV DNA with that of three other commercial assays for the detection of HBV DNA. These were the Versant 3.0 branched-chain DNA assay, the Cobas Amplicor HBV Monitor test, and the Cobas AmpliPrep-Cobas TaqMan hepatitis B virus assay (CAP-CTM). HBV DNA was measured in blood samples taken from two cohorts of patients with chronic hepatitis. HBV DNA levels measured with the Abbott RealTime assay were highly correlated with those measured with the other three tests over their respective dynamic ranges (r, 0.88 to 0.96). The sensitivity (detection limit, 10 IU/ml) and dynamic range of the Abbott RealTime assay (10(1) to 10(9) IU/ml) was superior to that of the Versant assay. The RealTime assay recognized both HBV strains belonging to genotypes A to G and those bearing polymerase gene mutations equivalently. In conclusion, this study demonstrates the utility of the Abbott RealTime assay for monitoring HBV DNA levels in patients with chronic hepatitis B. Its sensitivity and wide dynamic range should allow optimal monitoring of antiviral therapy and timely treatment adaptation.

Molecular testing in the diagnosis and management of chronic hepatitis B

Hepatitis B virus (HBV) is an enveloped virus with a small (3.2-kb) partially double-stranded DNA genome that causes acute and chronic infections. The impact of these infections on public health worldwide is enormous, with an estimated prevalence of 2 billion acute infections and 360 million chronic infections globally. This review focuses on chronic hepatitis B and the molecular assays used in its diagnosis and management. Background information, including that about features of the hepatitis B virion, viral replication, and epidemiology of infection, that is important for understanding chronic hepatitis B and molecular diagnostic tests for HBV is provided. To facilitate an understanding of the utility of molecular testing for chronic hepatitis B, the four stages of chronic hepatitis B infection that are currently recognized, as well as an additional entity, occult hepatitis B, that can be diagnosed only by sensitive nucleic acid amplification methods, are reviewed in detail, including available therapeutic agents. The molecular diagnostic content focuses on tests for HBV DNA quantification, genotyping, and mutation detection (including precore/core promoter and antiviral resistance mutations). The discussion of these tests encompasses their current utility and performance characteristics, drawing from current clinical guidelines and other studies from the literature. In recognition of the continual evolution of this field, the final section describes emerging molecular markers with future diagnostic potential.

Levels of hepatitis B virus (HBV) replication during the nonreplicative phase: HBV quantification by real-time PCR in Korea

The levels of HBV replication in the nonreplicative phase are not clear. We conducted this study to evaluate the levels of viral replication during the nonreplicative phase in chronic HBV-infected Korean patients using real-time PCR. A total of 125 patients were classified into three groups: inactive HBsAg carriers, inactive liver cirrhosis patients, and resolved chronic HBV-infected patients with loss of HBsAg. The real-time PCR detected HBV DNA in 112 cases (89.6%). The mean levels of HBV DNA were 3.84, 4.10, and 3.31 log copies/ml in the three groups, respectively (P <0.01). Ninety-five percent of inactive HBsAg carriers showed levels of HBV DNA lower than 6 x 10(4) copies/ml. In conclusion, we showed different levels of HBV DNA exactly in three groups during nonreplicative phases. We suggest that the cutoff level of HBV DNA in inactive HBsAg carriers should be readjusted to a lower level in future studies.

Comparison of Versant HBV DNA 3.0 and COBAS AmpliPrep-COBAS TaqMan assays for hepatitis B DNA quantitation: Possible clinical implications

We compared two commercial assays for HBV DNA quantitation, Versant HBV 3.0, System 340 (bDNA; Bayer Diagnostics) and COBAS AmpliPrep-COBAS TaqMan HBV Test (TaqMan; Roche Diagnostics). Analytical sensitivity, calculated on WHO International Standard, predicted 95% detection rate at 11.4 and 520.2IU/ml for TaqMan and bDNA, respectively. Specificity, established on 50 blood donor samples, was 100% and 84% for TaqMan and bDNA, respectively. When using clinical samples, HBV DNA was detected by TaqMan in 21/55 samples negative to bDNA. Mean values of HBV DNA obtained with bDNA were higher than those obtained with TaqMan (4.09log(10)+/-1.90 versus 3.39log(10)+/-2.41, p<0.001), and 24.4% of samples showed differences in viral load values >0.5log(10), without association with HBV genotype. There was a good correlation for HBV DNA concentrations measured by the two assays (r=0.94; p<0.001) within the overlapping range, and the distribution of results with respect to relevant clinical threshold recently confirmed (20,000 and 2000IU/ml) was similar. Approximately 50% of samples with low HBV DNA, appreciated by TaqMan but not by bDNA, were successfully sequenced in pol region, where drug resistance mutations are located.

Pre- and post-treatment predictors of the early achievement of HBeAg loss in lamivudine-resistant patients receiving adefovir therapy

BACKGROUND AND AIM

This study investigated the clinical variables that predict hepatitis B e antigen (HBeAg) loss in lamivudine-resistant patients receiving adefovir therapy.

METHODS

Fifty-six consecutive HBeAg-positive patients treated with adefovir for at least 12 months were enrolled in this study. All had serum alanine aminotransferase (ALT) levels over twice the upper limit of normal (ULN) as a result of lamivudine resistance. Predictors of HBeAg loss after switching from lamivudine to adefovir were examined.

RESULTS

During the follow-up period, 18 (32.1%) of 56 patients showed a loss of HBeAg. The estimated rates of HBeAg loss at 6, 12, and 18 months were 11.5%, 26.8%, and 42.9%, respectively. Univariate analysis revealed that pretreatment ALT levels >10 x ULN (P = 0.029), a viral load at 3 months of therapy (P = 0.017), and viral decline by >3 log(10) from baseline at 3 months (P < 0.001) were significantly associated with the loss of HBeAg within 12 months of therapy. With multivariate analysis using the stepwise logistic regression model, pretreatment ALT > 10 x ULN (odds ratio [OR], 4.22; 95% confidence interval [CI], 1.09-19.44; P = 0.044) and viral suppression >3 log(10) at 3 months (OR, 10.39; 95% CI, 1.86-58.07; P = 0.008) were identified as the two independent predictors of HBeAg loss.

CONCLUSIONS

Pretreatment ALT levels and the initial pattern of post-treatment viral decline are the strongest predictors of the early achievement of HBeAg loss following treatment with adefovir in lamivudine-resistant patients. These results may provide useful information for the optimal timing of adefovir rescue as well as for better monitoring after treatment.

Treatment of hepatitis B with lamivudine and tenofovir in HIV/HBV-coinfected patients: factors associated with response

As therapy for human immunodeficiency virus (HIV) infection evolves, optimizing hepatitis B virus (HBV) treatment and identifying factors that impact its response in the HIV/HBV-coinfected population is critical. We identified retrospectively 45 HBV/HIV-coinfected patients with detectable HBV DNA by the Bayer VERSANT HBV 3.0 bDNA assay (limit of quantification 2000 copies/mL) at baseline and/or year 1 of therapy. Patients were divided into three groups based on the active HBV agent in their antiretroviral regimen: group 1 (n = 15) received lamivudine; group 2 (n = 10), lamivudine plus tenofovir and group 3 (n = 20), lamivudine followed by lamivudine plus tenofovir. HBV genotypes and resistance profiles were determined by the Bayer Trugene HBV 1.0 assay. More patients in group 2 achieved HBV DNA suppression below 2000 copies/mL (80%), loss of HBe antigen (HBeAg) (40%) and loss of HBeAg and gain of anti-HBe (20%) than did patients in group 1 or 3. More patients with HBV genotype A, achieved HBV DNA suppression <2000 copies/mL than did patients with non-A genotypes [74% (26/35) vs 20% (2/10)], respectively (P = 0.003). Risk for virological nonresponse was significant in those with non-A genotypes [odds ratio (OR) 11.1; 95% CI: 2.0-50], previous HIV therapy (OR 6.5; 95% CI: 1.2-35) and <90% compliance (OR 3.7; 95% CI: 0.99-14.3). Simultaneous therapy with lamivudine/tenofovir suppresses HBV DNA more effectively than lamivudine or tenofovir added to lamivudine. More patients infected with HBV genotype A responded than the non-A patients, regardless of therapeutic regimen, compliance or prior HIV therapy.

Evaluation of DNA microarray results with quantitative gene expression platforms

We have evaluated the performance characteristics of three quantitative gene expression technologies and correlated their expression measurements to those of five commercial microarray platforms, based on the MicroArray Quality Control (MAQC) data set. The limit of detection, assay range, precision, accuracy and fold-change correlations were assessed for 997 TaqMan Gene Expression Assays, 205 Standardized RT (Sta)RT-PCR assays and 244 QuantiGene assays. TaqMan is a registered trademark of Roche Molecular Systems, Inc. We observed high correlation between quantitative gene expression values and microarray platform results and found few discordant measurements among all platforms. The main cause of variability was differences in probe sequence and thus target location. A second source of variability was the limited and variable sensitivity of the different microarray platforms for detecting weakly expressed genes, which affected interplatform and intersite reproducibility of differentially expressed genes. From this analysis, we conclude that the MAQC microarray data set has been validated by alternative quantitative gene expression platforms thus supporting the use of microarray platforms for the quantitative characterization of gene expression.

Evaluation of the COBAS AmpliPrep-total nucleic acid isolation-COBAS TaqMan hepatitis B virus (HBV) quantitative test and comparison to the VERSANT HBV DNA 3.0 assay

Quantitative detection of hepatitis B virus (HBV) in serum or plasma has become the most direct and reliable method for monitoring chronic hepatitis B. Here, we report the performance characteristics of a real-time PCR hepatitis B DNA quantitative assay, the COBAS TaqMan (CTM) HBV test (Roche Diagnostics, Meylan, France), in combination with an automated DNA extraction on the COBAS AmpliPrep (CAP) instrument using the total nucleic acid isolation kit (TNAI kit), a generic reagent for nucleic acid isolation (both from Roche Diagnostics). The linearity, accuracy, and specificity of the CAP-TNAI-CTM HBV test were evaluated using various reference panels and standards (HBV panel 2004 from Quality Control for Molecular Diagnostics, OptiQuant HBV panel from AcroMetrix, WHO International Standard for HBV, and Teragenix hepatitis B genotype panel). Quantitative results show that the CAP-TNAI-CTM HBV test performed well with respect to linearity, accuracy, and reproducibility from at least 100 to 500,000 HBV DNA IU/ml. Based on the log(10) IU of HBV DNA/ml measured, the intra-assay variation ranged from 2.49% to 8.46% and the interassay variation ranged from 1.88% to 7.83%. The test was extremely sensitive and could detect samples containing HBV DNA below the reported quantification threshold (<30 IU/ml). All HBV genotypes were correctly amplified, and no cross-contamination occurred during the automated sample preparation. In addition, 402 human serum samples were tested comparatively to the VERSANT HBV DNA 3.0 assay (bDNA; Bayer Diagnostics, Puteaux, France). The viral load results of the CAP-TNAI-CTM test and bDNA were significantly correlated, but the agreement between the two tests was poor, with large differences between results for individual samples. The hands-on time was estimated to be reduced from 2.30 h with bDNA to 45 min with the CAP-TNAI-CTM test, and up to 84 samples were completely processed within a working day. Overall, the performance characteristics of the CAP-TNAI-CTM test demonstrated that it provides a high-throughput sensitive and reliable method for quantitation of HBV DNA levels in the routine molecular laboratory.

Quantification of hepatitis B virus (HBV) DNA with a TaqMan HBV analyte-specific reagent following sample processing with the MagNA pure LC instrument

TaqMan hepatitis B virus (HBV) analyte-specific reagent (ASR; Roche Molecular Systems, Inc., Branchburg, NJ) is designed for the quantification of HBV DNA in serum or plasma. The performance characteristics of TaqMan HBV ASR following automated sample processing with the MagNA Pure LC instrument (MP; Roche Applied Science, Indianapolis, IN) were evaluated in this study. Analytical sensitivity and precision were assessed with commercially available HBV standards, while clinical serum specimens from HBsAg-seropositive patients and healthy blood donors were used to determine clinical sensitivity, specificity, and correlation with other commercially available assays. Analytical studies yielded a limit of detection of 2.4 IU/ml, with good linearity and correlation (R(2) = 0.9958) with expected HBV DNA titers over a wide range (6.0 x 10(0) to 2.1 x 10(8) IU/ml). Clinical sensitivity and specificity of the assay combined with automated sample processing were both 100%. Comparison of TaqMan HBV ASR and VERSANT HBV DNA 3.0 assay (bDNA; Bayer HealthCare LLC, Tarrytown, NY) results among clinical specimens yielded good correlation (R(2) = 0.9237), with a mean difference in titer of -0.213 log(10) IU/ml (95% confidence interval, -0.678 to 1.10 log(10) IU/ml). The overall test failure rate was 2.0% among 204 clinical serum specimens tested. Total time required for MP sample processing and automated postelution handling of 24 samples was 224 min, with 57 min of actual hands-on time. MP is a reliable, labor-saving platform suitable for use with TaqMan HBV ASR, providing sensitive and accurate quantification of HBV DNA levels over a range of 8 log(10) IU/ml.

Comparison of real-time PCR assays for monitoring serum hepatitis B virus DNA levels during antiviral therapy

The performance characteristics of the RealART and Molecular Beacons assays were compared with those of the Digene Hybrid Capture II assay (ultrasensitive). The results of the RealART and Digene Hybrid assays were related (r = 0.94; P < 0.001) and diverged by 2 orders of magnitude. The RealART assay can be used to effectively monitor serum hepatitis B virus DNA levels.

Real-time PCR assay for detection and quantification of hepatitis B virus genotypes A to G

The detection and quantification of hepatitis B virus (HBV) DNA play an important role in diagnosing and monitoring HBV infection as well as assessing therapeutic response. The great variability among HBV genotypes and the enormous range of clinical HBV DNA levels present challenges for PCR-based amplification techniques. In this study, we describe the development, evaluation, and validation of a novel real-time PCR assay designed to provide accurate quantification of DNA from all eight HBV genotypes in patient plasma specimens. A computer algorithm was used to design degenerate real-time PCR primers and probes based upon a large number (n = 340) of full-length genomic sequences including HBV genotypes A to H from Europe, Africa, Asia, and North and South America. Genotype performance was tested and confirmed using 59 genotype A to G specimens from two commercially available worldwide genotype panels. This assay has a dynamic range of at least 8 log(10) without the need for specimen dilution, good clinical intra- and interassay precision, and excellent correlation with the Bayer Diagnostics VERSANT HBV DNA 3.0 (branched DNA) assay (r = 0.93). Probit analysis determined the 95% detection level was 56 IU/ml, corresponding to 11 copies per PCR well. The high sensitivity, wide linear range, good reproducibility, and genotype inclusivity, combined with a small sample volume requirement and low cost, make this novel quantitative HBV real-time PCR assay particularly well suited for application to large clinical and epidemiological studies.

Management of chronic hepatitis B virus infection: current perspectives for the nurse practitioner

PURPOSE

To address the clinical management of chronic hepatitis B virus (HBV) infection.

DATA SOURCES

Studies from the National Library of Medicine that examine the natural history, prevention, and antiviral therapy of chronic HBV infection, with emphasis on recent studies.

CONCLUSIONS

Chronic infection with HBV is a frequent cause of cirrhosis, liver cancer, and liver-related mortality worldwide. Strategies to prevent infection, screen for liver cancer in HBV carriers, and treat chronic hepatitis B are all important in managing this disorder.

IMPLICATIONS FOR PRACTICE

Much can be done to prevent and treat infection. Both classes of drugs to treat hepatitis B, nucleoside analogues and interferons, have advantages and disadvantages. Selection of therapy should be based on biochemical, histological, and virological parameters as well as consideration of several practical issues.

A multiplex branched DNA assay for parallel quantitative gene expression profiling

We describe a novel method to quantitatively measure messenger RNA (mRNA) expression of multiple genes directly from crude cell lysates and tissue homogenates without the need for RNA purification or target amplification. The multiplex branched DNA (bDNA) assay adapts the bDNA technology to the Luminex fluorescent bead-based platform through the use of cooperative hybridization, which ensures an exceptionally high degree of assay specificity. Using in vitro transcribed RNA as reference standards, we demonstrated that the assay is highly specific, with cross-reactivity less than 0.2%. We also determined that the assay detection sensitivity is 25,000 RNA transcripts with intra- and interplate coefficients of variance of less than 10% and less than 15%, respectively. Using three 10-gene panels designed to measure proinflammatory and apoptosis responses, we demonstrated sensitive and specific multiplex gene expression profiling directly from cell lysates. The gene expression change data demonstrate a high correlation coefficient (R(2)=0.94) compared with measurements obtained using the single-plex bDNA assay. Thus, the multiplex bDNA assay provides a powerful means to quantify the gene expression profile of a defined set of target genes in large sample populations.

A randomized controlled study of preemptive lamivudine in patients receiving transarterial chemo-lipiodolization

Reactivation of hepatitis B virus (HBV) during chemotherapy is well documented. However, there are limited data on this complication in patients with hepatocellular carcinoma (HCC) undergoing transarterial chemotherapy. The aim of this study was to evaluate the efficacy of preemptive lamivudine therapy in reducing hepatitis due to HBV reactivation in patients with HCC undergoing transarterial chemo-lipiodolization (TACL) and to seek predictors of this event. A total of 73 consecutive HCC patients undergoing TACL using epirubicin 50 mg/m2 and cisplatin 60 mg/m2 at monthly intervals were prospectively and randomly assigned to receive lamivudine 100 mg daily from the start of TACL (preemptive group) or not (control group). During the study, 11 (29.7%) of 37 patients in the control group and 1 (2.8%) of 36 patients in the preemptive group developed hepatitis due to HBV reactivation (P = .002). In addition, there were significantly more incidences of overall hepatitis (P = .021) and severe grade of hepatitis (P = .035) in the control group. With multivariate Cox regression model, a baseline HBV DNA level of more than 10(4) copies/mL was the only independent predictor of hepatitis due to HBV reactivation during chemo-lipiodolization (P = .046). In conclusion, preemptive lamivudine therapy demonstrated excellent efficacy in reducing hepatitis due to HBV reactivation and hepatic morbidity during TACL. Preemptive therapy should be considered in HCC patients with an HBV DNA level of more than 10(4) copies/mL. Further studies are needed to confirm the value of this approach in patients with low-level viremia.

Comparison of the COBAS TaqMan HBV test with the COBAS Amplicor monitor test for measurement of hepatitis B virus DNA in serum

Quantitation of low hepatitis B virus (HBV) DNA levels in patients with chronic hepatitis B is important for monitoring natural history of disease and treatment efficacy. This study aimed to compare the quantitation range and analytical sensitivity of the newly developed COBAS TaqMan HBV test (TaqMan test) with the COBAS Amplicor HBV Monitor Test (Amplicor test), using the Eurohep HBV reference plasma and serum samples from patients. Serial dilutions (2.7x10(1)-2.7x10(8) copies/ml) of the Eurohep HBV reference plasma and 50 serum samples from chronic hepatitis B patients were tested by both assays. The TaqMan test could detect seven (2.7x10(2)-2.7x10(8) copies/ml) of eight dilutions of the reference plasma, while the Amplicor test could only detect three of them (2.7x10(3)-2.7x10(5) copies/ml). The HBV DNA values measured by the TaqMan test correlated very well with the theoretical Eurohep standard values (r=0.998, P<0.001). There were good correlations between the HBV DNA levels measured by the two assays on both the Eurohep reference plasma (r=0.993, P<0.001) and serum samples from patients (r=0.904, P<0.001). Compared to the Amplicor test, the TaqMan test had a higher sensitivity (50 vs. 300 copies/ml), shorter assay time (6 vs. 10 hr), and wider dynamic range (8 vs. 3 logs), and was more cost-effective in a clinical setting. These data indicate that the TaqMan test is an excellent tool for HBV DNA quantitation.

Utilization of a Liver Allograft from a Hepatitis B Surface Antigen Positive Donor

With today's donor organ shortage, enhanced efforts must be made to utilize organs that previously would have been declined. We report a 26-year-old man with chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) coinfection who received a liver transplant from an HBsAg-positive donor. HBV viremia (6,281,185 copies/ml) was seen early posttransplant despite lamivudine prophylaxis, but became negative with addition of adefovir. Virologic analysis revealed predominantly donor HBV strain immediately posttransplant. At 5 months there was an elevation of liver enzymes accompanied by histologic evidence of hepatitis. At this time, HCV-RNA was positive but HBV DNA was undetectable. Treatment with pegylated interferon and ribavirin resulted in sustained clearance of HCV RNA. Two years posttransplant, the patient has normal liver biochemistry and HCV and HBV viral load are undetectable with persistence of HBsAg. Our experience suggests that with effective antiviral therapy, the use of HBsAg seropositive donors is feasible in selected circumstances.

Recent developments in the diagnosis and monitoring of HBV infection and role of the genetic variability of the S gene

Recent developments in the laboratory diagnosis of hepatitis B virus infection include the optimization of key serologic markers, including hepatitis B virus surface antigen and antihepatitis B virus core antibody, as well as the development of automated nucleic acid amplification assays. There is still a lack of standardization for nucleic acid amplification assays that are used for the monitoring of antiviral therapy and follow-up of chronic infection and the clinical significance of hepatitis B virus DNA levels need to be clarified. Although highly sensitive automated nucleic acid amplification assays for blood donor screening are available, their implementation is still subject to discussion and certain countries rejected hepatitis B virus DNA testing for blood donation due to poor cost effectiveness. Genetic variability of hepatitis B virus constitutes a major challenge for diagnosis of hepatitis B virus infection, particularly with regard to hepatitis B virus surface antigen detection, antihepatitis B virus surface antigen quantification and nucleic acid amplification assays. The performances of hepatitis B virus surface antigen enzyme immunoassays in regard to genotype and surface antigen variability need to be further improved. Polyclonal antibody-based hepatitis B virus surface antigen enzyme immunoassays, although they cannot guarantee 100% sensitivity, demonstrate superior S gene mutant recognition to assays using monoclonal capture and tracer antibodies. Isolated antihepatitis B virus core reactivity is an unusual but frequent result, which requires a test algorithm for resolution and hepatitis B virus DNA detection with sensitive nucleic acid amplification assays in order to exclude occult hepatitis B virus infection.

Genetic variability of the S gene of hepatitis B virus: clinical and diagnostic impact

The genetic variability of hepatitis B virus (HBV) represents a challenge for the sensitivity of immunologic and molecular based assays. Based on sequence divergence in the entire genome of >8%, HBV genomes have been classified into eight groups designated A to H. The genotypes of HBV have distinct geographical distributions. Although preliminary clinical studies seem to indicate that there is an association between HBV genotype and natural history of infection and response to antiviral therapy, further evaluations on larger collectives of patients are necessary to give a clearer picture of the subject. The analytical sensitivity of HBsAg and anti-HBs assays may be dependent on HBV genotype or subtype. The influence of genotypic variability on the sensitivity of nucleic acid amplification tests (NAT) has so far been poorly investigated. Preliminary results show that new real-time NAT detect genotypes A to G with an equal sensitivity. Different mechanisms intervening at the translational or post-translational level, including conformational changes, hydrophobic changes, insertion of basic residues and reduced synthesis or secretion of HBsAg may account solely or in conjunction for escape mutations to the immune response and to detection in HBsAg immunassays. The clinical significance of S-gene mutants, needs in analogy to that of HBV genotypes, to be further investigated. HBV mutants are stable over time and can be transmitted horizontally or vertically. The sensitivity of HBsAg assays for mutant detection is continuously improved. Immunoassays based on polyclonal capture antibody show the highest sensitivity for the recognition of recombinant mutants or serum samples harboring mutant forms of HBsAg. However, they do not guarantee full sensitivity. Detection of HBsAg needs to be improved by the introduction of new HBsAg assays able to recognize so far described S-gene mutants and with a lower detection threshold than current immunoassays in order to detect smallest amounts of HBsAg in low level carriers. There is also a need for more complete epidemiological data on the prevalence of HBsAg mutants and strategies for the (differential) screening of mutants need to be developed and evaluated.