Quantitative analysis of hepatitis B virus DNA by real-lime amplification

Simple Detection of Hepatitis B Virus in Using Loop-Mediated Isothermal Amplification Method

INTRODUCTION

US Military and civilian personnel regularly deploy to regions that are endemic for the Hepatitis B virus (HBV), including the Western Pacific, Africa, Eastern Mediterranean, Southeast Asia, and Europe. When patients have life-threatening injuries that require any blood component that is not immediately available, they are typically transfused with locally collected fresh whole blood from a walking blood bank. Currently, there is no simple and easy method for sensitively screening fresh blood in deployed theaters of conflict.

MATERIALS AND METHODS

In order to fill the gap, we have developed a loop-mediated isothermal amplification (LAMP) assay to detect the presence of HBV in blood products. The primers were designed to target the gene of the pre-Surface/Surface antigen region of HBV. The amplification reaction mixture was incubated at 60°C for 60 min. The amplicon can be detected by a handheld fluorescence tube scanner or an immune-chromatography test strip.

RESULTS

We were able to detect down to 10 copies of viral DNA by LAMP reaction for HBV DNA extracted from HBV-positive plasma. We also identified the optimal heat treatment condition (125°C for 10 min) for plasma specimens without requiring DNA extraction for the LAMP assay. The sensitivity of the assay was evaluated with polymerase chain reaction (PCR) confirmed HBV-positive samples. Using LAMP, we detected HBV in 107 out of 127 (84%) samples.

CONCLUSION

This LAMP assay has the potential to be used in resource-limited settings to improve the safety of locally collected blood in endemic regions.

In-house quantitative real-time PCR for the diagnosis of hepatitis B virus and hepatitis C virus infections

The quantification of viral nucleic acids in serum by real-time PCR plays an important role in diagnosing hepatitis B virus and hepatitis C virus infection. In this study, we developed an assay using specific primers and probes to quantify hepatitis B virus DNA or hepatitis C virus RNA in serum from infected patients. For standardization and validation of the assay, an international panel of hepatitis B virus/hepatitis C virus and standard plasmids was used. A correlation coefficient of 0.983 and 0.963 for hepatitis B virus and hepatitis C virus, respectively, was obtained based on cycle threshold values and concentrations of DNA or RNA. The standard curve showed a linear relationship from 19 IU/mL to 1.9 × 10⁹ IU/mL of serum, with a coefficient of determination (r²) of 0.99. In sera from patients infected with hepatitis B virus or hepatitis C virus viral loads (19 IU/mL and 1.9 × 10⁹ IU/mL), we quantified viral loads with a detection limit of 1.9 × 10² IU/mL. The real-time quantitative PCR assay developed in this study provides an ideal system for routine diagnosis and confirmation of indeterminate serological results, especially in immunosuppressed patients.

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.

Methylation regulates hepatitis B viral protein expression

BACKGROUND

Hepatitis B virus (HBV) DNA has been shown to contain CpG islands that are methylated in human tissue, which suggests a role for methylation in regulating viral protein production. However, data are lacking about whether methylation regulates viral gene expression.

METHODS

To investigate the hypothesis that methylation of viral DNA regulates viral gene expression, unmethylated, partially methylated, and fully methylated viral DNA was transfected into HepG2 cells. In addition, a new assay was designed that specifically identifies methylated covalently closed circular DNA (cccDNA) in human liver tissue.

RESULTS

Transfection of methylated HBV DNA led to reduced HBV mRNA levels in HepG2 cells, decreased surface and core protein expression in these cells, and decreased secretion of HBV viral proteins into the cell supernatant. These data provide direct evidence that CpG islands regulate gene transcription of HBV. Furthermore, methylated cccDNA was found in tumor and nonneoplastic human liver tissues. Finally, an in vitro equivalent of cccDNA showed decreased viral protein production in HepG2 cells after DNA methylation.

CONCLUSION

Taken together, these data demonstrate that methylation of viral CpG islands can regulate viral protein production.

A review of the one-year incidence of resistance to lamivudine in the treatment of chronic hepatitis B : Lamivudine resistance

PURPOSE

The development of antiviral resistance is a recognized challenge to successful treatment of chronic hepatitis B (CHB), but it has been difficult to establish an accurate estimate of its incidence due to a number of factors: (a) lack of an accepted definition of antiviral resistance; (b) lack of a standardized assay to assess resistance; and (c) lack of consensus on patient selection criteria for resistance testing. Lamivudine, an effective and well-established antiviral agent, has been reported to show one-year resistance rates in CHB ranging from 6% to 32%, but methodologies used to calculate these rates vary considerably. This article reviews the clinical, statistical, and laboratory methodologies of clinical studies reporting one-year rates of antiviral resistance to lamivudine in CHB.

METHODS

Studies reporting one-year resistance rates to lamivudine in CHB were analyzed for methodologic differences and their influence on reported resistance rates.

RESULTS

Studies using only a genotypic definition of resistance reported one-year rates ranging from 14% to 32%. Studies assessing genotypic resistance in patients with evidence of virologic breakthrough reported much lower one-year resistance rates of 6.4-15.4%.

CONCLUSIONS

It is important when comparing resistance rates to antiviral drugs in CHB to consider the methodology and definition of resistance used because this can dramatically influence the results.

A review of the one-year incidence of resistance to lamivudine in the treatment of chronic hepatitis B : Lamivudine resistance

PURPOSE

The development of antiviral resistance is a recognized challenge to successful treatment of chronic hepatitis B (CHB), but it has been difficult to establish an accurate estimate of its incidence due to a number of factors: (a) lack of an accepted definition of antiviral resistance; (b) lack of a standardized assay to assess resistance; and (c) lack of consensus on patient selection criteria for resistance testing. Lamivudine, an effective and well-established antiviral agent, has been reported to show one-year resistance rates in CHB ranging from 6% to 32%, but methodologies used to calculate these rates vary considerably. This article reviews the clinical, statistical, and laboratory methodologies of clinical studies reporting one-year rates of antiviral resistance to lamivudine in CHB.

METHODS

Studies reporting one-year resistance rates to lamivudine in CHB were analyzed for methodologic differences and their influence on reported resistance rates.

RESULTS

Studies using only a genotypic definition of resistance reported one-year rates ranging from 14% to 32%. Studies assessing genotypic resistance in patients with evidence of virologic breakthrough reported much lower one-year resistance rates of 6.4-15.4%.

CONCLUSIONS

It is important when comparing resistance rates to antiviral drugs in CHB to consider the methodology and definition of resistance used because this can dramatically influence the results.

Comprehensive genetic and epigenetic analysis of occult hepatitis B from liver tissue samples

BACKGROUND

Occult infection with hepatitis B virus (HBV) is a type of chronic HBV infection that is characterized by the absence of a detectable hepatitis B surface antigen in the blood and by very low levels of HBV DNA in the blood and liver. The mechanisms leading to occult HBV infection remain poorly understood but include possible genetic mutations and deletions. Recently, it has been shown that HBV has CpG islands that are methylated, raising the possibility that epigenetic changes may also be important.

METHODS

The full-length genomes of isolates from 5 cases of occult HBV infection were cloned and analyzed for mutations and deletions. Additional studies were performed to examine for APOBEC3G (1 member of a family of deaminating proteins that are part of the innate immune system's defense against viral infection) hyperediting and methylation of viral DNA.

RESULTS

Numerous mutations and deletions were found in the genomes of occult HBV. However, similar types and locations of polymorphisms were also noted in the genome sequences of HBV isolated from control liver tissue samples obtained from individuals with nonoccult HBV infection. Evidence of APOBEC3G hyperediting was found in 1 case of occult HBV infection, but hyperedited sequences made up only a small proportion of the viral sequences. Methylation of HBV CpG islands 1 and 2 was evident in both occult and nonoccult HBV sequences, with island 2 more densely methylated in occult HBV sequences and island 1 more densely methylated in nonoccult HBV sequences.

CONCLUSION

Deletions and mutations are common in occult HBV but are also found in control nonoccult HBV, and no unique genetic signature for occult HBV was found. Methylation patterns differ between cases of occult and nonoccult HBV infection, suggesting that epigenetic changes may be relevant to occult HBV. Together, these findings suggest that multiple mechanisms can contribute to occult HBV infection.

Evaluation of the Abbott RealTime HBV DNA assay and comparison to the Cobas AmpliPrep/Cobas TaqMan 48 assay in monitoring patients with chronic cases of hepatitis B

The new Abbott RealTime hepatitis B virus (HBV) assay was compared to the Cobas AmpliPrep/Cobas TaqMan assay with 128 serum samples from patients with chronic hepatitis B. There was an excellent correlation (r = 0.961) between the two assays, with the Abbott RealTime test showing at least equivalent sensitivity and a slightly wider dynamic range than the Cobas TaqMan assay. By coupling high sensitivity with a large dynamic range, the Abbott RealTime HBV assay is useful in monitoring the response to antiviral therapy.

Hepatitis B viral DNA is methylated in liver tissues

The mechanisms that regulate hepatitis B virus (HBV) replication within the liver are poorly understood. Given that methylation of CpG islands regulates gene expression in human tissues, we sought to identify CpG islands in HBV-DNA and to determine if they are methylated in human tissues. In silico analysis demonstrated three CpG islands in HBV genotype A sequences, two of which were of particular interest because of their proximity to the HBV surface gene start codon (island 1) and to the enhancer 1/X gene promoter region (island 2). Human sera with intact virions that were largely unmethylated were used to transfect HepG2 cells and HBV-DNA became partially methylated at both islands 1 and 2 by day 6 following exposure of HepG2 to virus. Examination of three additional human sera and 10 liver tissues showed no methylation in sera but tissues showed methylation of island 1 in six of 10 cases and of island 2 in five of 10 cases. The cell line Hep3B, with integrated HBV, showed complete methylation of island 1 but no methylation of island 2. In conclusion, HBV-DNA can be methylated in human tissues and methylation may play an important role in regulation of HBV gene expression.

Antiviral effects of PNA in duck hepatitis B virus infection model

AIM

To study the efficacy of antiviral treatment with PNA for the duck model of HBV (DHBV)-infected ducks. PNA is a 2-amine-9-(2,3-dideoxy-2,3-dihydro-beta-D-arabinofuranosyl)-6-methoxy-9H-purine.

METHODS

The Sichuan Mallard ducklings in the hepatitis B virus model were treated with PNA, a new antiviral agent. DHBV DNA from the blood serum and liver tissues were measured at 0, 5, and 10 d during the treatment and at 3 d withdrawal by real-time PCR. The duck hepatitis B surface antigen (DHBsAg) in the liver cells was observed by Immunohistochemistry (IHC). Pathological changes in the liver tissues were also observed. Control group I was administered with distilled water and control group II was administered with 3-thiacytidine. Treatment group I was administered with PNA at a dose of 40 mg/kg and treatment group II was administered perorally (po) with PNA at a dose of 80 mg/kg. Treatment group III was administered with PNA at a dose of 20 mg/kg and treatment group IV was intravenously administered with PNA at a dose of 40 mg/kg. Each group contained 15 ducklings.

RESULTS

PNA can significantly lower the DHBV replication levels in serum and liver. Compared with control group II, there were no significant differences in inhibiting efficacy in treatment groups I and III (P>0.05) and there were significant differences in inhibiting efficacy in treatment groups II and IV (P<0.05). Interestingly, significant differences were observed at 3 d withdrawal. The DHBV replication levels in each group slightly increased at 3 d withdrawal, but rebounded slightly in the PNA treatment groups than in control group II (P<0.05). The DHBV replication levels in the treatment groups were lower than in control group I. The DHBV replication levels in sera had a positive relationship with that in the liver, but the DHBV replication levels in the liver was lower than that in sera. Pathological changes in the treatment groups were obviously improved and the changes were associated with liver viral DNA levels.

CONCLUSION

The results demonstrate that PNA is a strong inhibitor of DHBV replication in the DHBV-infected duck model.

Involvement of host cellular multivesicular body functions in hepatitis B virus budding

Hepatitis B virus (HBV) is a major human pathogen that chronically infects approximately 350 million people, causing liver disease and liver cancer. HBV virions bud into an endoplasmic reticulum (ER)-associated intracellular compartment, but the mechanisms of HBV assembly, budding, and release remain poorly understood. Budding of retroviruses and some other enveloped RNA viruses from plasma membranes requires host functions involved in protein sorting into late endosomal multivesicular bodies (MVBs). To determine whether budding of DNA-containing HBV virions at intracellular membranes also involves MVB functions, we used immunofluorescence to show that, in human hepatoma cells, HBV envelope protein colocalizes with MVB proteins AIP1/ALIX and VPS4B. We also found that a dominant negative (DN) AIP1 mutant inhibited production and/or release of enveloped virions without significant effects on intracellular nucleocapsid formation, whereas DN VPS4B inhibited both nucleocapsid production and budding. By contrast, DN AIP1 and VPS4 had no effect on the efficiency of release of enveloped, nucleocapsid-lacking HBV subviral particles, which are produced in vast excess over virions, and dramatically increased the release of unenveloped, naked nucleocapsids by an apparently nonlytic route. Thus, host MVB functions are required for efficient budding and release of enveloped HBV virions and may be a valuable target for HBV control. Moreover, HBV enveloped virions, enveloped subviral particles, and unenveloped nucleocapsids are all released by distinct pathways with separate host factor requirements.

Liver enzyme flares and occult hepatitis B in persons with chronic hepatitis C infection

BACKGROUND

Occult hepatitis B (HBV) has been reported in numerous clinical settings, but it remains unclear whether occult HBV contributes to liver damage. Given that typical chronic HBV infections often have periodic flairs in viral replication and liver damage, we hypothesized that occult HBV may also have flares in viral replication that are associated with increased liver enzymes.

STUDY DESIGN

We screened hepatitis B surface antigen negative injection drug users with untreated chronic hepatitis C viral (HCV) infection for unexplained ALT/AST flares. To further enrich for individuals with possible occult HBV flares, we studied those individuals whose flares were associated with IgM antibodies to hepatitis B core antigen. Serum samples were assayed for HBV DNA and serologies were performed in serum collected 6 months before, at the time, and 6 months after the flare. HCV RNA levels were also determined. Controls consisted of individuals who also had ALT/AST flares but who were negative for IgM antibodies to hepatitis B core antigen.

RESULTS

Seven study cases and eight control cases were identified. HBV DNA was detectable during the enzyme flares in 7/7 study cases versus 3/8 controls, p=0.026. HBV DNA levels during the flare were low, averaging 1943 +/- 2341 copies/ml, but were higher in study cases versus controls, p=0.002. No change in HCV levels was associated with the flares.

CONCLUSIONS

In this population at high risk for occult HBV, AST/ALT flares can be associated with detection of HBV DNA. These findings may link occult hepatitis B to liver injury.

Correlation between hepatitis B virus DNA levels and HBeAg quantity in patients under 20 years old with chronic hepatitis B virus infection

AIM: To investigate the relationshipt between hepatitis B virus (HBV) DNA contents and HBeAg quantity in HBV-infected patients under 20 years old.

METHODS: The serum HBV DNA contents and HBeAg quantity in 339 patients (age 1-20) with chronic HBV infection were examined by real time fluorescence quantitative polymerase chain reaction (FQ-PCR) and time-resolved fluoroimmunoassay (TRFIA) respectively, and the level of anine aminotransferase (ALT) was detected by rate method.

RESULTS: The patients with HBV DNA contents more than 10⁵ copies/mL, HBeAg quantity more than 0.3 NCU/mL, and normal ALT level accounted for 92.3% of the total cases. Positive correlation (r = 0.769, P < 0.001) and linear regression (b = 0.32, R² = 0.59, P < 0.001) existed between HBV DNA contents (on a log scale) and HBeAg quantity in the patients under 20 years old.

CONCLUSION: Serum HBV DNA contents and HBeAg quantity are changed simultaneously in HBV-infected patients under 20 years old, except in quite a few cases, so combined examination of HBV DNA and HBeAg may help to evaluate the state of chronic HBV infection more exactly.

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.

Rapid quantification of hepatitis B virus DNA by real-time PCR using efficient TaqMan probe and extraction of virus DNA

AIM: To rapidly quantify hepatitis B virus (HBV) DNA by real-time PCR using efficient TaqMan probe and extraction methods of virus DNA.

METHODS: Three standards were prepared by cloning PCR products which targeted S, C and X region of HBV genome into pGEM-T vector respectively. A pair of primers and matched TaqMan probe were selected by comparing the copy number and the Ct values of HBV serum samples derived from the three different standard curves using certain serum DNA. Then the efficiency of six HBV DNA extraction methods including guanidinium isothiocyanate, proteinase K, NaI, NaOH lysis, alkaline lysis and simple boiling was analyzed in sample A, B and C by real-time PCR. Meanwhile, 8 clinical HBV serum samples were quantified.

RESULTS: The copy number of the same HBV serum sample originated from the standard curve of S, C and X regions was 5.7 × 10⁴/mL, 6.3 × 10²/mL and 1.6 × 10³/mL respectively. The relative Ct value was 26.6, 31.8 and 29.5 respectively. Therefore, primers and matched probe from S region were chosen for further optimization of six extraction methods. The copy number of HBV serum samples A, B and C was 3.49 × 10⁹/mL, 2.08 × 10⁶/mL and 4.40 × 10⁷/mL respectively, the relative Ct value was 19.9, 30 and 26.2 in the method of NaOH lysis, which was the efficientest among six methods. Simple boiling showed a slightly lower efficiency than NaOH lysis. Guanidinium isothiocyanate, proteinase K and NaI displayed that the copy number of HBV serum sample A, B and C was around 10⁵/mL, meanwhile the Ct value was about 30. Alkaline failed to quantify the copy number of three HBV serum samples. Standard deviation (SD) and coefficient variation (CV) were very low in all 8 clinical HBV serum samples, showing that quantification of HBV DNA in triplicate was reliable and accurate.

CONCLUSION: Real-time PCR based on optimized primers and TaqMan probe from S region in combination with NaOH lysis is a simple, rapid and accurate method for quantification of HBV serum DNA.

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.

Antiviral effect of Phyllanthus nanus ethanolic extract against hepatitis B virus (HBV) by expression microarray analysis

Ethanolic extract of Phyllanthus nanus (P. nanus) treatment exhibited potent antiviral activity against Hepatitis B virus (HBV). The effects of these extracts on HBV in the HBV genome integrated cell lines--Alexander cells and HepG2 2.2.15 cells were examined. Experimental results showed that the ethanolic extract of P. nanus produced suppressive effect on HBsAg secretion and HBsAg mRNA expression. The extract also inhibited HBV replication as measured by HBV DNA level in vitro. In addition, using a duck HBV (DHBV) primary culture model, the P. nanus ethanolic extract suppressed viral replication of DHBV in DHBV infected primary duck hepatocytes. The gene expression pattern in Alexander cells that had been treated with the ethanolic extract of P. nanus was also revealed by microarray techniques. The microarray results indicated that there was up-regulation of expression of several genes, including annexin A7 (Axn7). The subcellular localization of Axn7 and anti-HBV effect of Axn7 over-expression in Alexander cells were also investigated. Results showed that expression of Axn7-GFP fusion protein are localized around the secretory vesicles and could cause a decrease in HBsAg secretion in Alexander cells. Axn7 protein might play an important role in the medicinal effect of the active principle(s) of P. nanus.

Hepatitis C and hepatitis B nucleic acids are present in intrahepatic cholangiocarcinomas from the United States

Intrahepatic cholangiocarcinomas (IHCs) are rare in the United States, but the prevalence is steadily increasing and risk factors are poorly understood. Tissues were obtained at the time of surgical resection, and 11 cases of IHC were retrospectively studied for the presence of hepatitis B virus (HBV) DNA and hepatitis C virus (HCV) RNA. Hemi-nested and real-time polymerase chain reaction assays were used to detect HBV DNA, and nested reverse transcriptase-polymerase chain reaction was used to detect HCV RNA. Genotypes were determined for both HBV and HCV. The cases were predominantly from women (10/11), with an average age at surgery of 63 years and an average tumor size of 6 cm. Three cases (27%) were positive for either HBV or HCV nucleic acids: HBV alone (n = 1), HCV alone (1), coinfection with HBV and HCV (1). Both HBV-positive cases were genotype A, and both HCV cases were genotype 1a. Hepatitis B and C viral copy numbers were low in all cases. Evidence for active HBV replication was found in both HBV-positive cases, as they were positive for covalently closed circular DNA. In this study, 27% of ICC cases contained HBV and/or HCV nucleic acids, suggesting an etiologic role for these viruses in some cases of IHC.

Real-time PCR in clinical microbiology: applications for routine laboratory testing

Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.

Splenic large B-cell lymphoma in patients with hepatitis C virus infection

Hepatitis virus infection, especially type C (hepatitis C virus [HCV]), has been suggested to be one of the important pathogenetic factors for low- and high-grade B-cell lymphoma, including splenic marginal zone lymphoma (SMZL), in southern Europe. Here, we analyzed the incidences of HCV and hepatitis B virus (HBV) infections, and the clinicopathologic features in 29 cases of splenic diffuse large B-cell lymphoma (DLBCL), 10 SMZL, 3 splenic mantle cell lymphoma, 1 hairy cell leukemia, 13 B-chronic lymphocytic leukemia, and 12 hepatosplenic T-cell and natural killer cell lymphoma. Fifteen (51.7%) splenic DLBCL cases were HCV antibody-positive, and another 6 (20.7%) had the HBsAg. The incidence of each was significantly (P < .01) higher than those of HCV (9.3%) and HBV (1.9%) infections in 54 node-based DLBCL cases. Four examined HCV-positive DLBCL cases showed no type II cryoglobulinemia. HCV RNA was detected in fresh tumor tissues from 6 of 7 examined DLBCL cases, and HBV DNA was present in another 2, as evaluated by real-time polymerase chain reaction. Immunohistologically, tumor cells in 5 of 7 examined DLBCL cases showed intracytoplasmic reactions for HCV NS3 and E2 proteins and the viral receptor CD81. Of 6 cases, 2 showed an intranuclear reaction for the HBV surface protein. By Southern blot analysis, no rearrangement of the Bcl2 gene was detected in the tumor tissue of 7 HCV-positive DLBCL cases. For the other types of malignant lymphoma, 1 case each of SMZL (10%) and hepatosplenic T-cell and natural killer cell lymphoma (8.3%) showed HCV infection. In conclusion, persistent human hepatitis virus infections, especially HCV, may play an important role in the tumorigenesis of splenic DLBCL in Japan.

Dynamic range and reproducibility of hepatitis B virus (HBV) DNA detection and quantification by Cobas Taqman HBV, a real-time semiautomated assay

The Cobas Taqman assay for hepatitis B virus (HBV) DNA showed linear detection over 7 logs for genotypes A to D. The coefficient of variation was 1.2% at > or =1,000 IU/ml and 22.0% at 10 IU/ml. In 97 clinical samples, the log HBV DNA/ml differed by 0.11 between Cobas Amplicor and Cobas Taqman (r2 = 0.97).

Evaluation of the COBAS amplicor HBV monitor assay and comparison with the ultrasensitive HBV hybrid capture 2 assay for quantification of hepatitis B virus DNA

Performance characteristics of the COBAS Amplicor HBV Monitor test (Roche Diagnostics), which measures hepatitis B virus (HBV) DNA quantitatively, were evaluated and compared with the Ultrasensitive HBV Hybrid Capture 2 (HC2; Digene Corporation) assay. Linearity and within-run precision were assessed for both methods by using eight HBV DNA-positive samples serially diluted to obtain a range of <100 to 500,000 HBV DNA copies/ml and run in triplicate. Agreement between the methods was studied with 100 clinical samples. HC2 assay performance near the limit of detection was investigated through repeat testing of 149 samples with HC2 and testing of 37 samples with HC2 results of <4,700 HBV DNA copies/ml by Amplicor assay and a qualitative PCR assay. The linearity experiment for Amplicor had regression of observed values compared to expected values (y = 1.073x - 0.247; R(2) = 0.993, n = 32; for HC2, y = 0.855x + 0.759, R(2) = 0.729, n = 18). Within-run standard deviation of log HBV DNA copies/ml ranged from 0.003 to 0.348 (Amplicor) and 0.027 to 0.253 (HC2). Agreement assessed by Deming regression was poor [Amplicor = 1.197(HC2) - 0.961; R(2) = 0.799, standard error of the estimate (SEE) = 0.710, n = 94]. Near the lower limit of detection, 32 of 149 repeat HC2 results were <4,700 HBV DNA copies/ml. Of the 37 samples with HC2 results of <4,700 HBV DNA copies/ml, HBV DNA was not detected in 15 samples, while HBV DNA was detected by at least one PCR method in 12 samples. Amplicor is linear from 200 to 200,000 HBV DNA copies/ml with undiluted samples, and this range can be expanded through dilution. Inconsistent HC2 results near the limit of detection justify use of a grey zone.

Real time TaqMan PCR detection and quantitation of HBV genotypes A-G with the use of an internal quantitation standard

BACKGROUND

Diagnostic assays for the accurate quantitation of hepatitis B virus (HBV) DNA levels from patients undergoing antiviral therapy are useful for monitoring and tailoring therapy. Such assays should give accurate results with all HBV genotypes, including a seventh genotype of hepatitis B virus, genotype G, that has recently been identified in specimens from HBV-positive patients in the United States and Europe.

OBJECTIVES

To characterize the performance characteristics of a quantitative real time TaqMan PCR assay, the High Pure System Viral Nucleic Acid/COBAS TaqMan HBV Test, for the detection and quantitation of HBV genotypes A-G from patient plasma and serum. This test was evaluated for limit of detection, dynamic range, reproducibility, accuracy, and genotype inclusivity.

STUDY DESIGN

Primers and TaqMan probes specific for HBV and an internal quantitation standard (QS) were designed and tested using a set of plasmid DNAs representing various genotyped specimens. In addition, sensitivity, dynamic range, precision, and correlation with the COBAS AMPLICOR HBV MONITOR Test were evaluated using HBV dilution panels and patient specimens.

RESULTS AND CONCLUSIONS

A real time TaqMan assay was developed that detects and quantifies DNA from genotypes A-G equivalently. The assay has a limit of detection of <50 copies/ml with plasma and serum, a dynamic range up to 10(9) copies/ml, and good precision and accuracy. Titers obtained with this method without dilutions show good correlation across the dynamic range with titers obtained with the COBAS AMPLICOR HBV MONITOR Test.

Occult hepatitis B viral DNA in liver carcinomas from a region with a low prevalence of chronic hepatitis B infection

Occult hepatitis B is defined by the presence of hepatitis B viral (HBV) DNA in the serum or liver in persons lacking hepatitis B surface antigen (HBsAg) in the serum. A high prevalence of occult HBV has been reported in hepatocellular carcinoma (HCC) from Asia, but little information is available on the prevalence of occult HBV in HCC from regions with a low prevalence of typical chronic hepatitis B infection. In a retrospective study, 19 cases of primary liver cancer were investigated for the presence of occult HBV DNA by amplification of the surface, core, and X gene. In addition, HBV copy numbers were quantitated by real time polymerase chain reaction, genotyped, and samples tested for covalently closed circular HBV DNA, which is a marker of active viral replication. Occult HBV was found in three of 19 cases (16%). Genotyping was successful in two cases, both of which were genotype A. HBV DNA copy numbers were low, all less than 10 copies/microg liver DNA. No closed circular HBV DNA was detected. Thus, in this study occult HBV was of genotype A and was found in a low percentage of cases of HCC and was associated with low tissue HBV DNA copy numbers and no detectable evidence for viral replication.

Rapid detection and quantitation of hepatitis B virus DNA by real-time PCR using a new fluorescent (FRET) detection system

BACKGROUND

The diagnosis of hepatitis B virus (HBV) has until recently been based on traditional serologic methods targeting viral antigens and antibodies to viral proteins. The development of molecular methods allowing for the quantitation of HBV DNA is proving clinically valuable for monitoring therapy and detecting early treatment failures.

OBJECTIVES

Here we report a new real-time (LightCycler) quantitative PCR for the detection of HBV DNA based on sequence specific hybridisation probes (designed in-house), targeting the HBV surface antigen.

STUDY DESIGN

The assay was evaluated using a 10-fold dilution series of standard HBV DNA [Eurohep standard reference 1, genotype A, HBsAg subtype adw with a unitage of 10(6) WHO. i.u./ml] and 89 clinical serum samples. The performance was measured against a quantified standard HBV DNA working reagent (NIBSC code 98/780) and the sensitivity compared with our conventional thermal-block PCR.

RESULTS AND CONCLUSION

Real-time PCR detected HBV DNA in 45% (40/89) and thermal-block PCR in 16% (14/75) of clinical samples. Results for 26 samples were below the detection limit of the thermal-block PCR but could be quantified by real-time (LightCycler) PCR. The LightCycler assay was at least 5 logs more sensitive than thermal-block PCR and could detect HBV in a linear range between 5 and 10(7) i.u. per reaction. The broad generic nature of the PCR primers coupled with the enhanced sensitivity and specificity of the fluorescent hybridisation probes makes this assay potentially valuable for both routine diagnostic and epidemiological work.

Quantitation of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) in the liver of HBV-infected patients by LightCycler real-time PCR

Antivirals for hepatitis B virus (HBV) reduce viral load and improve liver histology, however, their effect on covalently closed circular DNA (cccDNA), the HBV transcriptional template, has not been extensively examined. This study evaluated a newly designed LightCycler based quantitative cccDNA PCR assay. A linear range of 2.5 x 10(1) to 1 x 10(9) copies/assay using primers specific for HBV cccDNA and 2.5 x 10(1) to 2.5 x 10(9) copies/assay using primers specific for total HBV DNA (tDNA) was established. beta-Globin was used to estimate the number of cells in each PCR reaction. Enzymatic digestion with an ATP-dependent DNase improved the analytic specificity to a greater than 1:10000 ratio of cccDNA:RC DNA (relaxed circular DNA). One-tenth of the extracted DNA from 1mg of liver biopsy, was analyzed from six patients, three HBV-infected and three uninfected individuals, under blinded conditions; three were found positive and three negative for cccDNA and tDNA. Approximately 6 x 10(3) copies of cccDNA/mg of tissue were detected in a pre-transplant biopsy from an HBV-infected patient treated with lamivudine. Sequential post-transplant liver biopsies were negative for both HBV cccDNA and tDNA. An HBV-infected patient with cirrhosis who was antiviral therapy naïve had 3.7 x 10(4) copies of cccDNA/mg of liver tissue. Another treatment-naïve patient with a history of high HBV viral load had 1 x 10(5) copies of cccDNA/mg of tissue (4 x 10 (6) copies of tDNA/mg of tissue). Further studies are warranted but the high level of sensitivity, specificity, rapidity and accuracy provided by this novel assay with the LightCycler system indicate that it could be useful for monitoring antiviral therapy.

Identification of the minor component of a mixed stain by using mismatch primer-induced restriction sites in amplified mtDNA

We report a case in which STR typing failed to identify the minor component of a mixed saliva stain, but a mitochondrial restriction analysis succeeded in discriminating between the two components. To identify the nt16093 and nt16265 transitions, the template was amplified with the mismatch primers L16092-mm16085 and H16266-mm16269. In the presence of the transitions the mismatch primers created a BsaB I and a Cac8 I restriction site, respectively. Subsequently, aliquots were restricted separately using the enzymes Cac8 I and BsaB I which clearly identified the minor stain component.

Real-time quantitation of hepatitis B virus (HBV) DNA in tumorous and surrounding tissue from patients with hepatocellular carcinoma

Few data are available on the levels of HBV DNA in liver tissue of patients with hepatocellular carcinoma. In this study, HBV DNA was quantitated by a TaqMan real-time PCR method and results were normalised to an endogenous reference gene. The assay could detect reproducibly viral sequences from over 10(7) to less than 50 copies/microg of liver DNA. The HBV DNA content in liver samples from 11 HBsAg-positive patients (median: 10(5) copies/microg of DNA) was significantly higher (P < 0.001) compared to the viral DNA concentration detected in liver samples from 15 of 25 HBsAg-negative patients (median: 2.6 x 10(2) copies/microg). A liver DNA amount > or =1 HBV DNA copy per cell was detected in half of tissue samples from HBsAg-positive patients, and in none from HBsAg-negative ones. Liver tissue HBV DNA content was significantly higher in anti-HCV-negative than in anti-HCV-positive cases (P < 0.001). These results show that the quantitation of liver HBV DNA by real-time PCR can be useful to understand HBV state in hepatocellular carcinoma and viral interplay in patients with multiple viral infections.

A new and sensitive method for the quantification of HBV cccDNA by real-time PCR

The persistence of covalently closed circular (ccc) DNA of Hepatitis B virus (HBV) in liver cells is believed to be the major reason for relapse after completion of HBV antiviral therapy. Up to now, there is no sensitive method to quantify cccDNA in infected liver cells. We designed a set of primers to specifically amplify DNA fragments from HBV cccDNA but not from viral genomic DNA. A good linear range was obtained when 100-10(7) copies of HBV cccDNA were used as template in the quantitative real-time PCR. Not only is this method rapid, economical, highly sensitive, it can be used to monitor HBV cccDNA in infected human liver biopsies and to guide patients undergoing long-term anti-HBV therapy.