Quantification and genotyping of hepatitis B virus in a single reaction by real-time PCR and melting curve analysis

Discontinuation of lamivudine treatment for hepatitis flare after kidney or heart transplantation in hepatitis B surface antigen-positive patients: A retrospective case series

BACKGROUND

Limited data are available on the clinical course of hepatitis B virus (HBV) infection after discontinuation of lamivudine prescribed for kidney or heart posttransplantation hepatitis flare

OBJECTIVE

The purpose of this study was to investigate the reasons for discontinuation, subsequent reappearance of HBV DNA, and mortality in heart and kidney transplant recipients who discontinued lamivudine treatment.

METHODS

This retrospective case series followed up male and female hepatitis B surface antigen (HBsAg)-positive Taiwanese transplant recipients from the National Taiwan University Hospital, Taipei, Taiwan, between July 1989 and January 1999. Biochemical, virologic, and serologic parameters and liver-related mortality of patients who discontinued lamivudine 100 mg QD prescribed for posttransplantation hepatitis flare were compared with those in a group of patients who continued use of lamivudine administered for the same indication over the same period of time. Serum HBV DNA levels were checked in all patients before and after discontinuation of lamivudine, and after resumption of lamivudine treatment and in patients with breakthrough hepatitis flare.

RESULTS

A total of 39 HBsAg-positive transplant recipients (mean [SD] age, 45 [10.0] years) were identified during regular follow-up visits. Nine patients discontinued lamivudine use; 11 patients who continued it were selected as a control group. No significant between-group differences were observed in mean (SD) age (46 [14.0] vs 45 [6.9] years), sex (men/women,vs 1), type of transplant received (heart/kidney,vs ), or pretransplantation liver function test results. The reasons for discontinuation were informed patient decision (4 patients); YMDD mutation (2); self-discontinuation without physician consultation (2); and pregnancy (1). Of those who discontinued lamivudine, serum HBV DNA was undetectable at a mean of 30 (range, 9-47) months' follow-up in 6 (66.7%) of 9 patients. Lamivudine treatment was resumed in 3 patients on reappearance of HBV DNA, and a subsequent rapid decline in the serum HBV DNA was observed. The liver-related mortality rate was not significantly higher in patients who discontinued treatment compared with continuously treated patients (both, 0%). The between-group difference in overall mortality rates was not significant (22.2% and 18.2%, respectively).

CONCLUSIONS

This case series illustrated a variety of clinical situations in which discontinuation of lamivudine treatment prescribed for posttransplantation hepatitis flare may occur. However, liver-related mortality was not increased in these patients compared with those who continued lamivudine treatment.

High prevalence of occult hepatitis B virus infection in Taiwanese intravenous drug users

The epidemiology and impact of occult HBV infection in intravenous drug users remain largely unknown. The aim of the study was to investigate the prevalence of occult HBV infection among intravenous drug users in Taiwan. Molecular assays were used to determine the level of serum HBV DNA and the genotype in 304 intravenous drug users negative for both HBsAg and anti-HCV. Of 304 intravenous drug users, 125 (41.1%) were positive for serum HBV DNA. The genotype distribution of HBV was as follows: B, 55 (44%); C, 29 (23%); and mixed B and C infections, 41 (33%). The mean and median serum HBV DNA levels in 125 intravenous drug users with occult HBV infection were 4.0 +/- 0.6 and 4.0 log(10) copies/ml, respectively. The mean serum HBV DNA level in carriers with mixed genotype B and C infections was significantly higher than those infected with HBV genotype B or genotype C alone (mean, 4.2 +/- 0.6 log(10) vs. 3.9 +/- 0.5 log(10), and 3.9 +/- 0.7 log(10) copies/ml, P = 0.01 and 0.05, respectively). The amino acid sequence determination of HBV surface gene in 20 intravenous drug users with occult HBV infection selected at random showed no mutation of amino acid at codon 145. In conclusion, the prevalence of occult HBV infection and mixed HBV genotype infections are not uncommon in intravenous drug users residing in an HBV endemic areas. In addition, intravenous drug users with occult mixed genotype B and C infections have significantly higher viral loads than those with occult infection of single HBV genotype.

Simultaneous detection of five indices of hepatitis B based on an integrated automatic microfluidic device

Immunophenotyping evaluation is of particular importance for the clinical diagnosis, therapy, and prognosis of viral hepatitis. In this study, an integrated micro flow device has been developed to detect the differentiated antigens/antibodies for immunophenotyping of viral hepatitis. The sensors were fabricated with plasma-polymerized ethylenediamine film (PPF) and nanometer-sized gold particles (nanogold) on which the different hepatitis B antigens/antibodies (markers) were subsequently immobilized. Monitoring the changes in the potential signals before and after the antigen-antibody interaction provides the basis for an immunoassay that is simple, rapid, and cost-effective. It permits the detection of hepatitis B in the dynamic concentration range of 2 orders of magnitude (10(-6) g x L(-1) - 10(-4) g x L(-1)). Up to 7 successive assay cycles with retentive sensitivity were achieved for the sensors regenerated by 8 M urea. Moreover, the microfluidic device was applied to evaluate a number of practical specimens with analytical results in acceptable agreement with those clinically classified. The newly proposed multiparameter analysis technique provides a feasible alternative tool for the diagnosis and monitoring of hepatitis B.

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.

An immunocompetent mouse model for the tolerance of human chronic hepatitis B virus infection

An animal model for human hepatitis B virus (HBV) tolerance is needed to investigate the mechanisms. This model will also facilitate therapeutic strategies for the existing 350 million patients with chronic hepatitis B. We established a mouse model by hydrodynamic injection of an engineered, replication-competent HBV DNA into the tail veins of C57BL/6 mice. In 40% of the injected mice, HBV surface antigenemia persisted for > 6 months. Viral replication intermediates, transcripts, and proteins were detected in the liver tissues of the injected mice for up to 1 year. The tolerance toward HBV surface antigen in this model was shown to be due to an insufficient cellular immunity against hepatitis B core antigen, as was documented in humans. This animal model will accelerate further genetic and mechanistic studies of human chronic hepatitis B infection.

Precore/basal core promoter mutants and hepatitis B viral DNA levels as predictors for liver deaths and hepatocellular carcinoma

AIM: To conduct a retrospective study in 400 chronic hepatitis B patients in order to identify hepatitis B viral factors associated with complications of liver disease or development of hepatocellular carcinoma.

METHODS: The mean follow-up time was 83.6 ± 39.6 mo. Alpha-fetoprotein test and abdominal ultrasound were used for cancer surveillance. Hepatitis B basal core promoter mutants, precore mutants, genotypes, hepatitis B viral DNA (HBV DNA) level and hepatitis B e antigen (HBeAg) were measured. Univariate analysis and logistic regression were used to assess odds ratios for viral factors related to liver deaths and hepatocellular carcinoma development.

RESULTS: During follow-up, 38 patients had liver deaths not related to hepatocellular carcinoma. On multivariate analysis, older age [odds ratio: 95.74 (12.13-891.31); P < 0.0001], male sex [odds ratio: 7.61 (2.20-47.95); P = 0.006], and higher log₁₀ HBV DNA [odds ratio: 4.69 (1.16-20.43); P < 0.0001] were independently predictive for these liver related deaths. Also, 31 patients developed hepatocellular carcinoma. Multivariate analysis showed that older age [odds ratio: 26.51 (2.36-381.47); P = 0.007], presence of precore mutants [odds ratio: 4.23 (1.53-19.58); P = 0.02] and presence of basal core promoter mutants [odds ratio: 2.93 (1.24-7.57); P = 0.02] were independent predictors for progression to hepatocellular carcinoma.

CONCLUSION: Our results show that high levels of baseline serum HBV DNA are associated with non-hepatocellular carcinoma-related deaths of liver failure, while genetic mutations in the basal core promoter and precore regions are predictive for development of hepatocellular carcinoma.

Simultaneous quantification and genotyping of hepatitis B virus for genotypes A to G by real-time PCR and two-step melting curve analysis

Both the viral titer and the genotype significantly determine clinical outcomes and responses to antiviral treatment in chronic hepatitis B virus (HBV) infection. A method was developed for large-scale A-to-G genotyping with simultaneous viral quantification. The assay was run on a LightCycler instrument using hybridization probes. The genotype was determined from the melting points of the probes in a two-step manner. Set 1 amplicons differentiated genotypes B, E, and F from A, C, D, and G and simultaneously quantified viremia by real-time PCR. Melting curve analysis using the set 2-1 amplicon or the set 2-2 amplicon reaction mixture was then used to differentiate these genotype groups into single genotypes. HBV DNA quantification was consistent with that of the Amplicor assay and linear in a range from 10(2) to 10(13) copies/ml. By comparison with the restriction fragment length polymorphism method, 92.3% of 441 samples were accurately genotyped by the current assay. The method should be useful for genotyping and quantification of HBV DNA in areas where all genotypes exist.

Viral factors correlate with hepatitis B e antigen seroconverson in patients with chronic hepatitis B

BACKGROUND/AIMS

Seroconversion (SC) from hepatitis B envelope antigen (HBeAg) to anti-HBe usually indicates lower viral loads, resolved hepatitis activity and improved long-term outcomes. However, the role of viral factors in the development of SC remains largely unknown. We thus comprehensively studied these factors in 25 patients with sustained HBeAg SC and seven control patients with sustained loss of HBeAg.

METHODS

We determined viral factors in serum samples obtained 1 year before, 6 months before, 3 months before, at the time of, 6 months after and 1 year after HBeAg SC or HBeAg loss. Precore A1896 and basal core promoter T1762/A1764 mutants were determined by polymerase chain reaction (PCR)-based assays. Serum HBV levels were determined by a real-time PCR assay.

RESULTS

We found that decline of serum viral load, frequently accompanied by hepatitis exacerbation, occurred within 1 year before HBeAg SC. The proportions of precore and BCP mutations also increased gradually throughout the process of HBeAg SC. The virologic features were similar between HBeAg SC group and HBeAg loss group. Before HBeAg SC or loss, genotype B patients had higher serum viral loads and lower proportions of BCP mutation compared with genotype C patients.

CONCLUSION

Our findings suggested that viral factors correlate with the development of sustained HBeAg SC or loss.

Classification of hepatitis B virus genotypes by the PCR-Invader method with genotype-specific probes

Hepatitis B virus is a worldwide public health problem. A simple and effective test to identify viral genotypes would greatly aid efforts to understand and control the spread of this disease. A serial invasive signal amplification reaction assay (PCR-Invader assay) was developed for distinguishing the known eight genotypes (A-H) and four subgenotypes (Aa, Ae, Ba, Bj) of hepatitis B virus (HBV). The preS/S and core regions were amplified by multiplex PCR and delivered to 12 wells containing genotype-specific Invader probes. By observing the fluorescence patterns in the wells, HBV sub/genotypes can be assigned. A total of 505 serum samples containing HBV/HBsAg in Japan was examined by PCR-Invader and compared the results with those from ELISA assays with monoclonal antibodies against epitopes on gene products of the preS2 region and with a genotype-specific probe assay (GSPA) based on the preS1 region. Genotypes determined by the PCR-Invader agreed with those of the ELISA method in 98.2% of cases and with the GSPA method in 97.1% of cases. Co-infection with two distinct genotypes was correctly identified by the PCR-Invader in four serum samples, as determined by GSPA. Thus, the PCR-Invader assay is a useful tool for detecting the 10 known HBV sub/genotypes.

Cocirculation of measles virus genotype B2 and B3.1 in Central African Republic during the 2000 measles epidemic

Many African countries have begun implementation of national programs to eliminate measles by the year 2015. However, measles continues to be endemic in Africa. This study describes the first molecular epidemiological study of measles virus circulating in Central African Republic. Two hundred and ten blood samples were tested for measles IgM. Sixty-seven urine samples were collected during measles outbreak in Bangui in 2000 and 2004 and used for genotyping studies. Two different methods were used to determine measles virus genotypes; the recently described real-time PCR-based method and the nucleotide sequencing and phylogenetic analysis methods. These tests revealed the cocirculation of two distinct viruses in Bangui. The proposed subgroup of the B3 genotype, B3.1 was found in 14 samples. This virus has been found in other neighboring countries. More surprising, genotype B2 was found in samples from four patients. The first measles genotype B2 viruses were isolated in Gabon in 1984, but have not been detected until recently when they were identified during a measles outbreak in 2003 in South Africa. This suggests that the circulation of measles genotype B2 has continued in Central Africa during the last 20 years. This study provides the baseline for genetic surveillance of measles virus in Central African Republic. Knowledge of currently circulating measles virus genotype in Central African Republic will help in monitoring the success of measles elimination program.

Overlap lamivudine treatment in patients with chronic hepatitis B receiving adefovir for lamivudine-resistant viral mutants

Adefovir dipivoxil is effective against lamivudine-resistant hepatitis B virus (HBV) strains. Whether short-term overlap lamivudine is beneficial remains unknown, particularly in patients with decompensated chronic hepatitis B. We enrolled 30 patients who underwent 48-week adefovir treatment (10 mg daily) for exacerbation of hepatitis B, associated with lamivudine-resistant mutants. Nineteen (63.3%) patients had baseline evidence of hepatic decompensation. Lamivudine was combined for <or=1 month in eight (group I), 2-5 months in 10 (group II) and >or=6 months in 12 (group III). We analysed their serial alanine aninotransferase (ALT) levels, Child-Pugh (CP) score, serum viral load and lamivudine-resistant strains. We found that serum ALT became normalized in 20 (66.7%) and HBV-DNA decreased to <or=100 copies/mL in eight (26.7%) at the end of the 48-week treatment. The log(10) reduction of serum HBV-DNA was significantly smaller in group I patients compared with group II and III patients at week 24 and 48 of treatment [median (range): 3.0 (1.5-5.6) vs 4.5 (1.5-7.4), P = 0.032; and 3.4 (0.9-4.7) vs 5.2 (2.2-7.7), P = 0.008 respectively]. In contrast, the virologic responses at the end of the 48-week therapy were similar between group II and III patients. The improvement in serum ALT and CP score at week 48 was similar irrespective of baseline decompensation, liver cirrhosis and the duration of overlap lamivudine therapy. Our findings suggested that an overlap of lamivudine for >or=2 months might lead to better virological but not biochemical outcomes in patients receiving adefovir for lamivudine-resistance HBV. As our sample size was small and the study was not randomly controlled, further studies are needed.

Higher cut-off index value of immunoglobulin M antibody to hepatitis B core antigen in Taiwanese patients with hepatitis B

BACKGROUND

The cut-off index value of immunoglobulin M (IgM) antibody to hepatitis B core antigen (anti-HBc; AxSYM CORE-M, Abbott) for diagnosing acute hepatitis B is 1.2. A high false-positive rate of IgM anti-HBc was observed in acute flare-ups of chronic hepatitis B in Taiwanese patients. Thus the purpose of the present paper was to study the optimal index value of IgM anti-HBc in Taiwanese subjects.

METHODS

The peak index values of 42 IgM anti-HBc-positive patients were collected. There were 20 acute hepatitis B patients and 22 patients with chronic hepatitis B with acute flare. The biochemical, virological, and serological data were obtained.

RESULTS

There were significant differences in mean age (36 vs 47 years, P = 0.01), serum alanine aminotransferase level (2042 U/L vs 1193 U/L, P = 0.02) and peak index value of IgM anti-HBc (2.9 vs 1.5, P < 0.01) between patients with acute hepatitis B and those with acute flare of chronic hepatitis B. Eleven (50%) of 22 patients with chronic hepatitis B with acute flare had index value of >1.2. The optimal cut-off index value to differentiate acute hepatitis B from chronic hepatitis B with acute flare was 2.4-2.5, with a sensitivity of 90% and specificity of 90%.

CONCLUSIONS

The cut-off index value of IgM anti-HBc to differentiate acute hepatitis B from chronic hepatitis B with acute flare among Taiwanese patients should be set at 2.4-2.5 instead of 0.8-1.2.

Application of real-time PCR to quantify hepatitis B virus DNA in chronic carriers in The Gambia

BACKGROUND/AIM

The study aimed at developing a real-time quantitative PCR assay to monitor HBV serum virus load of chronic carriers enrolled in therapeutic trials.

METHOD

Quantitative real-time PCR assay was carried out using SYBR-Green signal detection and primers specific to the S gene. Thermal cycling was performed in an ABi 5700 sequence detection system. The assay was calibrated against an international HBV DNA standard and inter- and intra-assay reproducibility determined. Levels of viral load were monitored for 1-year in lamivudine treated carriers. Correlation between HBV DNA levels and HBeAg sero-status was determined in untreated carriers.

RESULTS

The qPCR assay showed good intra- and inter-assay reproducibility over a wide dynamic range (1.5 x 103 to 1.5 x 108 copies/mL) and correlated well with those from a commercial assay (r = 0.91, (p < 0.001). Viral load levels dropped dramatically but temporarily during and after a short course of lamivudine therapy. HBV DNA was a more reliable indicator of the presence of virus than HBe antigen and was detected in 77.0% (161/209) of HBeAg negative and in all HBeAg positive carriers.

CONCLUSION

This method is reliable, accurate, and reproducible. HBV DNA Quantification by qPCR can be used to monitor the efficacy of HBV therapy and useful in understanding the natural history of HBV in an endemic area.

Interferon alpha-2b with and without ribavirin in the treatment of hepatitis B e antigen-positive chronic hepatitis B: a randomized study

To study whether interferon (IFN) alpha and ribavirin combination therapy has a beneficial effect for hepatitis B e antigen (HBeAg)-positive chronic hepatitis B, we enrolled 119 such patients in a randomized study. Fifty-nine patients received 5 million units of IFN-alpha2b daily for 4 weeks followed by 5 million units three times a week for 28 weeks, plus 1,200 mg ribavirin daily. Sixty patients received the same dosage of IFN plus placebo. They were followed up for 24 weeks posttreatment, and 105 patients (88%) completed the entire course of 56 weeks. By intention-to-treat analysis, the rate of combined response (serum hepatitis B virus [HBV] DNA <2.5 pg/mL and HBeAg seroconversion) was 17% versus 25% between the IFN/ribavirin and IFN/placebo group, respectively, at the end of treatment (P = .35) and 25% vs. 20% at the end of follow-up (P = .32). Using quantitative real-time polymerase chain reaction assay, the log10 reduction of serum HBV DNA was 1.05 +/- 1.72 (mean +/- SD) versus 1.29 +/- 1.91 between the two groups at the end of treatment (P = .49) and was 2.15 +/- 2.15 versus 1.21 +/- 2.48 at the end of follow-up (P = .04). Prolonged observations in 83 patients suggested that the combined response was 29% (n = 17) versus 20% (n = 12) at 48 weeks after the end of treatment, respectively (P = .17). The safety profile was similar, except that the IFN/ribavirin group had a higher risk of anemia (15% vs. 0%; P = .002). In conclusion, for the treatment of HBeAg-positive chronic hepatitis B, adding ribavirin does not seem to increase the efficacy of IFN.

High prevalence and mapping of pre-S deletion in hepatitis B virus carriers with progressive liver diseases

BACKGROUND & AIMS

The interactions among pre-S deletion, precore (PC) mutation, and basal core promoter (BCP) mutation in various stages of chronic hepatitis B virus (HBV) infection remain unclear and were thus investigated in this study.

METHODS

The sequences of the pre-S region and the BCP (A1762T, G1764A) and PC (G1896A) mutations were determined in 46 HBV chronic carriers (CC) and 106 age-matched carriers with different stages of liver diseases, including 38 chronic hepatitis (CH), 18 cirrhosis (LC), and 50 hepatocellular carcinoma (HCC).

RESULTS

A higher prevalence of pre-S deletion and BCP and PC mutations was found in carriers with progressive liver diseases compared with the CC group. By logistic regression analysis, patients with pre-S deletion and BCP mutation were significantly associated with the development of progressive liver diseases than those without. Combination of mutations rather than single mutation was associated with the development of progressive liver diseases, especially in combination with pre-S deletion. Sequencing analysis showed that the deleted regions were more often in the 3' terminus of pre-S1 and the 5' terminus of pre-S2. Further mapping of these pre-S deletion sequences found that all the deletion regions encompassed T- and B-cell epitopes, and most of them lost 1 or more functional sites.

CONCLUSIONS

Our data indicate that patients with progressive liver diseases have a higher frequency of pre-S deletion.

Evolution of Hepatitis B virus in an acute hepatitis B patient co-infected with genotypes B and C

The interactions between different genotypes of Hepatitis B virus (HBV) in co-infected patients remain largely unknown, especially in acute infection. Here, the evolution of HBV strains was studied in an acute, self-limited hepatitis B patient co-infected with genotypes Ba (B2) and C. Virological analyses were performed at four time points after admission: T1 (5 days), T2 (11 days), T3 (22 days) and T4 (260 days). A dominant-genotype change from genotype C to Ba was found after anti-HBV e antigen (anti-HBe) seroconversion. Further clonal and phylogenetic analyses of the pre-S and pre-core/core regions of HBV were carried out to clarify the interactions between genotypes Ba and C. All clones propagated from T1 and T2 were of genotype C. In contrast, clones propagated from T3 (after anti-HBe seroconversion) were of genotype Ba, C and/or recombinant within the pre-S region. At T4, all clones were of genotype Ba with a 123 bp (from nt 3147 of the pre-S1 region to nt 54 of the pre-S2 region) in-frame pre-S deletion and had lost the start codon of the middle envelope protein and the nucleocapsid-binding site. Phylogenetic analysis showed that genetic distance was greater at T3 after seroconversion to anti-HBe. By using SimPlot, the breakpoint of one pre-S recombinant was located at nt 3069-3100 and the other two at nt 49-87. In conclusion, HBV genotype Ba may overtake genotype C as the predominant strain after anti-HBe seroconversion in acute hepatitis B. Recombination within the pre-S region emerged transiently and the pre-S deletion mutant was finally cleared.

Detection and monitoring of virus infections by real-time PCR

The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.

Genotyping of hepatitis B virus (HBV) by oligonucleotides microarray

Oligonuleotides (oligo) microarray is a promising method for virus genotyping. In this study, we developed an oligo microarray used for genotyping hepatitis B virus (HBV). It consists of 15 probes targeting HBV genotypes A-G and two genotypes of apes, and one conserved probe selected from the HBV pre-S region. To test a clinical sample, the gene targets of clinical samples were amplified and labelled with Cy5-dCTP in a PCR reaction using primers covering the flanking region of the HBV pre-S gene. Following purification, the labelled PCR products were hybridized to the microarray. In an analysis of 96 HBV patients' serum samples using our developed microarray, we identified 34 genotype B, 60 genotype C and 2 genotypes B/C coinfection samples. Sequencing results of 24 randomly selected samples agreed 100% with microarray data. Geographic distribution of genotypes C and B was also divergent, 95.7% (44/46) of genotype C and 64.0% (32/50) of genotype B samples were collected from Northern and Southern China, respectively. The accuracy of genotyping was confirmed by analyzing DNA sequences of 24 samples. It is demonstrated that low-density oligo microarray can serve as a reliable and time-saving method to HBV genotyping from patient's sera.

Transmission of occult hepatitis B virus by transfusion to adult and pediatric recipients in Taiwan

BACKGROUND/AIMS

The infectivity of occult hepatitis B virus (HBV), defined as HBsAg-negative but HBV DNA-positive, after transfusion has been low but not negligible. To address this, we investigated the incidence of post-transfusion HBV infection after receiving screened blood units in Taiwan.

METHODS

Consecutive HBV-naïve (anti-HBc-negative) recipients with normal ALT were followed for HBV DNA and serologic markers before and after transfusion. Among 4448 blood recipients, 467 (10.5%) were anti-HBc-negative. Post-transfusion 6-month follow-up was completed for 327. We identified 5 (1.5%) who developed hepatitis B viremia 1 week after transfusion. Three were children who later seroconverted to anti-HBc but with normal ALT indicating subclinical acute infection, despite all had anti-HBs from previous vaccination. One had transient transfusion-transmitted HBV without seroconversion to anti-HBc and one possibly had occult HBV infection. Our findings suggested the possibility that occult HBV infection was transmissible by transfusion. The incidence of post-transfusion acute HBV infection was 0.9% (100 per million units) in naïve recipients in Taiwan, a figure 7 approximately 40-fold higher than in developed countries. Moreover, some vaccinated children with anti-HBs were still susceptible.

CONCLUSIONS

Therefore, despite active immunization, sensitive screening assays for occult HBV infection such as nucleic acid amplification test could be considered in endemic areas.

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.

The use of real-time PCR methods in DNA sequence variation analysis

BACKGROUND

Real-time (RT) PCR methods for discovering and genotyping single nucleotide polymorphisms (SNPs) are becoming increasingly important in various fields of biological sciences. SNP genotyping is widely used to perform genetic association studies aimed at characterising the genetic factors underlying inherited traits. The detection and quantification of somatic mutations is an important tool for investigating the genetic causes of tumorigenesis. In infectious disease diagnostics there is an increasing emphasis placed on genotyping variation within the genomes of pathogenic organisms in order to distinguish between strains.

METHODS

There are several platforms and methods available to the researcher wishing to undertake SNP analysis using real-time PCR methods. These use fluorescent technologies for discriminating between the alternate alleles of a polymorphism. There are several real-time PCR platforms currently on the market. Two of the key technical challenges are allele discrimination and allele quantification.

CONCLUSIONS

Applications of this technology include SNP genotyping, the sensitive detection of somatic mutations and infectious disease subtyping.

Hepatitis B virus genotype and DNA level and hepatocellular carcinoma: a prospective study in men

BACKGROUND

Although chronic infection with hepatitis B virus (HBV) has been established as a cause of hepatocellular carcinoma (HCC), the roles of viral load and HBV genotype remain unclear.

METHODS

From 1988 through 1992, baseline blood samples were collected from 4841 Taiwanese men who were HBV carriers but had not been diagnosed with HCC. We used real-time polymerase chain reaction assays of plasma DNA samples to quantify HBV DNA levels (a measure of viral load) and determine HBV genotypes for 154 case patients who were diagnosed with HCC during 14 years of follow-up and 316 control subjects. Unconditional logistic regression was used to assess odds ratios (ORs) of HCC for HBV-related factors. All statistical tests were two-sided.

RESULTS

The risk of HCC increased with increasing HBV viral load (adjusted OR for the highest versus the lowest quintile of HBV DNA copies/mL = 7.26, 95% confidence interval [CI] = 3.54 to 14.89; P(trend)<.001). Genotype C HBV was associated with an increased risk of HCC compared with other HBV genotypes (adjusted OR = 5.11, 95% CI = 3.20 to 8.18). Both viral load and genotype were positively associated with HCC within 10-year age categories among subjects aged 30 years old to older than 60 years. Genotype C HBV was associated with increased viral load, and associations of HBV genotype and viral load with HCC risk were additive. The adjusted OR of HCC for those carrying genotype C HBV and with viral load in the highest quintile was 26.49 (95% CI = 10.41 to 67.42) compared with HBV carriers with other HBV genotypes and viral load in the lowest two quintiles.

CONCLUSIONS

Measurements of HBV viral load and genotype may help to define which male HBV carriers aged 30 years or older are at high risk for HCC.

Clinical relevance of hepatitis B virus genotype in children with chronic infection and hepatocellular carcinoma

BACKGROUND & AIMS

The aim of this study was to investigate the influence of hepatitis B virus (HBV) genotypes on the clinical outcome of chronic childhood HBV infection and hepatocellular carcinoma (HCC).

METHODS

A total of 460 HBV carrier children were followed-up for 15 years and 26 children with HBV-related HCC were recruited. HBV genotyping was examined at enrollment and the latest follow-up of these carrier children and at diagnosis in HCC children. Viral load was checked at enrollment for the carrier children. These carriers were grouped based on their initial hepatitis B e antigen (HBeAg) and antibody to hepatitis B e antigen (anti-HBe) status. The HBeAg positive (+) group was divided further into an HBeAg(+/+) group and HBeAg(+/-) group, depending on whether spontaneous HBeAg seroconversion occurred during the follow-up period.

RESULTS

Genotype B constituted 73%, 86%, and 76% in the HBeAg(+/+), HBeAg(+/-), and anti-HBe(+) groups, respectively. Genotype C was found in 27%, 8%, and 6% in the HBeAg(+/+), HBeAg(+/-), and anti-HBe(+) group, respectively. Genotype C carriers were more prevalent in the HBeAg(+/+) group than the other 2 groups (P = .01), and had a delayed HBeAg seroconversion compared with the genotype B carriers (P < .001). Changes of genotype during the follow-up period were rare (2.8%). In those with HCC, genotype B was also the major type (74%). There was no difference in the baseline viral load between genotypes B and C.

CONCLUSIONS

Although HBV genotype B dominates in children with chronic HBV infection and HCC in Taiwan, genotype C delays HBeAg seroconversion in pediatric chronic HBV infection.