Hepatitis B virus harboring nucleotide deletions in the core promoter region and genotype B correlate with low viral replication activity in anti-HBe positive carriers

High Frequency of Either Altered Pre-Core StartCodon or Weakened Kozak Sequence in the CorePromoter Region in Hepatitis B Virus A1 Strainsfrom Rwanda

Hepatitis B virus (HBV) is endemic in Rwanda and is a major etiologic agent for chronic liver disease in the country. In a previous analysis of HBV strains from Rwanda, the S genes of most strains segregated into one single clade of subgenotype, A1. More than half (55%) of the anti-HBe positive individuals were viremic. In this study, 23 complete HBV genomes and the core promoter region (CP) from 18 additional strains were sequenced. Phylogenetic analysis of complete genomes confirmed that most Rwandan strain formed a single unique clade, within subgenotype A1. Strains from 17 of 22 (77%) anti-HBe positive HBV carriers had either mutated the precore start codon (9 strains with either CUG, ACG, UUG, or AAG) or mutations in the Kozak sequence preceding the pre-core start codon (8 strains). These mutually exclusive mutations were also identified in subgenotypes A1 (70/266; 26%), A2 (12/255; 5%), and A3 (26/49; 53%) sequences from the GenBank. The results showed that previous, rarely described HBV variants, expressing little or no HBeAg, are selected in anti-HBe positive subgenotype Al carriers from Rwanda and that mutations reducing HBeAg synthesis might be unique for a particular HBV clade, not just for a specific genotype or subgenotype.

Variability in the precore and core promoter region of the hepatitis B virus genome

There is increasing evidence that hepatitis B virus (HBV) infections with different genotypes and subgenotypes differ in response to treatment and long-term prognosis. The differences emerge from variability within the genomes that leads to structural deviations at the pregenomic level and to changes at the translational level. Naturally occurring HBV strains covering the four major genotypes A-D were obtained from 393 patients and part of the genome was amplified using polymerase chain reaction (PCR), sequenced, and analyzed for mutational differences in the precore and core promoter regions. The study confirmed that core promoter and precore mutations occur at key positions (A1762T, G1764A, G1896A, and G1899A), and that the proportions of strains with seroconvertion in patients differ between the four HBV genotypes. A rare double mutation (C1857T together with G1897A) was observed, and C1856T was found together with the emerging G1898A mutation, which itself was found to be more widespread geographically than previously described. We found a novel mutation (T1850C), never before observed in human HBV strains but known from woodchuck hepatitis virus (WHV). A novel association of mutation C1773T with G1764T, C1766A, and G1757A was also found within a site already suggested to be a putative binding site for HNF-3. This novel association is proposed by us to be of importance for additional binding of HNH-2 to this site and is a better indicator of the emergence of the double mutation G1764T and C1766A than the G1757A mutation proposed previously.

African, Amerindian and European hepatitis B virus strains circulate on the Caribbean Island of Martinique

Ten Hepatitis B virus (HBV) genotypes, as well as numerous subgenotypes, have been described in well-characterized ethnogeographical populations. Martinique has been at a crossroads between Africa, Europe, India and the Americas because of the slave trade (17th-19th centuries), followed by an important immigration of Indian and West African workers. In this work, we aimed to study the molecular epidemiology of HBV infection in Martinique according to this unique settlement pattern. To that end, blood samples from 86 consecutive HBV-infected patients from the main hospitals of the island, were retrospectively analysed. Direct sequencing of the pre-S1 or pre-C-C region or complete genome sequencing, followed by phylogenetic analyses were performed. HBV genotypes were: HBV/A1 (68.6 %), HBV/A2 (10.5 %), HBV/D, mainly HBV/D3 and HBV/D4 (8.1 %), HBV/F (3.5 %), and also HBV/E (2.3 %), two strains isolated from two West-African patients. Moreover, 74 % of the HBeAg-negative strains harboured classical pre-C-C mutations, and most HBV/A1 strains also containing specific mutations. Finally, various patterns of deletion mutants in pre-S and pre-C-C regions were found. In conclusion, our findings point to historical and migration-related issues in HBV-genotype distribution suggesting that HBV/A1, but not HBV/E, was imported from Africa during the slave trade, and further supporting the hypothesis that HBV/E has emerged recently in West Africa (<150 years). Potential origins of 'European' HBV/A2 and HBV/D3, 'Amerindian' HBV/F, and HBV/D4 strains are also discussed. Such HBV genetic diversity, beyond its epidemiological interest, may have a clinical impact on the natural history of HBV infection in Martinique.

Mutations within enhancer II and BCP regions of hepatitis B virus in relation to advanced liver diseases in patients infected with subgenotype B3 in Indonesia

Studies on the characteristics of mutations within the hepatitis B virus (HBV) genome, their roles in the pathogenesis of advanced liver diseases, and the involvement of host properties of HBV-infected individuals have not been conducted in subgenotype B3-infected populations. For addressing this issue, 40 cases with HBV surface antigen (HBsAg)-positive advanced liver diseases, including advanced liver cancer and cirrhosis (male 31, female 9, age 54.4 ± 11.6-year-old), were collected and compared with 109 cases with chronic hepatitis B (male 71, female 38, age 38.0 ± 13.4-year-old). Mutations in enhancer II (Enh II) and basal core promoter (BCP)/precore regions were analyzed by PCR-direct sequencing method. HBV viral load was examined by real-time PCR. For all examined regions, the prevalence of mutation was significantly higher in cases with advanced liver diseases. Multivariate analysis showed that, in patients older than 45 years, C1638T and T1753V mutations constituted independent risk factors for the advancement of liver diseases. The presence of C1638T and T1753V mutations may serve as predictive markers for the progression of liver diseases in Indonesia and other countries, where subgenotype B3 infection is prevalent.

Short Communication: Hepatitis B Virus Harboring Nucleotide Deletions in the Basal Core Promoter in HBe-Positive HIV-Coinfected Patients Under Lamivudine Therapy

The presence of HBV genomes with deletions at the basal core promoter (BCP) is associated with more aggressive liver disease. This 3-year longitudinal analysis of two HIV-HBV-coinfected patients allowed identification of three deletions with dissimilar abundance and permanence into the HBV quasispecies composition. These deletions may contribute to HBV pathogenesis in HIV-coinfected individuals.

Infectivity of blood components with low hepatitis B virus DNA levels identified in a lookback program

BACKGROUND

Japanese Red Cross (JRC) blood centers implemented anti-hepatitis B core antigen (HBc) screening in 1989 and 50-minipool (MP)-nucleic acid testing (NAT) in 2000. A systematic lookback study has been conducted to determine the hepatitis B virus (HBV) transmission risk of donations drawn in the pre-hepatitis B surface antigen (HBsAg) and/or MP-NAT window phase and by donors with occult HBV infection.

STUDY DESIGN AND METHODS

JRC blood centers have been storing aliquots of every blood donation since 1996. On the basis of the complete repository tube archives, all donations from repeat donors received from 1997 to 2004 were subjected to a lookback study. When repeat donors turned positive for HBV viral marker(s), repository tubes from their previous donations were tested for HBV with individual-donation (ID)-NAT. The frequency of ID-NAT-only-positive donations and the HBV transmission risk by the transfusion of those components were investigated.

RESULTS

HBV ID-NAT was performed on 15,721 repository tubes, and 158 tubes (1.01%) were found positive for the presence of HBV DNA. Of these 158 ID-NAT-only-positive donations, 95 (60%) were derived from carriers with low anti-HBc titers. Of 63 patients transfused with ID-NAT-only-positive components, 12 (19%) proved to be infected with HBV. Only 1 of 33 components with low anti-HBc titers could be identified as infectious, whereas 11 of 22 anti-HBc-negative components proved to be infectious. None of the 16 identified hepatitis B surface antibody-positive components showed serologic evidence of infection.

CONCLUSION

The clinically observed HBV infection risk caused by blood components from occult HBV carriers with low anti-HBc titers who slip through the JRC screening system is more than 10-fold lower than the transmission risk by donations in the pre-HBsAg and/or MP-NAT window phase.

Mutations affecting the replication capacity of the hepatitis B virus

The genetic variability of the hepatitis B virus (HBV) encounters two compounding forces: a high viral copy number produced during active replication and the lack of proofreading activity in the HBV polymerase, resulting in a high mutational rate. A large pool of quasispecies is generated in which the fittest virus, i.e. the virus that replicates best, becomes the dominant species. Immune and antiviral selection pressures result in vaccine/immunoglobulin escape mutants and antiviral resistant variants. Viruses encoding changes associated with antiviral resistance often have reduced replication in vitro, but the accumulation of additional mutations helps restore viral fitness. These compensatory mutations may occur not only in the polymerase gene but also in other genes such as the overlapping envelope gene, the precore gene, or in regulatory regions such as the basal core promoter. In this report we aim to review the new findings that have appeared in recent months.

The DNA-Chip technology as a new molecular tool for the detection of HBV mutants

Genetic variability of the Hepatitis B virus (HBV) strongly impacts the natural history of infection and the efficiency of diagnosis, vaccination and treatment. A genotypc assay able to provide genetic information on all HBV genes would be a very important tool for clinicians and epidemiologists. The DNA-Chip technology has proved to be powerful and convenient for the diagnosis of infectious diseases due to bacteria and viruses. We have designed a genotyping assay based on polymerase chain reaction and DNA-Chip for HBV Starting from a unique specimen, analysis of polymorphisms at 150 positions along the genome and 383 mutations is possible as well as the determination of the genotype. Preliminary experiments with plasmas from infected patients show that results obtained with this reagent are strongly correlated with those obtained with sequencing.

Etiological investigation of fatal liver failure during the course of chronic hepatitis B in southeast China

BACKGROUND

The purpose of this study was to clarify the relationships between patients who had fatal liver failure during the course of chronic hepatitis B and those who were also superinfected with hepatitis A, C, D, or E virus, as well as their hepatitis B virus e system status, so that suitable measures could be adopted to decrease the mortality of patients with chronic hepatitis B.

METHODS

This study detected superinfections of hepatitis A, C, D, or E virus and the hepatitis B virus e system status in cases of fatal liver failure during the course of chronic hepatitis B by enzyme-lined immunosorbent assay.

RESULTS

The frequency of superinfections of hepatitis A, C, D, and E virus was 1.4% (4/282), 6.4% (18/282), 1.8% (5/282), and 28.4% (80/282), respectively, overall, 37.9% (107/282). Hepatitis E was prominent and steady in superinfection rates during the past 12 years. In 62.1% (175/282) of patients, the causes of fatal liver failure were not clear. The serological status frequency of HBeAg(+) and anti-HBe(-), HBeAg(-) and anti-HBe(-), and HBeAg(-) and anti-HBe(+) was 20.6% (22/107), 23.4% (25/107), and 56.1% (60/107), respectively, in the group with superinfections of hepatitis A, C, D, or E virus and 31.4% (55/175), 21.1% (37/175), and 47.4% (83/175), respectively, in the group in which causes were not clear. The serological status HBeAg(+) and anti-HBe(-) was more frequent in the group in which causes were not clear than in the group with superinfections of hepatitis A, C, D, or E virus (P < 0.05). Statistically, there were no differences (P > 0.05) between the serological status HBeAg(-), anti-HBe(-) and HBeAg(-), anti-HBe(+) between the two groups.

CONCLUSIONS

These results suggest that superinfection (107/282) is an important factor in fatal liver failure. The mortality of chronic hepatitis B can be decreased by strict food sanitation and the use of safe blood products. There were no significant relationships between hepatitis B e antigen seroconversion and fatal liver failure during the course of chronic hepatitis B.

HBx M130K and V131I (T-A) mutations in HBV genotype F during a follow-up study in chronic carriers

BACKGROUND

Around 400 million people worldwide are chronically infected with Hepatitis B virus (HBV). An estimated 10% of these chronic patients develop progressive liver damage including cirrhosis and Hepatocellular Carcinoma (HCC). The HBx gene encodes a protein of 154 amino acids which is a transactivator and has been associated with HBV pathogenesis. A change in the amino acid sequences at positions 130 and 131 in the HBV-X protein (M130K and V131I) produced by T-A point mutations at the nucleic acids level has been associated with severe liver damage and HCC in patients from China and Africa. Further, such changes have been proposed as a prognostic marker for progressive liver damage and HCC. The purpose of this study was to determine if T-A mutations are present in HBV chronic carriers with genotype F (the major genotype in Costa Rica) and further, if these mutations are associated with HBV disease progression in Costa Rica HBV patients from 1972 to 1985.

RESULTS

Serum samples from 50 HBV positive individuals were amplified and directly sequenced, 48 belonged to genotype F, 1 from genotype D and another was classified as D or E. T-A mutations were absent in 17 acute patients who recovered, but was present in 12 of 29 chronic carrier samples (42.8%), in one sample the T-A mutations were detected as early as 29 days after clinical onset of disease. In 17 carriers with available liver biopsies, T-A mutations were found in 8 sera of 13 (61.5%) classified as moderate or severe, and none in 4 biopsies with mild liver damage. However, it was not possible to demonstrate a statistical association between the presence of T-A mutations and moderate/severe liver damage, using a Fischer exact test, 1 tail, p = 0.05. In 4 patients HCC was diagnosed, and 2 of them presented the T-A mutations in their sera.

CONCLUSION

T-A mutations were found in HBV genotype F in chronic carriers but not in patients who recovered from acute infection. These mutations could be developing early during infection although the possibility of infection with the mutant virus could not be excluded. More studies are necessary to establish if the T-A mutation can be used as a prognostic marker for severity of liver disease in patients infected with HBV.

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Detection for genotypes of hepatitis B virus in Hunan Province of China by nested PCR with multiplex pairs of primers

AIM: To determine the genotypes of hepatitis B virus (HBV) in Hunan Province of China by nested PCR with multiplex pairs of genotype-specific primers.

METHODS: Ten outer and inner primers were designed on the basis of the conserved nature of nuleotide sequences in regions of the Pre-S1 through S genes, in which 8 inner primers were devided into mix A and B to amplify HBV of genotype A, B, C and D, E, F respectively. The two different products from one sample in second-round PCR were separately electrophoresed on a 3% agarose gel. Genotypes of HBV were determined directly by the size of PCR products. To test its reliability and veracity, we compared new nested PCR with popular PCR-RFLP, followed by repeated experiments. This nested PCR was also used in the genotyping of HBVs in 220 Hunan patients with chronic hepatitis B to know the distribution of HBV genotype in Hunan Province of China.

RESULTS: The results showed complete concordence between the two assays and 100% recurrence in the repeated experiments. Of the 220 Hunan patients, 190 (86.4%) were genotype B and 30 (13.6%) were genotype C.

CONCLUSION: This new nested PCR can help to determine HBV genotypes clearly and directly with reliable and accurate results. With the application of this new method, the predominant HBV genotypes in Hunan are confirmed to be genotypes B and C.

Two distinct types of hepatitis B virus core promoter variants in Yemeni blood donors

Genetic variations in the basic core promoter (BCP) region of hepatitis B virus (HBV) occur during the natural history of chronic HBV infection. This study investigates the presence of basic core promoter variations in 28 asymptomatic Yemeni blood donors, correlating variations with HBeAg phenotype and viral load. The core promoter/precore and surface gene region of HBV DNA were amplified using nested PCRs and the PCR products were sequenced either directly or after cloning. HBeAg and viral load were measured when HBV DNA was detectable. Sequencing of 18 surface PCR products indicated that all were of genotype D. Two distinct types of variants were identified in the basic core promoter: substitution only (N = 14) and major deletion (N = 9). The commonest substitutions were located at nucleotide positions 1753, 1762, and 1764; 10/14 (71.4%) were associated with the precore 1896A substitution resulting in the premature stop of the precore reading frame and 6/14 (42.9%) had viral loads above 400 copies/ml. Two forms of deletion variants were found: 8 bp deletion (1763-1770) (N = 2) and a novel 12 (1746-1757) + 8 bp (1763-1770) deletion (N = 7). The deletion sequences were never associated with the precore 1896A substitution and all had viral load below 400 copies/ml with negative HBeAg phenotype. The polymorphism 1773C was found in 9/14 (64.3%) substitution sequences whereas all deletion sequences had 1773T. Two donors had mixed sequences of basic core promoter substitution and major deletions (both 8 bp and 12 + 8 bp). While the deletion variants in these two donors were similar to others found in isolation, the substitutions were of a different pattern. Further studies are required to understand the selection process behind these variants.

Rapid detection of hepatitis B virus mutations using real-time PCR and melting curve analysis

Current methods of detecting hepatitis B virus (HBV) mutations are time consuming, labor intensive, and not suitable for screening large numbers of samples. In the present study, we documented the advantages of a system that exploits differences in thermal stability between perfect match and mismatch hybrids, and thereby distinguishes between wild-type and mutants. Hybridization probes were designed complementary to specific wild-type HBV sequences in surface (S), precore, and basal core promoter (BCP) regions of the HBV genome (nt 587, 1896, and 1762/1764, respectively). Two probes were designed for each mutation: anchor probes were 3' labeled with fluorescein and sensor probes, 5' labeled with LC-Red 640, and 3' phosphorylated. Temperatures for each probe melted from amplification products were then determined in a melting program. Sera from 12 patients, each containing identified HBV mutants (6 S-escape, 1 precore, 1 BCP, and 4 mixed precore and BCP), and 5 control sera from patients with wild-type virus were analyzed. Genomic sequences of mutant and wild-type viruses were confirmed by direct sequencing. Real-time polymerase chain reaction (PCR) with fluorescent hybridization probes accurately identified each mutant and wild-type genome. Melting temperatures obtained from probe-product duplexes for the 3 mutants were distinguished from wild-type (>4.0 degrees C, minimal) within 45 minutes. The sensitivity of the system was 100 copies/mL and as few as 5% of mutant among wild-type virus were detected. In conclusion, real-time PCR with fluorescent hybridization probes is a specific, sensitive, quantitative, and rapid means of detecting clinically relevant HBV mutants.