Variability in hepatitis B virus DNA: phylogenetic, epidemiological and clinical implications

Synthesis of specifically deuterated nucleotides for NMR studies on RNA

Abstract We propose a strategy for NMR structure determination of RNA based on deuteration and use of specific labeling patterns. This strategy involves the use of NTPs that are deuterated in the ribose ring except for specific positions, e.g. H2', and that are either unlabeled or uniformly labeled in (13)C and (15)N in either the ribose or the base or both. Incorporation of these NTPs into an RNA sequence reduces both resonance line-width and spectral overlap. A limited number of combinations of these differently labeled NTPs in an RNA sequence suffices to obtain all relevant proton resonance assignments and structure parameters necessary for structure determination of larger systems (≫ 50 nucleotides). We describe the in vitro synthesis of the deuterated and/or (13)C/(15)N-labeled NTPs from glucose via separate enzymatic reactions. First, enzymes from the pentose-phosphate pathway efficiently convert glucose into ribose and enzymes from nucleotide biosynthesis and salvage pathways subsequently convert the ribose into nucleosides triphosphates (NTPs). The enzymes from the pentosephosphate pathway are all commercially available; the remaining enzymes have been purified from over-expressing strains. Separate enzymatic reactions were used to convert (2)H(7)- (13)C(6)-glucose into [1',3',4',5',5″-(2)H(5)-1',2',3',4',5',2,4,5,6-(13)C(9)-1,3-(15)N(2)]UTP and (2)H(7)-glucose into [1',3',4',5',5″-(2)H(5)]ATP, [1',3',4',5',5″-(2)H(5)]GTP, and [1',3',4',5',5″-(2)H(5)] CTP. The synthesis yields up to 1 gram of NTPs from 1 gram of glucose, which is about 5 to 10 times as efficient extraction for E. Coli grown on glucose. The synthesis presented here, is a modification of the method described by Tolbert & Williamson (1,2). (1)D and (2)D NMR spectra were acquired to demonstrate the utility of the new labeling patterns. The enzymatically synthesized NTPs were used in the synthesis of a 31-nucleotide RNA derived from the primer binding site of Hepatitis B virus genomic RNA to asses their efficiency in transcription.

Immune-induced evolutionary selection focused on a single reading frame in overlapping hepatitis B virus proteins

Viruses employ various means to evade immune detection. Reduction of CD8(+) T cell epitopes is one of the common strategies used for this purpose. Hepatitis B virus (HBV), a member of the Hepadnaviridae family, has four open reading frames, with about 50% overlap between the genes they encode. We computed the CD8(+) T cell epitope density within HBV proteins and the mutations within the epitopes. Our results suggest that HBV accumulates escape mutations that reduce the number of epitopes. These mutations are not equally distributed among genes and reading frames. While the highly expressed core and X proteins are selected to have low epitope density, polymerase, which is expressed at low levels, does not undergo the same selection. In overlapping regions, mutations in one protein-coding sequence also affect the other protein-coding sequence. We show that mutations lead to the removal of epitopes in X and surface proteins even at the expense of the addition of epitopes in polymerase. The total escape mutation rate for overlapping regions is lower than that for nonoverlapping regions. The lower epitope replacement rate for overlapping regions slows the evolutionary escape rate of these regions but leads to the accumulation of mutations more robust in the transfer between hosts, such as mutations preventing proteasomal cleavage into epitopes.

Variability of the PreS1/PreS2/S regions of hepatitis B virus in Hungary

Infection with the hepatitis B virus can occur perinatally, parenterally, or sexually, and it can cause acute or chronic liver diseases. Phylogenetic analysis of the virus has led to its classification into eight genotypes (A-H), which show a characteristic worldwide distribution. The aim of this study was to reveal the HBV genotypes present in Hungary and to investigate a nosocomial and an intrafamilial outbreak. The collected samples were tested by nested PCR, and a 650-nucleotide-long segment of the preS1/preS2/S region was sequenced. As no previous genotype data were available from Hungary, sera of 24 HBsAg-positive patients were collected from different regions of the country. They also served as control samples for the molecular epidemiologic study. Nineteen of them carried genotype D of hepatitis B virus, and five of them carried genotype A. Twenty-nine patients from a haemato-oncology unit were affected in a nosocomial outbreak. The patients had haematological and/or oncological diseases, most of them were immunosuppressed. In twenty-eight cases, based on phylogenetic analysis of the viruses, there was presumably a common source of infection, and an epidemiological investigation showed that the infections seemed to be hospital-acquired. In the intrafamilial outbreak, two asymptomatic carrier children infected their foster mother. The three sequences were totally identical.

Genotypic distribution of hepatitis B virus in the Czech Republic: a possible association with modes of transmission and clinical outcome

OBJECTIVE

The relationship between hepatitis B virus (HBV) genotype with disease or treatment outcome is beginning to be characterized. However, the link between genotype and disease transmission route has not been closely examined. We addressed this question in high-risk populations in Prague, Czech Republic.

DESIGN

Patients with HBV infection were consecutively recruited into the study at an outpatient clinic between June 2000 and March 2001. Their serum samples were analysed for HBV S gene segments by polymerase chain reaction (PCR) test. The amplified product sequences were compared to those of known HBV genotypes. Patients were evaluated for other virus co-infections, and parenteral and sexual exposure histories.

RESULTS

Of 57 consecutively recruited patients with evidence of HBV infection, 45 (79%) had PCR-detectable S gene sequences. Only genotypes A (n = 33; 73%) and D (n = 12; 27%) were found. There was no difference in the development of chronic infection between the two genotypes. Of nine patients co-infected with TTV, all were infected with HBV genotype A. There was a trend towards an association between number of lifetime sex partners and genotype A but not genotype D.

CONCLUSIONS

In Prague, the number of HBV genotypes appears to be limited compared to other northern European countries, suggesting that the virus has recently spread in the high-risk populations. While a large proportion of HBV infections occur in intravenous drug users, a subset of HBV genotype A may be transmitted by sexual contact. An HBV subtype may influence modes of transmission of HBV.

High hepatitis B virus (HBV) DNA viral load as the most important risk factor for HBV reactivation in patients positive for HBV surface antigen undergoing autologous hematopoietic cell transplantation

The risk factors for hepatitis due to hepatitis B virus (HBV) reactivation in patients positive for hepatitis B surface antigen (HBsAg) treated with autologous hematopoietic cell transplantation (HCT) are unknown. We evaluated 137 consecutive patients (23 positive for HBsAg, 37 positive for hepatitis B surface antibody, and 77 negative for HBV) who underwent HCT. Serial serum ALT were measured before transplant and after transplant at 1 to 4 weekly intervals for the first year and then at 2 to 12 weekly intervals thereafter. Before HCT, basic core promoter (T(1762)/A(1764)) and precore (A(1896)) HBV variants were determined in HBsAg-positive and HBV DNA-positive (by polymerase chain reaction assay) patients by direct sequencing and serum HBV DNA quantitation using the Digene Hybrid Capture II assay. Cox proportional hazards analysis was used to assess the association between pretransplantation HBV virologic and host factors and occurrence of hepatitis due to HBV reactivation. After HCT, hepatitis due to HBV reactivation was more common in HBsAg-positive patients than in HBsAg-negative patients (hazard ratio, 33.3; 95% confidence interval [CI], 7.35-142.86; P <.0001). HBsAg-positive patients with detectable serum HBV DNA before HCT (on Digene assay) had a significantly higher risk of hepatitis due to HBV reactivation than HBsAg-positive patients with no detectable serum HBV DNA (adjusted hazard ratio, 9.35; 95% CI, 1.65-52.6; P =.012). Thus, we found that hepatitis due to HBV reactivation is common in HBsAg-positive patients undergoing autologous HCT. A high HBV DNA level (>10(5) copies/mL) was the most important risk factor for HBV reactivation, and its lowering by administration of nucleoside analogues before transplantation should be considered.

Molecular, immunological and clinical properties of mutated hepatitis B viruses

Hepatitis B virus (HBV) is at the origin of severe liver diseases like chronic active hepatitis, liver cirrhosis and hepatocellular carcinoma. There are some groups of patients with high risk of generation of HBV mutants: infected infants, immunosuppressed individuals (including hemodialysis patients), patients treated with interferon and lamivudine for chronic HBV infection. These groups are the target for molecular investigations reviewed in this paper. The emergence of lamivudine- or other antiviral-resistant variants, rises concern regarding long term use of these drugs. Infection or immunization with one HBV subtype confers immunity to all subtypes. However, reinfection or reactivation of latent HBV infection with HBV mutants have been reported in patients undergoing transplant and those infected with HIV. Mutations of the viral genome which are not replicative incompetent can be selected in further course of infection or under prolonged antiviral treatment and might maintain the liver disease. Four open reading frames (ORF) which are called S-gene, C-gene, X-gene and P-gene were identified within the HBV genome. Mutations may affect each of the ORFs. Mutated S-genes were described to be responsible for HBV-infections in successfully vaccinated persons, mutated C-genes were found to provoke severe chronic liver diseases, mutated X-genes could cause serious medical problems in blood donors by escaping the conventional test systems and mutated P-genes were considered to be the reason for chemotherapeutic drug resistance. This paper reviews molecular, immunological and clinical aspects of the HBV mutants.

Frequent integration of precore/core mutants of hepatitis B virus in human hepatocellular carcinoma tissues

The development of hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC) frequently follows persistent HBV infection and may arise in individuals who are hepatitis B e antigen (HBeAg) negative, indicating the possible presence of precore/core mutants. It is unclear whether precore/core mutants are associated with tumour development or are selected for after chromosomal integration of the wild-type viral DNA. We studied the status and sequence variation of the precore/core region of HBV in 56 patients with HBV-associated HCC and in various corresponding non-tumour tissues by Southern blot analysis, polymerase chain reaction and direct sequencing. Southern blot showed that integrated HBV DNA existed in 43 of 56 HCC tissues. Sequence analysis revealed mutations in 65% of the HCC (26/40) and 45% (14/31) of the corresponding non-tumour tissues. The mutation at nucleotide (nt) 1896, known to prevent HBeAg synthesis, was detected in 40% (16/40) of the tumours and in 35.4% (11/31) of the non-tumour tissues. Other mutations were found at nt 1899 (eight of 40 in HCC; three of 31 in non-tumour tissues), nt 1898 (seven of 40 in HCC; two of 31 in non-tumour tissues), nt 1912 (seven of 40 in HCC; none of 31 in non-tumour tissues) and nt 1886 (three of 40 in HCC; none of 31 in non-tumour tissues). To determine whether this finding merely reflected the prevalence of such mutants in this geographical region, HBV DNA from the sera of patients (also in this region) with acute and chronic hepatitis were sequenced. The nt 1896 mutant was found in 5.6% (one of 18) of patients with acute hepatitis B and in 22.8% (nine of 35) of patients with chronic hepatitis B. However, the nt 1898 mutation was not found in any of these sera. The precore/core mutant was observed with increasing frequency from acute hepatitis to chronic hepatitis, non-tumour and HCC, and this difference in frequency was significant between HCC and acute hepatitis B groups (P < 0.01), suggesting that the precore/core mutant or hepatocytes harbouring this mutant may be under immune selection and that such mutations may facilitate integration and subsequent tumour development.