Nucleotide Sequence of the Hypervariable Pre-S2 Surface Antigen Region of Pakistani HBV Isolates (original) (raw)
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Journal of General Virology, 1993
A 681 nucleotide fragment of the hepatitis B virus (HBV) genome was sequenced that corresponded to the complete gene for hepatitis B surface antigen (HBsAg) in 80HBsAg-and hepatitis B e antigen (HBeAg)positive sera of diverse geographical origins. These and 42 previously published HBV sequences within the S gene were used for the construction of a dendrogram. In this comparison, each of the 122 HBsAg genes was found to be related to one or other of the six previously identified genomic groups of HBV, A to F. The HBV strains within each genomic group showed a characteristic geographical distribution. Group A genomes were represented by 23 strains mainly originating in northern Europe and sub-Saharan Africa. The group B and C genomes, represented by 17 and 28 strains respectively, were confined to populations with origins in eastern Asia and the Far East. The group D genomes, represented by 38 strains, were found worldwide, but were the predominant strains in the Mediterranean area, the Near and Middle East, and in south Asia. Group E genomes, represented by nine strains, were indigenous to western sub-Saharan Africa as far south as Angola. There were indications that the F group, made up of six strains, represented the genomic group of HBV among populations with origins in the New World. Thus, HBV has diverged into genomic groups according to the distribution of mankind in the different continents. As well as giving information on the genetic relationship of HBV strains of different geographical origin, this study also provides information on the primary structure of HBsAg in different regions of the world. Such data might prove valuable in explaining the reported failures to obtain protection with current HBV vaccines. 0001-1477 © 1993 SGM
Journal of General Virology, 1992
The surface (S) genes of 12 hepatitis B viruses (HBVs) encoding nine different serotypes of hepatitis B surface antigen (HBsAg) were amplified by the polymerase chain reaction and sequenced. These represented the eight strains of HBV, PI to P8, defined at an international workshop on HBsAg subtypes in Paris in 1975, and the adrqsubtype. The S genes from additional HBV strains, one ayw4, one adw4 and one aywl, of sub-Saharan African origin, were also sequenced. The relationship of these 12 new S gene sequences to those of the 20 published previously was investigated by constructing a phylogenetic tree, which confirmed a previous classification into four groups, designated A to D, based on 18 complete HBV genomes. When relating our sequenced S genes to these genomic groups, aywl of African origin and P6 (adw2) were both allocated to group A, the reference P1 (aywl of Vietnamese origin) was allocated to group B, P5 (ayr), P8 (adr) and adrqwere all related to group C, and P2 (ayw2) and P3 (ayw3) could both be allocated to group D. Interestingly, the S genes of w4 serotype viruses, i.e. P4 (ayw4) and P7 (adw4q-), differed by 4% or more from both previous groups and from each other, suggesting their classification into two new groups, for which the designations E and F are proposed. Genomes specifying ayw were also found in groups A and B; previously sequenced genomes specifying the ayw subtype have all been confined to group D. There were indications that the epitope for subdeterminants of w resided at amino acid positions 125 to 127. Thus, at positions 125 and 127, aywl, ayw2 and adw2 had T and P residues, respectively, whereas M and T residues were at the corresponding positions ofayw3. Both ayw4 and adw4 had L at residue 127, and all strains expressing r, apart from P5, had an I instead of a T residue at position 126.
Hepatology, 2012
To evaluate whether hepatitis B virus (HBV) preS/S gene variability has any impact on serum hepatitis B surface antigen (HBsAg) levels and to analyze the replication capacity of naturally occurring preS/S variants, sera from 40 untreated patients with HBV-related chronic liver disease (hepatitis B e antigen [HBeAg]-positive, n 5 11; HBeAg-negative, n 5 29) were virologically characterized. Additionally, phenotypic analysis of three different preS/S variant isolates (carrying a 183-nucleotide deletion within the preS1 region, the deletion of preS2 start codon, and a stop signal at codon 182 within the S gene, respectively) was performed. HBV infecting 14 (35%) patients had single or multiple preS/S genomic mutations (i.e., preS1 and/or preS2 deletions, preS2 start codon mutations, C-terminally truncated and/or ''a'' determinant mutated S protein). Presence of preS/S variants negatively correlated with HBsAg titers (r 5 20.431; P 5 0.005) and its prevalence did not significantly differ between HBeAg-positive and HBeAg-negative patients. No correlation was found between HBsAg and HBV DNA levels in patients infected with preS/S mutants, whereas a significant correlation was found between HBsAg and viremia levels (r 5 0.607; P 5 0.001) in patients infected with wild-type HBV strains. HepG2 cells replicating the abovementioned three preS/S variants showed significant reduction of HBsAg secretion, retention of envelope proteins in the endoplasmic reticulum, less efficient virion secretion and nuclear accumulation of significantly higher amounts of covalently closed circular DNA compared with wild-type HBV replicating cells. Conclusion: In patients infected with preS/S variants, HBV DNA replication and HBsAg synthesis/secretion appear to be dissociated. Therefore, the use of HBsAg titer as diagnostic/prognostic tool has to take into account the frequent emergence of preS/S variants in chronic HBV infection. (HEPATOLOGY 2012;56:434-443) See Editorial on Page 411 H epatitis B virus (HBV) belongs to the Hepadnaviridae family, which comprises hepatotropic DNA viruses sharing with HBV most of the genetic structure and replicative characteristics. 1 HBV is one of the smallest viruses in nature and its genome presents a highly compact genetic organization. It consists of a partially double-stranded relaxed circular DNA of approximately 3,200 nucleotides in length and contains four partially overlapping open-reading frames: preS/S, pre-C-C, P, and X. The preS/S openreading frame encodes three different, structurally related envelope proteins termed the large (L), middle (M), and small (S) protein that are synthesized from alternative initiation codons. The three proteins share the same carboxy-terminus part but have different aminoterminal extensions. In particular, the S protein-corresponding to the HBV surface antigen (HBsAg)-consists of only 226 amino acids (aa), the M protein contains an extra N-terminal extension of 55 aa, and the L
[Structure and expression of human hepatitis B virus surface antigen]
Molekuliarnaia biologiia
In view of the growing occurrence rate of the virus-induced hepatitis B and also of the special role played by this particular virus (HBV) in the application of recombinant genetic techniques to the study of complex biological systems, an attempt was made to survey the available evidence concerning the widely investigated and practically the most important part of the viral genome, viz. the gene coding for the surface antigen (HBsAg) and the protein itself. The possible antigenic structure of the protein was investigated using data on the primary structure of 11 cloned HBsAg gene variants and on the synthesis of peptides simulating its immunological properties. Special emphasis was placed on quantitative assessment of antigenicity and immunogenicity. Expression of the gene in homologous systems was studied using cultures of eukaryotic tissues: both as part of HBV nucleotide sequences incorporated into the chromosome and as part of extrachromosomal DNA. The latest findings on HBsAg g...
Typing of hepatitis B virus genomes by a simplified polymerase chain reaction
Journal of Medical Virology, 1990
The amplification of hepatitis B virus (HBV) DNA sequences in sera for molecular epidemiology of HBV is an important application of the polymerase chain reaction (PCR) with regard to HBV. To simplify the PCR for this purpose, the optimal concentrations of SDS and detergents for carrying out the proteinase K digestion and the amplification of DNA by Taq polymerase were evaluated. It was found that by using 1% deoxycholic acid as detergent for the proteinase K step and diluting the digest 10 times before carrying out the PCR, the phenol extraction of DNA became superfluous. The sensitivity of this procedure equalled that of PCR after phenol extraction on comparable amounts of serum. Four pairs of oligonucleotide primers were compared for amplification of HBV DNA sequences in 48 sera previously subtyped with respect to hepatitis B surface antigen (HBsAg), and in eight sera with different genotypes of HBV, representing the subtypes of HBsAg P I to P8, defined at an international meeting [Courouce-Pauty et al.: "HBs Antigen Subtypes." Basel: Karger, 19761. Two primer pairs, selected from conserved regions in the X and S genes of HBV, gave a positive PCR with sera harbouring all the eight different strains of HBV, resulting in DNA fragments consistent with the sizes deduced from genome sequence data. Two other primer pairs were selected in order to discriminate genotypes with regard to differences between d/y and w/r strains. With these primer sets total agreement was obtained with previous results from subtyping with regard to d/y and w/r with all 48 sera, but more complex results were obtained with P I to P8, which partially, however, confirm a recent grouping of HBV genomes based on genetic relatedness [Okamoto et al.:
Large surface proteins of hepatitis B virus containing the pre-s sequence
Journal of virology, 1984
The sequence of hepatitis B virus DNA contains an open reading frame which codes for a not-yet-identified protein of at least 389 amino acids. Only the products starting at the third (GP33/GP36) or the fourth (P24/GP27) initiation signal have been characterized as components of the viral surface antigen. We found a larger protein, P39, and its glycosylated form, GP42, in hepatitis B virus particles and viral surface antigen filaments. Immunological cross-reactions showed that P39/GP42 is partially homologous to P24/GP27 and GP33/GP36. The unique portion of its sequence bound monoclonal antibodies which had been induced by immunization with hepatitis B virus particles. Proteolytic cleavage patterns and subtype-specific size differences suggested that the sequence of P39 starts with the first initiation signal of the open reading frame. Its amino-terminal part (pre-s coded) is exposed at the viral surface and, probably, is highly immunogenic. A model is presented of how the open readi...
A unique insertion in the S gene of surface antigen?Negative hepatitis B virus chinese carriers
Hepatology, 1995
The presence of unique hepatitis B virus (HBV) variants has been investigated in two Chinese patients with chronic liver disease, whose sera were positive for HBV-DNA by dot blot hybridization or polymerase chain reaction (PCR) but hepatitis B surface antigen (HBsAg)negative by conventional polyclonal antibody based immunoassays. PCR amplification of HBV-DNA followed by direct sequencing showed an insertion of six nucleotides, which introduced two additional amino acids between codons 122 and 123 in one patient (Isolate l), whereas a nine nucleotide insertion in the other patient (Isolate 2) gave rise to three amino-acids between codons 123 and 124 immediately upstream from the 'a' determinant in the S gene. These insertions have not been described previously in any published sequences of the known subtypes and were absent from sequences of 30 HBsAg-positive Chinese patients from the same region. In the cases under study, the insertion is associated with four consecutive adenine molecules from nucleotides 516 to 519. It seems likely that this area is a hot spot for insertions in HBV. We found none of the previously described amino-acid deletions or substitutions in the pre-S1, pre-S2 and S genes, which are involved in unusual antigenic profiles. This finding suggests that genetic mutations in the S gene outside the 'a' determinant may be responsible for failure to detect HBsAg in some Chinese patients with chronic hepatitis caused by HBV infection. (HEPATOLOGY 1995;21:273-278.) The existence of hepatitis B virus (HBV) variants has been suspected for some time because of the observation that viral DNA can be detected in the serum, liver, and blood mononuclear cells of some patients with chronic liver disease and hepatocellular carcinoma, as well as in some normal individuals, without
Variability in the immunogenic preS region of Pakistani hepatitis B virus isolates
VirusDisease, 2019
This paper reports the genetic variability of hepatitis B virus in Pakistan population. The worldwide prevalence of hepatitis B virus is estimated to be around 350 million that causes significant mortality especially in developing countries like Pakistan. In this study, genetic diversity of HBV was checked by using preS domain of HBV. About seventy-five samples were selected for study. Among these samples nine samples showed positive results after PCR and gel analysis. These nine samples were named SBS001-SBS008. After gel purification these samples were ligated in T/A cloning vector and transformed with E. coli DH5a. After successful cloning and positive restriction analysis these samples were subjected to DNA sequencing. Sequencing results showed that eight samples (SBS002-SBS008) have a deletion of 33 nucleotides at N-terminal that is characteristics of genotype D while SBS001 belongs to genotype C. Silent mutations and amino acid changes were also searched in this highly variable region of genome. Based upon this study it was concluded that genotype D is the most common genotype in Pakistan.