Nucleotide sequence of a hepatitis B virus genome of subtype adw isolated from a Philippine: Comparison with the reported three genomes of the same subtype

Estacio, R C; Chavez, Carlita C.; Okamoto, Hiroaki; Lingao, Augusto L.; Reyes, Marita T.; Domingo, Ernesto O.; Matsui, Makoto

doi:10.1111/j.1440-1746.1988.tb00241.x

Cited by 38 publications

(22 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Of the South African isolates, 40n9 % (A14, A15, A16, A21, A22, A24, A26, A28 and A36) cluster with published sequences, forming the first subgroup of A, while the remaining 59n1 % (A17, A18, A19, A20, A23, A25, A27, A29, A30, A32, A39 and A40) cluster separately to form a discrete genotypic segment, which we referred to as subgroup Ah. Also clustering in subgroup Ah were three isolates from GenBank, A45 (a Zimbabwean isolate), A04 (a French isolate ; Tran et al, 1991) and A42 (a clone isolated from the Philippines ; Estacio et al, 1988). A05 and A46, which are variants of A04, also cluster with subgroup Ah.…”

Section: Resultsmentioning

confidence: 99%

A unique segment of the hepatitis B virus group A genotype identified in isolates from South Africa.

Bowyer

Staden²,

Kew³

et al. 1997

Journal of General Virology

158

160

View full text Add to dashboard Cite

The preS2/S genes of hepatitis B virus isolated from 29 acutely or chronically infected individuals in the Gauteng province of South Africa were sequenced. Phylogenetic analysis of these sequences in comparison with global isolates from the GenBank database showed that 24 sequences clustered with genotypic group A, three with genotypic group D and one each with genotypic groups B and C. Group A isolates had greater identity with groups D (variation of 6n6 %) and E (6n8 %) than with the Eastern groups B (7n4 %) and C (8n1 %) and were most different from group F (11n0 %). Of the South

show abstract

Section: Resultsmentioning

confidence: 99%

A unique segment of the hepatitis B virus group A genotype identified in isolates from South Africa.

Bowyer

Staden²,

Kew³

et al. 1997

Journal of General Virology

158

160

View full text Add to dashboard Cite

show abstract

“…1). They were classified into genotype A, and clustered with subgroup A 0 with isolates reported previously from France [Stuyver et al, 1999], the Philippines [Estacio et al, 1988] and South Africa [Owiredu et al, 2001b;Kramvis et al, 2002]. They differed distinctly from HBV isolates of genotype A without A 0 in carriers from Western countries with nucleotide differences ranging from 4.1-6.2% (Table II).…”

Section: Phylogenetic Analysismentioning

confidence: 97%

Genotype, serotype, and phylogenetic characterization of the complete genome sequence of hepatitis B virus isolates from Malawian chronic carriers of the virus

Sugauchi

Orito

Kato

et al. 2002

Journal of Medical Virology

View full text Add to dashboard Cite

Hepatitis B virus (HBV) genotypes have distinct geographical distribution. HBV sequences among hepatitis B carriers in Malawi have not been evaluated thus far. HBsAg serotype and genotype of HBV was determined in 20 serum samples from Malawian chronic HBV carriers, and two complete genomes and 13 entire pre-S2/S genes were sequenced directly. Genotype A HBV isolates were found in all of the samples, and serotype with adw2 and ayw2 were detected in three and 17 samples, respectively. In phylogenetic analyses, two complete genomes were classified into a subgroup A' that was described previously in South African isolates of the virus, and were separated from HBV isolates in Western countries with nucleotide differences ranging from 4.1-6.2%. The separation of subgroup A' was also evident in the tree topology of the entire pre-S1/S2, X and precore/core region, but not evident in the small-S region. The nucleotide divergences in subgroup A' were higher than those among genotype A without subgroup A' in the complete genomes as well as each of four open reading frames. All of the 13 pre-S2/S sequences were classified into the subgroup A', and clustered with known HBV isolates with ayw2 in carriers from South Africa and Zimbabwe. Three amino acids in the pre-S2/S gene were characteristic of subgroup A' with ayw2. In conclusion, unique HBV isolates of subgroup A' with ayw2 are prevalent in Malawi, and subgroup A' with a relatively higher nucleotide diversity may be a HBV isolate characteristic of the indigenous population of some African countries.

show abstract

“…The databank accession numbers for genotype A were: V00866 [38], X02763 [39] and M57663 [40]. Sequences D23678 [41] and M54923 [Sastrosoewignjo et al, unpublished] were used as representatives of genotype B. Sequences V00867 [38] and X04615 [42] were used as representatives of genotype C. Sequences X02496 [43] and M32138 [44] were used as representatives of genotype D, X75657 [5] served as a representative of genotype E, and both X69798 [45] and X75663 [5] served as representatives of genotype F. The resulting pregenomic RNA sequences had a 130-base terminal redundancy and would correspond to the sequences of naturally occurring pregenomic RNA (although unpolyadenylated) within an accuracy of 8 bases.…”

Section: Hbv Pregenomic Sequencesmentioning

confidence: 99%

The Hepatitis B Virus Pregenome: Prediction of RNA Structure and Implications for the Emergence of Deletions

Kidd‐Ljunggren

Zuker²,

Hofacker³

et al. 2000

Intervirology

View full text Add to dashboard Cite

The terminally redundant pregenomic RNA of human hepatitis B virus (HBV) comprises some 3,330 nucleotides and is a replicative intermediate in the production of the circular DNA genome. Deletions are known to arise in the HBV genome during the course of chronic infection and are sometimes associated with interferon therapy. These deletions are limited to small parts of the genome such as the 357-nucleotide pre-S1 region. Long RNA molecules such as the HBV pregenome have considerable structural flexibility and will undergo secondary structure shifts between energetically favourable states in a continuous and semi-random fashion. Since prediction of structure elements that are highly conserved in different forms of one RNA molecule is now feasible by computer modelling, we have analysed the whole HBV pregenome by two different RNA structure prediction algorithms and by new methods that exploit these algorithms. Significantly, the ends of pregenomic RNA were predicted to undergo both short-range and long-range interactions, which has relevance to our knowledge of the virus replicative cycle. By incorporating phylogenetic information relating to the 6 recognised genotypes of HBV, it was possible to highlight short secondary structures that may be common to all HBV strains. For example, although the pre-S1 region was predicted to undergo local folding of a loosely defined nature, most observed pre-S1 deletions mapped to all or part of an arm carrying a better-defined structure. The loss of such sequences may be mechanistically attributable to polymerase skipping during reverse transcription, and the possible advantages of such deletions are considered.

show abstract

Nucleotide sequence of a hepatitis B virus genome of subtype adw isolated from a Philippine: Comparison with the reported three genomes of the same subtype

Cited by 38 publications

References 25 publications

A unique segment of the hepatitis B virus group A genotype identified in isolates from South Africa.

A unique segment of the hepatitis B virus group A genotype identified in isolates from South Africa.

Genotype, serotype, and phylogenetic characterization of the complete genome sequence of hepatitis B virus isolates from Malawian chronic carriers of the virus

The Hepatitis B Virus Pregenome: Prediction of RNA Structure and Implications for the Emergence of Deletions

Contact Info

Product

Resources

About