1887

Abstract

Phylogenetic analysis of hepatitis B virus (HBV) has led to its classification into eight genotypes, A to H. The dominant genotype in South Africa is genotype A, which consists of two subgenotypes, A1 and A2. Subgenotype A1 (previously subgroup A′) predominates over subgenotype A2 (previously subgroup A minus A′). The complete genome of HBV isolated from 18 asymptomatic carriers of the virus and five acute hepatitis B patients was amplified; the resulting amplicons were cloned and sequenced. All acute hepatitis isolates belonged to subgenotype A1 and had no distinguishing mutations relative to the isolates from asymptomatic carriers, which had a distribution of ten subgenotype A1, two subgenotype A2 and six genotype D. The presence of the previously described amino acid residues that distinguish subgenotype A1 (subgroup A′) from the remainder of genotype A in the S and polymerase genes was confirmed. Moreover, the large number of subgenotype A1 isolates sequenced allowed identification in the other open reading frames of additional nucleotide and amino acid changes that are characteristic of subgenotype A1. In particular, nucleotide mutations at positions 1809–1812 that alter the Kozak sequence of the precore/core open reading frame, and A in the precore region, were found exclusively in subgenotype A1 isolates. Unique sequence alterations of the transcriptional regulatory elements were also found in subgenotype A1 isolates. The mean nucleotide divergence of subgenotype A1 was greater than that of subgenotype A2, suggesting that this subgenotype has been endemic for a longer time in the South African black population than had subgenotype A2.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.19749-0
2004-05-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/jgv/85/5/vir851211.html?itemId=/content/journal/jgv/10.1099/vir.0.19749-0&mimeType=html&fmt=ahah

References

  1. Ahn S., Kramvis A., Kawai S., Spangenberg H., Li J., Kimbi G., Kew M., Wands J., Tong S. 2003; Sequence variation upstream of the precore AUG start codon of hepatitis B virus reduces HBe-antigen production. Gastroenterology 125:1370–1378
    [Google Scholar]
  2. Arauz-Ruiz P., Norder H., Visona K. A., Magnius L. O. 1997; Genotype F prevails in HBV infected patients of hispanic origin in Central America and may carry the precore stop mutant. J Med Virol 51:305–312
    [Google Scholar]
  3. Arauz-Ruiz P., Norder H., Robertson B. H., Magnius L. O. 2002; Genotype H: a new Amerindian genotype of hepatitis B virus revealed in Central America. J Gen Virol 83:2059–2073
    [Google Scholar]
  4. Arii M., Takada S., Koike K. 1992; Identification of three essential regions of hepatitis B virus X protein for trans-activation function. Oncogene 7:397–403
    [Google Scholar]
  5. Baptista M., Kramvis A., Kew M. C. 1999; High prevalence of 1762T 1764A mutations in the basic core promoter of hepatitis B virus isolated from black Africans with hepatocellular carcinoma compared with asymptomatic carriers. Hepatology 29:946–953
    [Google Scholar]
  6. Biegalke B. J., Geballe A. P. 1990; Translational inhibition by cytomegalovirus transcript leaders. Virology 177:657–667
    [Google Scholar]
  7. Bowyer S. M., van Staden L., Kew M. C., Sim J. G. 1997; A unique segment of the hepatitis B virus group A genotype identified in isolates from South Africa. J Gen Virol 78:1719–1729
    [Google Scholar]
  8. Das K., Xiong X., Yang H., Westland C. E., Gibbs C. S., Sarafianos S. G., Arnold E. 2001; Molecular modeling and biochemical characterization reveal the mechanism of hepatitis B virus polymerase resistance to lamivudine (3TC) and emtricitabine (FTC). J Virol 75:4771–4779
    [Google Scholar]
  9. Degnin C. R., Schleiss M. R., Cao J., Geballe A. P. 1993; Translational inhibition mediated by a short upstream open reading frame in the human cytomegalovirus gpUL4 (gp48) transcript. J Virol 67:5514–5521
    [Google Scholar]
  10. de Smit M. H., van Duin J. 1993; Translational initiation at the coat-protein gene of phage MS2: native upstream RNA relieves inhibition by local secondary structure. Mol Microbiol 9:1079–1088
    [Google Scholar]
  11. Estacio R. C., Chavez C. C., Okamoto H., Lingao A. L., Reyes M. T., Domingo E., Mayumi M. 1988; Nucleotide sequence of a hepatitis B virus genome of subtype adw isolated from a Philippino: comparison with the reported three genomes of the same subtype. J Gastroenterol Hepatol 3:215–222
    [Google Scholar]
  12. Felsenstein J. 1995; phylip (Phylogeny Inference Package). Department of Genetics, University of Washington; Seattle, Washington:
  13. Fouillot N., Tlouzeau S., Rossignol J. M., Jean-Jean O. 1993; Translation of the hepatitis B virus P gene by ribosomal scanning as an alternative to internal initiation. J Virol 67:4886–4895
    [Google Scholar]
  14. Grethe S., Heckel J. O., Rietschel W., Hufert F. T. 2000; Molecular epidemiology of hepatitis B virus variants in nonhuman primates. J Virol 74:5377–5381
    [Google Scholar]
  15. Gunther S., Li B. C., Miska S., Kruger D. H., Meisel H., Will H. 1995; A novel method for efficient amplification of whole hepatitis B virus genomes permits rapid functional analysis and reveals deletion mutants in immunosuppressed patients. J Virol 69:5437–5444
    [Google Scholar]
  16. Hannoun C., Norder H., Lindh M. 2000; An aberrant genotype revealed in recombinant hepatitis B virus strains from Vietnam. J Gen Virol 81:2267–2272
    [Google Scholar]
  17. Hwang W. L., Su T. S. 1998; Translational regulation of hepatitis B virus polymerase gene by termination-reinitiation of an upstream minicistron in a length-dependent manner. J Gen Virol 79:2181–2189
    [Google Scholar]
  18. Kidd-Ljunggren K., Oberg M., Kidd A. H. 1995; The hepatitis B virus X gene: analysis of functional domain variation and gene phylogeny using multiple sequences. J Gen Virol 76:2119–2130
    [Google Scholar]
  19. Kozak M. 1986; Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283–292
    [Google Scholar]
  20. Kozak M. 1987; At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells. J Mol Biol 196:947–950
    [Google Scholar]
  21. Kramvis A., Kew M. C. 1998; Structure and function of the encapsidation signal of hepadnaviridae. J Viral Hepat 5:357–367
    [Google Scholar]
  22. Kramvis A., Kew M. C. 1999; The core promoter of hepatitis B virus. J Viral Hepat 6:415–427
    [Google Scholar]
  23. Kramvis A., Bukofzer S., Kew M. C., Song E. 1997; Nucleic acid sequence analysis of the precore region of hepatitis B virus from sera of southern African black adult carriers of the virus. Hepatology 25:235–240
    [Google Scholar]
  24. Kramvis A., Weitzmann L., Owiredu W. K., Kew M. C. 2002; Analysis of the complete genome of subgroup A′ hepatitis B virus isolates from South Africa. J Gen Virol 83:835–839
    [Google Scholar]
  25. Laskus T., Rakela J., Steers J. L., Wiesner R. H., Persing D. H. 1994; Precore and contiguous regions of hepatitis B virus in liver transplantation for end-stage hepatitis B. Gastroenterology 107:1774–1780
    [Google Scholar]
  26. Mayerat C., Mantegani A., Frei P. C. 1999; Does hepatitis B virus (HBV) genotype influence the clinical outcome of HBV infection?. J Viral Hepat 6:299–304
    [Google Scholar]
  27. Moolla N., Kew M., Arbuthnot P. 2002; Regulatory elements of hepatitis B virus transcription. J Viral Hepat 9:323–331
    [Google Scholar]
  28. Mphahlele M. J., Francois G., Kew M., Van Damme P., Hoosen A., Meheus A. 2002; Epidemiology and control of hepatitis B: implications for eastern and southern Africa. S Afr J Epidemiol Infect 17:12–17
    [Google Scholar]
  29. Nassal M., Schaller H. 1996; Hepatitis B virus replication – an update. J Viral Hepat 3:217–226
    [Google Scholar]
  30. Neurath A. R., Kent S. B., Strick N., Parker K. 1986; Identification and chemical synthesis of a host cell receptor binding site on hepatitis B virus. Cell 46:429–436
    [Google Scholar]
  31. Nicholas K. B., Nicholas H. B. Jr 1997; GeneDoc: analysis and visualization of genetic variation.
    [Google Scholar]
  32. Norder H., Courouce A. M., Magnius L. O. 1992a; Molecular basis of hepatitis B virus serotype variations within the four major subtypes. J Gen Virol 73:3141–3145
    [Google Scholar]
  33. Norder H., Hammas B., Lofdahl S., Courouce A. M., Magnius L. O. 1992b; Comparison of the amino acid sequences of nine different serotypes of hepatitis B surface antigen and genomic classification of the corresponding hepatitis B virus strains. J Gen Virol 73:1201–1208
    [Google Scholar]
  34. Norder H., Hammas B., Lee S. D., Bile K., Courouce A. M., Mushahwar I. K., Magnius L. O. 1993; Genetic relatedness of hepatitis B viral strains of diverse geographical origin and natural variations in the primary structure of the surface antigen. J Gen Virol 74:1341–1348
    [Google Scholar]
  35. Norder H., Courouce A. M., Magnius L. O. 1994; Complete genomes, phylogenetic relatedness, and structural proteins of six strains of the hepatitis B virus, four of which represent two new genotypes. Virology 198:489–503
    [Google Scholar]
  36. Norder H., Ebert J. W., Fields H. A., Mushahwar I. K., Magnius L. O. 1996; Complete sequencing of a gibbon hepatitis B virus genome reveals a unique genotype distantly related to the chimpanzee hepatitis B virus. Virology 218:214–223
    [Google Scholar]
  37. Odemuyiwa S. O., Mulders M. N., Oyedele O. I., Ola S. O., Odaibo G. N., Olaleye D. O., Muller C. P. 2001; Phylogenetic analysis of new hepatitis B virus isolates from Nigeria supports endemicity of genotype E in West Africa. J Med Virol 65:463–469
    [Google Scholar]
  38. Okamoto H., Tsuda F., Sakugawa H., Sastrosoewignjo R. I., Imai M., Miyakawa Y., Mayumi M. 1988; Typing hepatitis B virus by homology in nucleotide sequence: comparison of surface antigen subtypes. J Gen Virol 69:2575–2583
    [Google Scholar]
  39. Owiredu W. K., Kramvis A., Kew M. C. 2001; Hepatitis B virus DNA in serum of healthy black African adults positive for hepatitis B surface antibody alone: possible association with recombination between genotypes A and D. J Med Virol 64:441–454
    [Google Scholar]
  40. Ozawa K., Ayub J., Young N. 1988; Translational regulation of B19 parvovirus capsid protein production by multiple upstream AUG triplets. J Biol Chem 263:10922–10926
    [Google Scholar]
  41. Page R. 1996; treeview: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358
    [Google Scholar]
  42. Pontisso P., Ruvoletto M. G., Gerlich W. H., Heermann K. H., Bardini R., Alberti A. 1989; Identification of an attachment site for human liver plasma membranes on hepatitis B virus particles. Virology 173:522–530
    [Google Scholar]
  43. Rogozin I. B., Kochetov A. V., Kondrashov F. A., Koonin E. V., Milanesi L. 2001; Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ‘weak’ context of the start codon. Bioinformatics 17:890–900
    [Google Scholar]
  44. Ryabova L. A., Pooggin M. M., Hohn T. 2002; Viral strategies of translation initiation: ribosomal shunt and reinitiation. Prog Nucleic Acid Res Mol Biol 72:1–39
    [Google Scholar]
  45. Stuyver L., De Gendt S., Van Geyt C., Zoulim F., Fried M., Schinazi R. F., Rossau R. 2000; A new genotype of hepatitis B virus: complete genome and phylogenetic relatedness. J Gen Virol 81:67–74
    [Google Scholar]
  46. Sugauchi F., Orito E., Kato H. 8 other authors 2003; Genotype, serotype, and phylogenetic characterization of the complete genome sequence of hepatitis B virus isolates from Malawian chronic carriers of the virus. J Med Virol 69:33–40
    [Google Scholar]
  47. Takahashi K., Akahane Y., Hino K., Ohta Y., Mishiro S. 1998; Hepatitis B virus genomic sequence in the circulation of hepatocellular carcinoma patients: comparative analysis of 40 full-length isolates. Arch Virol 143:2313–2326
    [Google Scholar]
  48. Takahashi K., Brotman B., Usuda S., Mishiro S., Prince A. M. 2000; Full-genome sequence analysis of hepatitis B virus strains recovered from chimpanzees infected in the wild: implications for an origin of HBV. Virology 267:58–64
    [Google Scholar]
  49. Uy A., Wunderlich G., Olsen D. B., Heermann K. H., Gerlich W. H., Thomssen R. 1992; Genomic variability in the preS1 region and determination of routes of transmission of hepatitis B virus. J Gen Virol 73:3005–3009
    [Google Scholar]
  50. Verschoor E. J., Warren K. S., Langenhuijzen S., Heriyanto Swan., A R, Heeney J. L. 2001; Analysis of two genomic variants of orang-utan hepadnavirus and their relationship to other primate hepatitis B-like viruses. J Gen Virol 82:893–897
    [Google Scholar]
  51. Vieth S., Manegold C., Drosten C., Nippraschk T., Gunther S. 2002; Sequence and phylogenetic analysis of hepatitis B virus genotype G isolated in Germany. Virus Genes 24:153–156
    [Google Scholar]
  52. WHO 2002 Hepatitis B. World Health Organization Department of Communicable Diseases Surveillance Reponse WHO/CDS/CSR/LYO/2002.2: Hepatitis B;
    [Google Scholar]
  53. Xia X. 2000 Data Analysis in Molecular Biology and Evolution Dordrecht: Kluwer;
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.19749-0
Loading
/content/journal/jgv/10.1099/vir.0.19749-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error