1887

Abstract

Hepatitis B virus (HBV) was partitioned into type, subtype and isolate categories and the average evolutionary distances within and between categories was plotted at each of 54 points along the genome. The graphs showed alternating variable and conserved domains within and between HBV subtypes and revealed that some specimens assigned to different groups are more similar across several contiguous intervals than specimens belonging to the same group. Isolates were screened individually to determine their conformation to type and mosaic structure was identified in 14/65 specimens. Two entire clades (six specimens) of genotype B had a B/C sequence switch in the core gene region, whereas six genotype D specimens showed D/A switching in one or more regions of the genome. Genotype E was not separate from genotype D in the X and C subgenomic regions. The nature and distribution of polymorphic sites in mosaic regions was mapped at both the nucleotide and protein levels and the position of the variant fragments was related to mutational hot spots and linear epitopes of HBV. Mosaic structure was demonstrated statistically in 11 isolates using bootstrap resampling and recombination, rather than random change, appeared to be the mechanism responsible. The sequence between and including the two DR regions was represented in all putative recombinants. The distribution of genetic distances over subgenomic regions showed that substitution rates are not constant among the lineages of HBV in the preS regions. Genotype F is the most diverse group. Only genotypes A, C and F partition consistently into subtypes.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-81-2-379
2000-02-01
2020-01-29
Loading full text...

Full text loading...

/deliver/fulltext/jgv/81/2/0810379a.html?itemId=/content/journal/jgv/10.1099/0022-1317-81-2-379&mimeType=html&fmt=ahah

References

  1. Beasley, R. P. & Hwang, L.-Y. ( 1984; ). Epidemiology of hepatocellular carcinoma. In Viral Hepatitis and Liver Disease, pp. 209-224. Edited by G. N. Vyas, J. L. Dienstag & J. H. Hoofnagle. Orlando, FL: Grune & Stratton.
  2. Bollyky, P. L., Rambaut, A., Harvey, P. H. & Holmes, E. C. ( 1996; ). Recombination between sequences of hepatitis B virus from different genotypes. Journal of Molecular Evolution 42, 97-102.[CrossRef]
    [Google Scholar]
  3. Botha, J. F., Dusheiko, G. M., Ritchie, M. J. J., Mouton, H. W. K. & Kew, M. C. ( 1984; ). Hepatitis B virus carrier state in black children in Ovamboland: role of perinatal and horizontal infection. Lancet 1, 1210-1212.
    [Google Scholar]
  4. Bowyer, S. M. (1998). Epidemiology and molecular characterization of HBV strains from the northern provinces of Namibia. In National Institute for Virology, Annual Report 1997, pp. 38–39. Johannesburg: National Institute for Virology.
  5. Bowyer, S. M., van Staden, L., Kew, M. C. & Sim, J. G. M. ( 1997; ). A unique segment of the hepatitis B virus group A genotype identified in isolates from South Africa. Journal of General Virology 78, 1719-1729.
    [Google Scholar]
  6. Boyer, J. C., Bebenek, K. & Kunkel, T. A. ( 1992; ). Unequal HIV-1 reverse transcriptase error rates with RNA and DNA templates. Proceedings of the National Academy of Sciences, USA 89, 6919-6923.[CrossRef]
    [Google Scholar]
  7. Chisari, F. V. & Ferrari, C. ( 1995; ). Hepatitis B virus immunopathogenesis. Annual Reviews in Immunology 13, 29-60.[CrossRef]
    [Google Scholar]
  8. Dusheiko, G. M., Bowyer, S. M., Paterson, A., Song, E., Dibisceglie, A. & Kew, M. C. ( 1985; ). Clinical and serological events accompanying changes in hepatitis B viral replication: case reports. Liver 5, 77-83.
    [Google Scholar]
  9. Edmunds, W. J., Medley, G. F., Nokes, D. J., O’Callaghan, C. J., Whittle, H. C. & Hall, A. J. ( 1996; ). Epidemiological patterns of hepatitis B virus (HBV) in highly endemic areas. Epidemiology and Infection 117, 313-325.[CrossRef]
    [Google Scholar]
  10. Foster, G. R. & Thomas, H. C. ( 1993; ). Recent advances in the molecular biology of hepatitis B virus: mutant virus and the host response. Gut 34, 1-3.[CrossRef]
    [Google Scholar]
  11. Ganem, D. ( 1991; ). Assembly of hepadnaviral virions and subviral particles. In Hepadnaviruses, Current Topics in Microbiology and Immunology, pp. 61-83. Edited by W. S. Mason & C. Seeger. New York: Springer–Verlag.
  12. Georgi-Geisberger, P., Berns, H., Loncarevic, I. F., Yu, Z.-Y., Tang, Z.-Y., Zentgraf, H. & Schröder, C. H. ( 1992; ). Mutations on free and integrated hepatitis B virus DNA in a hepatocellular carcinoma: footprints of homologous recombination. Oncology 49, 386-395.[CrossRef]
    [Google Scholar]
  13. Girones, R. & Miller, R. L. ( 1989; ). Mutation rate of the hepadnavirus genome. Virology 170, 595-597.[CrossRef]
    [Google Scholar]
  14. Günther, S., Fischer, L., Puli, I., Sterneck, M. & Will, H. ( 1999; ). Naturally occurring variants of hepatitis B. In Advances in Viral Research, pp. 25-137. Edited by K. Maramorosch, F. A. Murphy & A. J. Shatkin. San Diego: Academic Press.
  15. Heijtink, R. A., van Hattum, J., Schalm, S. W. & Masurel, N. ( 1982; ). Co-occurrence of HBsAg and anti-HBs: two consecutive infections or a sign of advanced chronic liver disease? Journal of Medical Virology 10, 83-90.[CrossRef]
    [Google Scholar]
  16. Hino, O., Tabata, S. & Hotta, Y. ( 1991; ). Evidence for increased in vitro recombination with insertion of human hepatitis B virus DNA. Proceedings of the National Academy of Sciences, USA 88, 9248-9252.[CrossRef]
    [Google Scholar]
  17. Kew, M. C., Miller, R. H., Chen, H.-S., Tennant, B. C. & Purcell, R. H. ( 1993; ). Mutant woodchuck hepatitis virus genomes from virions resemble rearranged hepadnaviral integrants in hepatocellular carcinoma. Proceedings of the National Academy of Sciences, USA 90, 10211-10215.[CrossRef]
    [Google Scholar]
  18. Kidd-Ljunggren, K., Couroucé, A.-M., Öberg, M. & Kidd, A. H. ( 1994; ). Genetic conservation within subtypes in the hepatitis B virus pre-S2 region. Journal of General Virology 75, 1485-1490.[CrossRef]
    [Google Scholar]
  19. Kidd-Ljunggren, K., Öberg, M. & Kidd, A. H. ( 1995; ). The hepatitis B virus X gene: analysis of functional domain variation and gene phylogeny using multiple sequences. Journal of General Virology 76, 2119-2130.[CrossRef]
    [Google Scholar]
  20. Köck, J. & Schlicht, H.-J. ( 1993; ). Analysis of the earliest steps of hepadnavirus replication: genome repair after infectious entry into hepatocytes does not depend on viral polymerase activity. Journal of Virology 67, 4867-4874.
    [Google Scholar]
  21. Kremsdorf, D., Garreau, F., Capel, F., Petit, M.-A. & Bréchot, C. ( 1996; ). In vivo selection of a hepatitis B virus mutant with abnormal viral protein expression. Journal of General Virology 77, 929-939.[CrossRef]
    [Google Scholar]
  22. Magnius, L. O. & Norder, H. ( 1995; ). Subtypes, genotypes and molecular epidemiology of the hepatitis B virus reflected by sequence variability of the S-gene. Intervirology 38, 24-34.
    [Google Scholar]
  23. Miller, R. H. ( 1988; ). Close evolutionary relatedness of the hepatitis B virus and murine leukemia virus polymerase gene sequences. Virology 164, 147-155.[CrossRef]
    [Google Scholar]
  24. Mizokami, M., Orito, E., Ohba, K.-I., Ikeo, K., Lau, J. Y. N. & Gojobori, T. ( 1997; ). Constrained evolution with respect to gene overlap of hepatitis B virus. Journal of Molecular Evolution 44 (Suppl. 1), 83–90.[CrossRef]
    [Google Scholar]
  25. Norder, H., Hammas, B., Lofdahl, S., Couroucé, A.-M. & Magnius, L. O. ( 1992; ). 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. Journal of General Virology 73, 1201-1208.[CrossRef]
    [Google Scholar]
  26. Norder, H., Hammas, B., Lee, S.-D., Bile, K., Couroucé, 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. Journal of General Virology 74, 1341-1348.[CrossRef]
    [Google Scholar]
  27. Norder, H., Couroucé, 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.[CrossRef]
    [Google Scholar]
  28. Ohba, K.-I., Mizokami, M., Ohno, T., Suzuki, K., Orito, E., Lau, J. Y. N., Ina, Y., Ikeo, K. & Gojobori, T. ( 1995; ). Relationships between serotypes and genotypes of hepatitis B virus: genetic classification of HBV by use of surface genes. Virus Research 39, 25-34.[CrossRef]
    [Google Scholar]
  29. Okamoto, H., Imai, M., Kametani, M., Nakamura, T. & Mayumi, M. ( 1987; ). Genomic heterogeneity of hepatitis B virus in a 54-year-old woman who contracted the infection through materno-fetal transmission. Japanese Journal of Experimental Medicine 57, 231-236.
    [Google Scholar]
  30. 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. Journal of General Virology 69, 2575-2583.[CrossRef]
    [Google Scholar]
  31. Pathak, V. K. & Wei-Shau, H. ( 1997; ). ‘Might as well jump!’ Template switching by retroviral reverse transcriptase, defective genome formation, and recombination. Seminars in Virology 8, 141-150.[CrossRef]
    [Google Scholar]
  32. Pourquier, P., Jensen, A. D., Gong, S. S., Pommier, Y. & Rogler, C. E. ( 1999; ). Human DNA topoisomerase I-mediated cleavage and recombination of duck hepatitis B virus DNA in vitro. Nucleic Acids Research 27, 1919-1925.[CrossRef]
    [Google Scholar]
  33. Raimondo, G., Burk, R. D., Lieberman, H. M., Muschel, J., Hadziyannis, S. J., Will, H., Kew, M. C., Dusheiko, G. M. & Shafritz, D. A. ( 1988; ). Interrupted replication of hepatitis B virus in liver tissue of HBsAg carriers with hepatocellular carcinoma. Virology 166, 103-112.[CrossRef]
    [Google Scholar]
  34. Schirmacher, P., Wang, W., Stahnke, G., Will, H. & Rogler, C. E. ( 1995; ). Sequences and structures at hepadnaviral integration: recombination sites implicate topoisomerase I in hepadnaviral DNA rearrangements and integration. Journal of Hepatology 22, 21-23.
    [Google Scholar]
  35. Siepel, A. C. & Korber, B. T. (1995). Scanning the database for recombinant HIV-1 genomes. In Human Retroviruses and AIDS, pp. III-35–III-60. Edited by G. Myers, B. H. Mellors, J. W. Hahn, L. E. Henderson, B. Korber, K.-T. Jeang, F. E. McCutchen & G. N. Pavlakis. New Mexico: Los Alamos National Laboratory.
  36. Simmonds, P., Mellor, J., Sakuldamrongpanich, T., Nuchaprayoon, C., Tanprasert, S., Holmes, E. C. & Smith, D. B. ( 1996; ). Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: comparison with classifications based upon sequence similarity. Journal of General Virology 77, 3013-3024.[CrossRef]
    [Google Scholar]
  37. Smith, J. M. ( 1992; ). Analyzing the mosaic structure of genes. Journal of Molecular Evolution 34, 126-129.
    [Google Scholar]
  38. Stephens, J. C. ( 1985; ). Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Molecular & Biological Evolution 2, 539-556.
    [Google Scholar]
  39. Tabor, E., Gerety, R. J., Smallwood, L. A. & Barker, L. F. ( 1977; ). Coincident hepatitis B surface antigen and antibodies of different subtypes in human serum. Journal of Immunology 118, 369-370.
    [Google Scholar]
  40. Tavis, J. E., Perri, S. & Ganem, D. ( 1994; ). Hepadnavirus reverse transcription initiates within the stem-loop of RNA packaging signal and employs a novel strand transfer. Journal of Virology 68, 3536-3543.
    [Google Scholar]
  41. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680.[CrossRef]
    [Google Scholar]
  42. 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. Journal of General Virology 73, 3005-3009.[CrossRef]
    [Google Scholar]
  43. Vardas, E., Mathai, M., Blaauw, D., McAnerney, J., Coppin, A. & Sim, J. ( 1999; ). Preimmunization epidemiology of hepatitis B virus infection in South African children. Journal of Medical Virology 58, 111-115.[CrossRef]
    [Google Scholar]
  44. Wang, G.-H. & Seeger, C. ( 1993; ). Novel mechanism for reverse transcription in hepatitis B viruses. Journal of Virology 67, 6507-6512.
    [Google Scholar]
  45. Will, H., Reiser, W., Weimer, T., Pfaff, E., Büscher, M., Sprengel, R., Cattaneo, R. & Schaller, R. ( 1987; ). Replication strategy of human hepatitis B virus. Journal of Virology 61, 904-911.
    [Google Scholar]
  46. Yang, Z. & Summer, J. ( 1995; ). Illegitimate replication of linear hepadnavirus DNA through nonhomologous recombination. Journal of Virology 69, 4029-4036.
    [Google Scholar]
  47. Yang, Z., Lauder, I. J. & Lin, H. J. ( 1995; ). Molecular evolution of the hepatitis B virus genome. Journal of Molecular Evolution 41, 587-596.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-81-2-379
Loading
/content/journal/jgv/10.1099/0022-1317-81-2-379
Loading

Data & Media loading...

Most cited articles

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