Variation of the hepatitis C virus 5′ non-coding region: implications for secondary structure, virus detection and typing Free

Abstract

Variation in the 5′ non-coding region (5′NCR) of hepatitis C virus (HCV) was investigated in detail by comparing 314 5′NCR sequences of viruses of genotypes 1 to 6. Evidence was obtained for the existence of associations between particular 5′NCR sequence motifs and virus types and subtypes. No recombination was observed between the 5′NCR and coding regions of different genotypes, implying that the sequence of subgenomic regions such as the 5′NCR can be used to deduce virus genotype. The distribution of polymorphic sites within the 5′NCR is used to propose improved oligonucleotide primers for virus detection and quantification that would be equally efficient in detecting RNA of different virus genotypes. The accuracy of two different genotyping methods (RFLP and the line probe assay) based on analysis of sequence polymorphisms in the 5′NCR is predicted from the sequences surveyed to be 97% and 83% respectively for types 1 to 6, with higher accuracies for distinguishing between subtypes 1a/1b, 2a/2b or 3a/3b. Several sites of genotype-specific polymorphism were covariant and maintained the base pairings required for a secondary structure model of the 5′NCR. Other sites of variation suggest minor modifications to this model and have implications for the probable functions of the 5′NCR

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-76-7-1749
1995-07-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/jgv/76/7/JV0760071749.html?itemId=/content/journal/jgv/10.1099/0022-1317-76-7-1749&mimeType=html&fmt=ahah

References

  1. Andonov A., Chaudhary R. K. 1994; Genotyping of Canadian hepatitis C virus isolates by PCR. Journal of Clinical Microbiology 32:2031–2034
    [Google Scholar]
  2. Andonov A., Chaudhary R. K. 1995; Subtyping of hepatitis C virus isolates by a line probe assay using hybridization. Journal of Clinical Microbiology 33:254–256
    [Google Scholar]
  3. Besnard N. C., Andre P. M. 1994; Automated quantitative determination of hepatitis C virus viremia by reverse transcription PCR. Journal of Clinical Microbiology 32:1887–1893
    [Google Scholar]
  4. Bhattacherjee V., Prescott L. E., Pike I., Rodgers B., Bell H., El-zayadi A. R., Kew M. C., Conradie J., Lin C. K., Marsden H., Saeed A. A., Parker D., Yap P. L., Simmonds P. 1995; Use of NS-4 peptides to identify type-specific antibody to hepatitis C virus genotypes 1, 2, 3, 4, 5 and 6. Journal of General Virology 76:1737–1748
    [Google Scholar]
  5. Brown E. A., Zhang H., Ping H.-L., Lemon S. M. 1992; Secondary structure of the 5′ nontranslated region of hepatitis C virus and pestivirus genomic RNAs. Nucleic Acids Research 20:5041–5045
    [Google Scholar]
  6. Bukh J., Purcell R. H., Miller R. H. 1992a; Sequence analysis of the 5′ noncoding region of hepatitis C virus. Proceedings of the National Academy of Sciences, USA 89:4942–4946
    [Google Scholar]
  7. Bukh J., Purcell R. H., Miller R. H. 19926; Importance of primer selection for the detection of hepatitis C virus RNA with the polymerase chain reaction assay. Proceedings of the National Academy of Sciences, USA 89:187–191
    [Google Scholar]
  8. Bukh J., Purcell R. H., Miller R. H. 1993; At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative El gene of isolates collected worldwide. Proceedings of the National Academy of Sciences, USA 90:8234–8238
    [Google Scholar]
  9. Bukh J., Purcell R. H., Miller R. H. 1994; Sequence analysis of the core gene of 14 hepatitis c virus genotypes. Proceedings of the National Academy of Sciences, USA 91:8239–8243
    [Google Scholar]
  10. Castillo I., Bartolome J., Quiroga J. A., Carreno V. 1992; Comparison of several PCR procedures for detection of serum HCV-RNA using different regions of the HCV genome. Journal of Virological Methods 38:71–79
    [Google Scholar]
  11. Chan S. W., Mcomish F., Holmes E. C., Dow B., Peutherer J. F., Follett E., Yap P. L., Simmonds P. 1992; Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants. Journal of General Virology 73:1131–1141
    [Google Scholar]
  12. Chaudhary R. K., Andonov A., Maclean C. 1993; Detection of hepatitis C virus infection with recombinant immunoblot assay, synthetic immunoblot assay, and polymerase chain reaction. Journal of Clinical Laboratory Analysis 7:164–167
    [Google Scholar]
  13. Chayama K., Tsubota A., Arase Y., Saitoh S., Koida I., Ikeda K., Matsumoto T., Kobayashi M., Iwasaki S., Koyama S., Morinaga T., Kumada H. 1993; Genotypic subtyping of hepatitis C virus. Journal of Gastroenterological Hepatology 8:150–156
    [Google Scholar]
  14. Cuypers H. T. M., Bresters D., Winkel I. N., Reesink H. W., Weiner A. J., Houghton M., van der Poel C. L., Leslie P. N. 1992; Storage conditions of blood samples and primer selection affect the yield of cDNA polymerase chain reaction products of hepatitis C virus. Journal of Clinical Microbiology 30:3220–3224
    [Google Scholar]
  15. Davidson F., Simmonds P., Ferguson J. C., Jarvis L. M., Dow B. C., Follett E. A. C., Seed C. R. G., Krusius T., Lin C., Medgyesi G. A., Kiyokawa H., Olim G., Duraisamy G., Cuypers T., Saeed A. A., Teo D., Conradie J., Kew M. C., Lin M., Nuchaprayoon C., Ndimbie O. K., Yap P. L. 1995; Survey of major genotypes and subtypes of hepatitis C virus using RFLP of sequences amplified from the 5′ non-coding region. Journal of General Virology 76:1197–1204
    [Google Scholar]
  16. Davis G. L., Lau J. Y. N., Urdea M. S., Neuwald P. D., Wilber J. C., Lindsay K., Perrillo R. P., Albrecht J. 1994; Quantitative detection of hepatitis C virus RNA with a solid-phase signal amplification method: definition of optimal conditions for specimen collection and clinical application in interferon-treated patients. Hepatology 19:1337–1341
    [Google Scholar]
  17. Dusheiko G. M., Simmonds P. 1994; Sequence variability of hepatitis C virus and its clinical relevance. Journal of Viral Hepatitis 1:1–13
    [Google Scholar]
  18. Fukushi S., Katayama K., Kurihara C., Ishiyama N., Hoshino F. B., Ando T., Oya A. 1994; Complete 5′ non-coding region is necessary for the efficient internal initiation of hepatitis C virusRNA. Biochemical and Biophysical Research Communications 199:425–432
    [Google Scholar]
  19. Garson J. A., Brillanti S., Ring C., Perini P., Miglioli M., Barbara L. 1992; Hepatitis-c viraemia rebound after successful interferon therapy in patients with chronic non-a, non-b-hepatitis. Journal of Medical Virology 37:210–214
    [Google Scholar]
  20. Gil B., Qian C., Riezuboj J. I., Civeira M. P., Prieto J. 1993; Hepatic and extrahepatic HCV RNA strands in chronic hepatitis C – different patterns of response to interferon treatment. Hepatology 18:1050–1054
    [Google Scholar]
  21. Giuberti T., Marin M. G., Ferrari C., Marchelli S., Schianchi C., Antoni A. M. D., Pizzocolo G., Fiaccadori F. 1994; Hepatitis C virus viremia following clinical resolution of acute hepatitis C. Journal of Hepatology 20:666–671
    [Google Scholar]
  22. Gretch D., Corey L., Wilson J., Delarosa C., Willson R., Carithers R., Busch M., Hart J., Sayers R., Han J. 1994; Assessment of hepatitis C virus RNA levels by quantitative competitive RNA polymerase chain reaction: high-titer viremia correlates with advanced stage of disease. Journal of Infectious Diseases 169:1219–1225
    [Google Scholar]
  23. Gunji T., Kato N., Mori S., Ootsuyama Y., Hijikata M., Imawari M., Shimotohno K. 1992; Correlation between the serum level of hepatitis c virus RNA and disease activities in acute and chronic hepatitis C. International Journal of Cancer 52:726–730
    [Google Scholar]
  24. Hagiwara H., Hayashi N., Mita E., Takehara T., Kasahara A., Fusamoto H., Kamada T. 1993; Quantitative analysis of hepatitis C virus RNA in serum during interferon alfa therapy. Gastroenterology 104:877–883
    [Google Scholar]
  25. Honda M., Kaneko S., Unoura M., Kobayashi K., Murakami S. 1993; Sequence analysis of putative structural regions of hepatitis C virus isolated from 5 japanese patients with hepatocellular carcinoma. Archives of Virology 128:163–169
    [Google Scholar]
  26. Jarvis L. M., Watson H. G., Mcomish F., Peutherer J. F., Ludlam C. A., Simmonds P. 1994; HCV genotype variation in haemophiliacs. Journal of Infectious Diseases 170:1018–1022
    [Google Scholar]
  27. Kato N., Ootsuyama Y., Tanaka T., Nakagawa M., Nakazawa T., Muraiso K., Ohkoshi S., Hijikata M., Shimotohno K. 1992; Marked sequence diversity in the putative envelope proteins of hepatitis C viruses. Virus Research 22:107–123
    [Google Scholar]
  28. Kato N., Yokosuka O., Hosoda K., Ito Y., Ohto M., Omata M. 1993; Quantification of hepatitis C virus by competitive reverse transcription polymerase chain reaction – increase of the virus in advanced liver disease. Hepatology 18:16–20
    [Google Scholar]
  29. Kleter G. E. M., Van doorn L. J., Brouwer J. T., Schalm S. W., Heijtink R. A., Quint W. G. V. 1994; Sequence analysis of the 5′ untranslated region in isolates of at least four genotypes of hepatitis C virus in the Netherlands. Journal of Clinical Microbiology 33:306–310
    [Google Scholar]
  30. Kobayashi Y., Watanabe S., Konishi M., Yokoi M., Kakehashi R., Kaito M., Kondo M., Hayashi Y., Jomori T., Suzuki S. 1992; Quantitation and typing of serum hepatitis C virus RNA in patients with chronic hepatitis C treated with interferon-beta. Hepatology 18:1319–1325
    [Google Scholar]
  31. Lau J. Y. N., Mizokami M., Kolberg J. A., Davis G. L., Prescott L. E., Ohno T., Perrillo R. P., Lindsay K. L., Gish R. G., Qian K.-P., Kohara M., Simmonds P., Urdea M. S. 1995; Application of hepatitis C virus genotyping systems in United States patients with chronic hepatitis C. Journal of Infectious Diseases 171:281–289
    [Google Scholar]
  32. Mcomish F., Chan S.-W., Dow B. C., Gillon J., Frame W. D., Crawford R. J., Yap P. L., Follett E. A. C., Simmonds P. 1993; Detection of three types of hepatitis C virus in blood donors: Investigation of type-specific differences in serological reactivity and rate of alanine aminotransferase abnormalities. Transfusion 33:7–13
    [Google Scholar]
  33. Mcomish F., Yap P. L., Dow B. C., Follett E. A. C., Seed C., Keller A. J., Cobain T. J., Krusius T., Kolho E., Naukkarinen R., Lin C., Lai C., Leong S., Medgyesi G. A., Hejjas M., Kiyokawa H., Fukada K., Cuypers T., Saeed A. A., Alrasheed A. M., Lin M., Simmonds P. 1994; Geographical distribution of hepatitis C virus genotypes in blood donors – an international collaborative survey. Journal of Clinical Microbiology 32:884–892
    [Google Scholar]
  34. Murphy D. G., Willems B., Villeneuve J.-P., Delage G. 1994; Sequence analysis of the 5′ noncoding region reveals the existence of multiple hepatitis C virus genotypes in Quebec, Canada. In Viral Hepatitis and Liver Disease pp 296–300 Edited by Nishioka K., Suzuki H., Mishiro S., Oda T. Tokyo: Springer–Verlag;
    [Google Scholar]
  35. Okamoto H., Okada S., Sugiyama Y., Tanaka T., Sugai Y., Akahane Y., Machida A., Mishiro S., Yoshizawa H., Miyakawa Y., Mayumi M. 1990; Detection of hepatitis C virus RNA by a two-stage polymerase chain reaction with two pairs of primers deduced from the 5′-noncoding region. Japanese Journal of Experimental Medicine 60:215–222
    [Google Scholar]
  36. Okamoto H., Sugiyama Y., Okada S., Kurai K., Akahane Y., Sugai Y., Tanaka T., Sato K., Tsuda F., Miyakawa Y., Mayumi M. 1992; Typing hepatitis C virus by polymerase chain reaction with type-specific primers: application to clinical surveys and tracing infectious sources. Journal of General Virology 73:673–679
    [Google Scholar]
  37. Okamoto H., Tokita H., Sakamoto M., Horikita M., Kojima M., Iizuka H., Mishiro S. 1993; Characterization of the genomic sequence of type V (or 3a). hepatitis C virus isolates and PCR primers for specific detection. Journal of General Virology 74:2385–2390
    [Google Scholar]
  38. Okamoto H., Kojima M., Sakamoto M., Iizuka H., Hadiwandowo S., Suwignyo S., Miyakawa Y., Mayumi M. 1992; The entire nucleotide sequence and classification of a hepatitis C virus isolate of a novel genotype from an Indonesian patient with chronic liver disease. Journal of General Virology 75:629–635
    [Google Scholar]
  39. Shindo M., Di bisceglie A. M., Cheung L., Shih J. W.-K., Cristiano K., Feinstone S. M., Hoofnagle J. H. 1991; Decrease in serum hepatitis C viral RNA during alpha-interferon therapy for chronic hepatitis C. Annals of Internal Medicine 115:700–704
    [Google Scholar]
  40. Simmonds P., Holmes E. C., Cha T. A., Chan S.-W., Mcomish F., Irvine B., Beall E., Yap P. L., Kolberg J., Urdea M. S. 1993a; Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. Journal of General Virology 74:2391–2399
    [Google Scholar]
  41. Simmonds P., Mcomish F., Yap P. L., Chan S. W., Lin C. K., Dusheiko G., Saeed A. A., Holmes E. C. 1993b; Sequence variability in the 5′ non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity. Journal of General Virology 74:661–668
    [Google Scholar]
  42. Simmonds P., Rose K. A., Graham S., Chan S. W., Mcomish F., Dow B. C., Follett E. A. C., Yap P. L., Marsden H. 1993c; Mapping of serotype-specific, immunodominant epitopes in the NS-4region of hepatitis C virus (HCV) – use of type-specific peptides to serologically differentiate infections with HCV type 1, type 2, and type 3. Journal of Clinical Microbiology 31:1493–1503
    [Google Scholar]
  43. Simmonds P., Alberti A., Alter H. J., Bonino F., Bradley D. W., Brechot C., Rouwer J. T., Chan S. W., Chayama K., Chen D. S., Choo Q. L., Colombo M., Cuypers H. T. M., Date T., Dusheiko G. M., Esteban J. I., Fay O., Hadziyannis S. J., Han J., Hatzakis A., Holmes E. C., Hotta H., Houghton M., Irvine B., Kohara M., Kolberg J. A., Kuo G., Lau J. Y. N., Lelie P. N., Maertens G., Mcomish F., Miyamura T., Mizokami M., Nomoto A., Prince A. M., Reesink H. W., Rice C., Roggendorf M., Schalm S. W., Shikata T., Shimotohno K., Stuyver L., Trepo C., Weiner A., Yap P. L., Urdea M. S. 1994a; A proposed system for the nomenclature of hepatitis C viral genotypes. Hepatology 19:1321–1324
    [Google Scholar]
  44. Simmonds P., Smith D. B., Mcomish F., Yap P. L., Kolberg J., Urdea M. S., Holmes E. C. 1994b; Identification of genotypes of hepatitis C virus by sequence comparisons in the core, El and NS–4regions. Journal of General Virology 75:1053–1061
    [Google Scholar]
  45. Stuyver L., Rossau R., Wyseur A., Duhamel M., Vanderborght B., Van Heuverswyn H., Maertens G. 1993; Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. Journal of General Virology 74:1093–1102
    [Google Scholar]
  46. Stuyver L., Vanarnhem W., Wyseur A., Hernandez F., Delaporte E., Maertens G. 1994; Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and nonstructural 5b regions and identification of five additional subtypes. Proceedings of the National Academy of Sciences, USA 91:10134–10138
    [Google Scholar]
  47. Takamizawa A., Mori C., Fuke I., Manabe S., Murakami S., Fujita J., Onishi E., Andoh T., Yosiiida I., Okayama H. 1991; Structure and organization of the hepatitis C virus genome isolated from human carriers. Journal of Virology 65:1105–1113
    [Google Scholar]
  48. Tokita H., Okamoto H., Tsuda F., Song P., Nakata S., Chosa T., Iizuka FI., Mishiro S., Miyakawa Y., Mayumi M. 1994a; Flepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proceedings of the National Academy of Sciences, USA 91:11022–11026
    [Google Scholar]
  49. Tokita H., Shrestha S. M., Okamoto H., Sakamoto M., Hirokita M., Iizuka H., Shrestha S., Miyakawa Y., Mayumi M. 1994b; Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group. Journal of General Virology 75:931–936
    [Google Scholar]
  50. Tsukiyama Kohara K., Iizuka N., Kohara M., Nomoto A. 1991; Internal ribosome entry site within hepatitis C virus RNA. Journal of Virology 66:1476–1483
    [Google Scholar]
  51. Tsukiyama Kohara K., Yamaguchi K., Maki N., Ohta Y., Miki K., Mizokami M., Ohba K., Tanaka S., Hattori N., Nomoto A., Kohara M. 1993; Antigenicities of group I and group II hepatitis C virus polypeptides – molecular basis of diagnosis. Virology 192:430–437
    [Google Scholar]
  52. Van Doorn L. J. 1994 In Detection and Characterization of the Hepatitis C Virus Rotterdam: Erasmus University;
    [Google Scholar]
  53. Van Doorn L. J., Kleter B., Stuyver L., Maertens G., Brouwer H., Schalm S., Heijtink R., Quint W. 1994; Analysis of hepatitis C virus genotypes by a line probe assay and correlation with antibody profiles. Journal of Hepatology 21:122–129
    [Google Scholar]
  54. Wakita T., Wands J. R. 1994; Specific inhibition of hepatitis C virus expression by antisense oligodeoxynucleotides – in vitro model for selection of target sequence. Journal of Biological Chemistry 269:14205–14210
    [Google Scholar]
  55. Wang C. Y., Sarnow P., Siddiqui A. 1993; Translation of human hepatitis C virus RNA in cultured cells is mediated by an internal ribosome-binding mechanism. Journal of Virology 67:3338–3344
    [Google Scholar]
  56. Wang C. Y., Sarnow P., Siddiqui A. 1994; A conserved helical element is essential for internal initiation of translation of hepatitis C virus RNA. Journal of Virology 68:7301–7307
    [Google Scholar]
  57. Xu L. Z., Martinotpeignoux M., Marcellin P., Benhamou J. P., Larzul D. 1994; Comparison of the sensitivity of nested PCR in the 5′ non-coding and the NS5 regions of the HCV genome. Journal of Hepatology 20:598–602
    [Google Scholar]
  58. Young K. K. Y., Resnick R. M., Myers T. W. 1993; Detection of hepatitis C virus RNA by a combined reverse transcription polymerase chain reaction assay. Journal of Clinical Microbiology 31:882–886
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-76-7-1749
Loading
/content/journal/jgv/10.1099/0022-1317-76-7-1749
Loading

Data & Media loading...

Most cited Most Cited RSS feed