Comparative rates of nucleotide sequence variation in the hypervariable region of E1/E2 and the NS5b region of hepatitis C virus in patients with a spectrum of liver disease resulting from a common source of infection

Virology

Volumn 301, Issue 2, 2002, Pages 354-364

  Duffy, Margaret ^a   Salemi, Marco ^b   Sheehy, Noreen ^a   Vandamme, Anne Mieke ^b   Hegarty, John ^c   Curry, Michael ^c   Nolan, Niamh ^c   Kelleher, Dermot ^d   McKiernan, Susan ^d   Hall, William W ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^c ST VINCENT S UNIVERSITY HOSPITAL   (Ireland)

^d ST JAMES S HOSPITAL   (Ireland)

Author keywords

Anti D; Evolution; Hepatitis C virus; HVR1; Phylogenetic; Quasispecies; Variability

Indexed keywords

IMMUNOGLOBULIN;

ARTICLE; COHORT ANALYSIS; CONTROLLED STUDY; DISEASE COURSE; DISEASE SEVERITY; EVOLUTION; FEMALE; GENDER; HEPATITIS; HEPATITIS C VIRUS; HUMAN; LIVER CIRRHOSIS; LIVER DISEASE; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; VIRUS GENOME;

HEPATITIS C VIRUS;

EID: 0036402567     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1006/viro.2002.1597     Document Type: Article

References (45)

1. Abe, K., Inchauspe, G., and Fujisawa, K. (1995). Genomic characterization and mutation rate of hepatitis C virus isolated from a patient who contracted hepatitis during an epidemic of non-A, non-B hepatitis in Japan. J. Gen. Virol. 73, 2725-2729.
2. Allain, J. P., Dong, Y., Vandamme, A.-M., Moultan, V., and Salemi, M. (2000). Evolutionary rate and genetic drift of hepatitis C virus are not correlated with the host immune response: Studies of infected donor-recipient clusters. J. Virol. 74, 2541-2549.
3. Barrett, S., Ryan, E., and Crowe, J. (1999). Association of the HLA-DBR1*01 allele with spontaneous viral clearance in an Irish cohort infected with hepatitis C virus via contaminated anti-D immunoglobulin. J. Hepat. 30, 973-983.
4. Booth, J. C. L., Kumar, U., Webster, D., Monjardino, J., and Thomas, H. C. (1998). Comparison of the rate of sequence variation in the hyper-variable region of the E2/NS1 region of hepatitis C virus in normal and hpyogammaglobulinemic patients. Hepatitis 27, 223-227.
5. Bukh, J., Purcell, R. H., and Miller, R. H. (1993). At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative E1 gene of isolates collected worldwide. Proc. Natl. Acad. Sci. USA 90, 8234-8238.
6. Choo, Q. L., Richman, K. H., Han, J. H., Berger, K., Lee, C., Dong, C., Gallegoe, C., Coit, D., Medina-Selby, R., and Barr, P. J. (1991). Genetic organisation and diversity of the hepatitis C virus. Proc. Natl. Acad. Sci. 88, 2451-2455.
7. Christie, J. M., Chapel, H., Chapman, R. W., and Rosenberg, W. M. (1999). Immune selection and genetic sequence variation in core and envelope regions of hepatitis C virus. Hepatitis 30, 1037-1044.
8. Cramp, M. E., Carucci, P., Underhill, J., Naoumov, N. V., Williams, R., and Donaldson, P. T. (1998). Association between HLA class II genotype and spontaneous clearance of hepatitis C viraemia. J. Hepat. 29, 207-213.
9. Curran, R., Jameson, C. L., Craggs, J. K., Grabowska, A. M., Thomson, B. J., Robins, A., Irving, W. L., and Ball, J. K. (2002). Evolutionary trends of the first hypervariable region of the hepatitis C virus E2 protein in individuals with differing liver disease severity. J. Virol. 83, 11-23.
10. Desmet, V. J., Gerber, M., Hoofnagle, J. H., Manns, M., and Scheuer, P. J. (1994). Classification of chronic hepatitis: Diagnostic, grading and staging. Hepatology 19, 1513-1520.
11. Enomoto, N., Sakuma, I., Asahina, Y., Kurosaki, M., Murakami, T., Yamamoto, C., Izumi, N., Marumo, F., and Sato, C. (1995). Comparison of full-length sequences of interferon-sensitive and resistant hepatitis C virus 1b: Sensitivity to interferon is conferred by amino acid substitutions in the NS5A region. J. Clin. Invest. 96, 224-230.
12. Fanning, L. J., Levis, J., Kenny-Walshe, E., Whelton, M., O'Sullivan, K., and Shanahan, F. (2001). HLA class II genes determine the natural variance of hepatitis C viral load. Hepatology 33, 224-230.
13. Fanning, L. J., Levis, J., Kenny-Walshe, E., Wynne, F., Whelton, M., and Shanahan,. F. (2000). Viral clearance in hepatitis C (1b) infection: Relationship with human leukocyte antigen class II in a homogeneous population. Hepatology 31, 1334-1337.
14. Farci, F., Shimoda, A., Colans, A., Diaz, G., Peddis, G., Melpolder, J., Strazzera, A., Chien, D., Munoz, S., Balestrieri, A., Purcell, R., and Alter, H. (2000). The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. Science 288, 339-344.
15. Forns, X., Thimme, R., Govindarajan, S., Emerson, S. U., Purcell, R. H., Chisari, F. V., and Bukh, J. (2000). Hepatitis C virus lacking the hypervariable region 1 of the second envelope protein is infectious and causes acute resolving or persistent infection in chimpanzees. Proc. Natl. Acad. Sci. USA 97, 13318-13323.
16. Gonzalez-Peralta, R. P., Qian, K., She, J. Y., Davis, G. L., Ohno, T., Mizokami, M., and Lau, J. Y. (1996). Clinical implications of viral quasispecies heterogeneity in chronic hepatitis C. J. Med. Virol. 49, 242-247.
17. Higashi, Y., Kakumu, S., Yoshioka, K., Wakita, T., Mizokami, M., Ohba, K., Ito, Y., Ishikawa, T., Takayanagi, M., and Nagai, Y. (1993). Dynamics of genome change in the E2/NS1 region of hepatitis C virus in vivo. Virology 197, 659-668.
18. Honda, M., Kaneko, S., Sakai, A., Unoura, M., Murakami, S., and Kobayashi, K. (1994). Degree of diversity of hepatitis C virus quasispecies and progression of liver disease. Hepatology 20, 1144-1151.
19. Kato, N., Ootsuyama, Y., Ohkoshi, S., Nakazawa, T., Seikiya, H., Hijikata, M., and Shimotohno, K. (1992). Characterisation of hypervariable regions in the putative envelope protein of hepatitis C virus. Biochem. Biophys. Res. Commun. 189, 119-127.
20. Kato, N., Seikiya, H., Ootsuyama, Y., Nakazawa, T., Hijikata, M., Ohkoshi, S., and Shimotohno, K. (1993). Humoral immune response to hyper-variable region 1 of the putative envelope glycoprotein (gp70) of hepatitis C virus. J. Virol. 67, 3923-3930.
21. Kenny-Walshe, E. (1999). Clinical outcomes after hepatitis C infection from contaminated anti-D immune globulin. Irish Hepatology Research Group. N. Engl. J. Med. 340, 1228-1233.
22. Knodell, R. G., Ishak, K. G., Black, W. C., Chen, T. S., Craig, R., Kaplowitz, N., Kiernan, T. W., and Wollman, J. (1981). Formation and application of a numerical scoring system for assessing histological activity in asymptomic chronic active hepatitis. Hepatology 1, 431-435.
23. Koizumi., K, Enomoto, N., Kuroski, M., Murakami, T., Izumi, N., Marumo, F., and Sato, C. (1995). Diversity of quasispecies in various disease stages of chronic hepatitis C virus infection and its significance in interferon treatment. Hepatology 22, 30-35.
24. Korber, B., and Myers, G. (1992). Signature pattern analysis: A method for assessing viral sequence relatedness. AIDS Res. Hum. Retroviruses 8, 1549-1560.
25. Maddison, W. P., and Maddison, D. R. (1992). Interactive analysis of phylogeny and character evolution using the computer program MacClade. Folia Primatol. 53, 190-202.
26. McAllister, J., Casino, C., Davidson, F., Power, J., Lawler, E., Yap, P. L., Simmonds, P., and Smith, D. B. (1998). Long term evolution of the hypervariable region of hepatitis C virus in a common-source-infected cohort. J. Virol. 76, 4893-4905.
27. McKiernan, S. H., Hagen, R., Curry, M., McDonald, G. S., Nolan, N., Crowley, J., Hegarty, J., and Lawlor, E., Kelleher, D. (2000). The MHC is a major determinant of viral status, but not fibrotic stage, in individuals infected with hepatitis C. Gastroenterology 118, 1124-1130.
28. Minton, E. J., Smillie, D., Neal, K. R., Irving, W. L., Underwood, J. C., and James, W. (1998). Association between MHC class II alleles and clearance of circulating hepatitis C virus. J. Infect. Dis. 179, 1309-1310.
29. Naito, M., Hayashi, N., Moribe, T., Hagiwara, H., Mita, E., Kanazawa, Y., Kashara, A., et al. (1995). Hepatitis C viral quasispecies in hepatitis C virus carriers with normal liver enzymes and patients with type C chronic liver disease. Hepatology 22, 407-412.
30. Okamoto, H., Kojima, M., Okada, S., Yoshizawa, H., Iizuka, H., Tanaka, T., Muchnore, E. E., Peterson, D. A., Ito, Y., and Mishiro, S. (1992). Genetic drift of hepatitis C virus during an 8.2 year infection in a chimpanzee: Variability and stability. Virology 190, 894-899.
31. Penin, F., Combet, C., Germanidis, G., Frainais, P. O., Deleage, G., and Pawlotsky J. M. (2001). Conservation of the conformation and positive charges of hepatitis C virus E2 envelope glycoprotein hypervariable region 1 points to a role in cell attachment. J. Virol. 75, 5703-5710.
32. Power, J. P., Lawlor, E., Davidson, F., Holmes, E. C., Yap, P. L, and Simmonds, O. (1995). Molecular epidemiology of an outbreak of infection with hepatitis C virus in recipients of anti-D immunoglobulin. Lancet 345, 1211-1213.
33. Puntoriero, G., Meola, A., Lahm, A., Zucchelli, S., Ercole, B. B., Tafi, R., Pezzanera, M., Mondelli, M. U., Cortese, R., Tramontano, A., Galfre, G., and Nicosia, A. (1998). Towards a solution for hepatitis C virus hypervariability: Mimotopes of the hypervariable region 1 can induce antibodies cross-reacting with a large number of viral variants. EMBO J. 17, 3521-3533.
34. Ray, S. C., Wang, Y. M., Laeyendecker, O., Tichehurst, J. R., Villano, S. A., and Thomas, D. L (1999). Acute hepatitis C virus structural gene sequences as predictors of persistent viremia: Hypervariable region 1 as a decoy. J. Virol. 73, 2938-2946.
35. Salemi, M., Strimmer, K., Hall, W. W., Duffy, M., Delaporte, E., Mboup, S., Peeters, M.,. and Vandamme, A.-M. (2001). Dating the common ancestor of SIVcpz and HIV-1 group M and the origin of HIV-1 subtypes using a new method to uncover clock-like molecular evolution. FASEB J. 15, 276-278.
36. Salemi, M., and Vandamme, A.-M. (2002). Hepatitis C virus evolutionary patterns studied through analysis of full genome sequences. J. Mol. Evol. 54, 62-70.
37. Sobolev, B. N., Poroikov, V. V., Olenina, L. V., Kolesanova, E. F., and Archakov, A. I. (2000). Comparative analysis of amino acid sequences from envelope proteins isolated from different hepatitis C virus variants: Possible role of conservative and variable regions. J. Viral Hepat. 7, 368-374.
38. Strimmer, K., and Von Haeseler, A. (1997). Likelihood mapping: A method to visualise phylogenetic content of a sequence alignment. Proc. Natl. Acad. Sci. USA 94, 6815-6819.
39. Tanaka, T., Kato, N., Nakagawa, M., Ootsuyama, Y., Cho, M. J., Naka-zawa, T., Hijikata, M., Ishimura, Y., and Shimotohno, K. (1992). Molecular cloning of hepatitis C virus genome from a single Japanese carrier: Sequence variation within the same individual and among infected individuals. Virus Res. 23, 39-53.
40. Taniguchi, S., Okamoto, H., Sakamoto, M., Kojima, M., Tsuda, F., Tanaka, T., Munekata, E., Muchmore, E. E., Peterson, D. A., and Mishiro S. (1993). A structurally flexible and antigenically variable N-terminal domain of the hepatitis C virus E2/NS1 protein: Implication for an escape from antibody. Virology 195, 297-301.
41. Thio, C. L., Thomas, D. L, Goedert, J. L., Vlahov, D., Nelson, K. E., Hilgartner, M. W., O'Brien, S. J., Karacki, P., Marti, D., Astemborski, J., and Carrington, M. J. (2001). Racial differences in HLA class II associations with hepatitis C virus outcome. J. Infect. Dis. 184, 16-21.
42. Van Doorn, L. J., Capriles, I., Maertens, G., Deleys, R., Murray, K., Kos, T., Schellehens H., and Quint S. (1995). Sequence evolution of the hypervariable region in the putative envelope region E2/NS1 of hepatitis C virus is correlated with specific humoral immune responses. J. Virol. 69, 773-778.
43. Vejbaesya, S., Songsivilai, S., Tanwandee, T., Rachaibun, S., Chantangpol, R., and Dharakul, T. (2000). HLA association with hepatitis C infection. Hum. Immunol. 61, 348-353.
44. Weiner, A. J., Brauer, M. J., Rosenblatt, J., Richman, K. H., Tung, J., Crawford, K., Bonino, F., Saracco Gchoo, Q. L., and Houghton, M. (1991). Variable and hypervariable domains are found in the region of HCV corresponding to the flavivirus envelope and NS1 proteins and the pestivirus envelope glycoproteins. Virology 180, 842-848.
45. Weiner, A. J., Geysen, H. M., Christopherson, C., Hall, J. E., Mason, T. J., Saracco, G., Bonino, F., Crawford, K., Marion, C. D., and Crawford, K. A. (1992). Evidence for immune selection of hepatitis C virus (HCV) putative envelope glycoprotein variants: Potential role in chronic HCV infections. Proc. Natl. Acad. Sci. USA 89, 3468-3472.