Acute hepatitis C virus structural gene sequences as predictors of persistent viremia: Hypervariable region 1 as a decoy

Journal of Virology

Volumn 73, Issue 4, 1999, Pages 2938-2946

  Ray, Stuart C ^a   Wang, Yu Ming ^c   Laeyendecker, Oliver ^a   Ticehurst, John R ^a,b   Villano, Stephen A ^a   Thomas, David L ^a,d  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^c THIRD MILITARY MEDICAL UNIVERSITY   (China)

^d Division of Infectious Diseases   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE;

ADULT; AMINO ACID SEQUENCE; ANTIBODY TITER; ARTICLE; CONTROLLED STUDY; ENVELOPE GENE; FEMALE; GENE MUTATION; GENE SEQUENCE; GLYCOSYLATION; HEPATITIS C VIRUS; HUMAN; IMMUNOREGULATION; MAJOR CLINICAL STUDY; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PERSISTENT VIRUS INFECTION; PRIORITY JOURNAL; RNA STRUCTURE; RNA TRANSLATION; VIREMIA; VIRUS CHARACTERIZATION; VIRUS GENOME; VIRUS REPLICATION;

EID: 0032976214     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.73.4.2938-2946.1999     Document Type: Article

References (61)

1. Abe, K., G. Inchauspe, and K. Fujisawa. 1992. 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. Alter, M. J., H. S. Margolis, K. Krawczynski, F. N. Judson, A. Mares, W. J. Alexander, P. Y. Hu, J. K. Miller, M. A. Gerber, R. E. Sampliner, E. Meeks, and M. J. Beach. 1992. The natural history of community acquired hepatitis C in the United States. N. Engl. J. Med. 327:1899-1905.
3. Anonymous. 1997. Hepatitis C: global prevalence. Weekly Epidemiol. Rec. 72:341-348.
4. Bassett, S. E., K. M. Brasky, and R. E. Lanford. 1998. Analysis of hepatitis C virus-inoculated chimpanzees reveals unexpected clinical profiles. J. Virol. 72:2589-2599.
5. Bassett, S. E., D. L. Thomas, K. M. Brasky, and R. E. Lanford. 1999. Viral persistence, antibody to E1 and E2, and hypervariable region 1 sequence stability in hepatitis C virus-inoculated chimpanzees. J. Virol. 73:1118-1126.
6. Bonhoeffer, S., E. C. Holmes, and M. A. Nowak. 1995. Causes of HIV diversity. Nature 376:125.
7. Bradley, D. W., K. Krawczynski, J. W. Ebert, K. A. McCaustland, Q. L. Choo, M. A. Houghton, and G. Kuo. 1990. Parenterally transmitted non-A, non-B hepatitis: virus-specific antibody response patterns in hepatitis C virus-infected chimpanzees. Gastroenterology 99: 1054-1060.
8. Bukh, J., R. H. Purcell, and R. H. Miller. 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.
9. Bukh, J., M. Yanagi, S. U. Emerson, and R. H. Purcell. 1998. Course of infection and evolution of monoclonal hepatitis C virus (HCV) in chimpanzees transfected with a cDNA clone of genotype 1a, abstr. 131. Presented at the Fifth International Meeting on Hepatitis C Virus and Related Viruses: Molecular Virology and Pathogenesis, 25-28 June 1998, Venice, Italy.
10. Cao, J., N. Sullivan, E. Desjardin, C. Parolin, J. Robinson, R. Wyatt, and J. Sodroski. 1997. Replication and neutralization of human immunodeficiency virus type 1 lacking the V1 and V2 variable loops of the gp120 envelope glycoprotein. J. Virol. 71:9808-9812.
11. Reference deleted.
12. Choo, Q. L., K. H. Richman, J. H. Han, K. Berger, C. Lee, C. Dong, C. Gallegos, D. Coit, A. Medina-Selby, P. J. Barr, A. J. Weiner, D. W. Bradley, G. Kuo, and M. Houghton. 1991. Genetic organization and diversity of the hepatitis C virus. Proc. Natl. Acad. Sci. USA 88:2451-2455.
13. Farci, P., A. Shimoda, D. Wong, T. Cabezon, D. De Gioannis, A. Strazzera, Y. Shimizu, M. Shapiro, H. J. Alter, and R. H. Purcell. 1996. Prevention of hepatitis C virus infection in chimpanzees by hyperimmune serum against the hypervariable region 1 of the envelope 2 protein. Proc. Natl. Acad. Sci. USA 93:15394-15399.
14. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
15. Felsenstein, J. 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164-166.
16. Garfein, R. S., M. C. Doherty, D. Brown, D. L. Thomas, S. A. Villano, E. Monterroso, and D. Vlahov. 1998. Hepatitis C virus infection among short-term injection drug users. J. Acquired Immune Defic. Syndr. 18:S11-S19.
17. Gretch, D., L. Corey, J. Wilson, C. Dela Rosa, R. Willson, R. Carithers, M. Busch, J. Hart, M. Sayers, and J. Han. 1994. Assessment of hepatitis C virus RNA levels by quantitative competitive RNA polymerase chain reaction: high titer viremia correlates with advanced stage of disease. J. Infect. Dis. 169:1219-1225.
18. Hadziyannis, E., M. W. Fried, and F. S. Nolte. 1997. Evaluation of two methods for quantitation of hepatitis C virus RNA. Mol. Diagn. 2:39-46.
19. Hoffman, T. L., E. B. Stephens, O. Narayan, and R. W. Doms. 1998. HIV type I envelope determinants for use of the CCR2b, CCR3, STRL33, and APJ coreceptors. Proc. Natl. Acad. Sci. USA 95:11360-11365.
20. Jukes, T. H., and T. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York, N. Y.
21. Kao, J.-H., P.-J. Chen, M.-Y. Lai, T.-H. Wang, and D.-S. Chen. 1995. Quasispecies of hepatitis C virus and genetic drift of the hypervariable region in chronic type C hepatitis. J. Infect. Dis. 172:261-264.
22. Kato, N., Y. Ootsuyama, H. Sekiya, S. Ohkoshi, T. Nakazawa, M. Hijikata, and K. Shimotohno. 1994. Genetic drift in hypervariable region 1 of the viral genome in persistent hepatitis C virus infection. J. Virol. 68:4776-4784.
23. Kato, N., Y. Ootsuyama, T. Tanaka, M. Nakagawa, T. Nakazawa, K. Muraiso, S. Ohkoshi, M. Hijikata, and K. Shimotohno. 1992. Marked sequence diversity in the putative envelope proteins of hepatitis C viruses. Virus Res. 22:107-123.
24. Kiyosawa, K., T. Sodeyama, E. Tanaka, Y. Gibo, K. Yoshizawa, Y. Nakano, S. Furuta, Y. Akahane, K. Nishioka, and R. H. Purcell. 1990. Interrelationship of blood transfusion, non-A, non-B hepatitis and hepatocellular carcinoma: analysis by detection of antibody to hepatitis C virus. Hepatology 12:671-675.
25. Kobayashi, M., E. Tanaka, A. Matsumoto, T. Ichijo, and K. Kiyosawa. 1997. Antibody response to E2/NS1 hepatitis C virus protein in patients with acute hepatitis C. J. Gastroenterol. Hepatol. 12:73-76.
26. Korber, B., and G. Myers. 1992. Signature pattern analysis: a method for assessing viral sequence relatedness. AIDS Res. Hum. Retroviruses 8:1549-1560.
27. Kumar, U., J. Monjardino, and H. C. Thomas. 1994. Hypervariable region of hepatitis C virus envelope glycoprotein (E2/NS1) in an agammaglobulinemic patient. Gastroenterology 106:1072-1075.
28. Kurosaki, M., N. Enomoto, F. Marumo, and C. Sato. 1993. Rapid sequence variation in the hypervariable region of hepatitis C virus during the course of chronic infection. Hepatology 18:1293-1299.
29. Lau, J. Y., G. L. Davis, J. Kniffen, K. P. Qian, M. S. Urdea, C. S. Chan, M. Mizokami, P. D. Neuwald, and J. C. Wilber. 1993. Significance of serum hepatitis C virus RNA levels in chronic hepatitis C. Lancet 341:1501-1504.
30. Lechmann, M., H. G. Ihlenfeldt, I. Braunschweiger, G. Giers, G. Jung, B. Matz, R. Kaiser, T. Sauerbruch, and U. Spengler. 1996. T- and B-cell responses to different hepatitis C virus antigens in patients with chronic hepatitis C infection and in healthy anti-hepatitis C virus-positive blood donors without viremia. Hepatology 24:790-795.
31. Liu, S. L., A. G. Rodrigo, R. Shankarappa, G. H. Learn, L. Hsu, O. Davidov, L. P. Zhao, and J. I. Mullins. 1996. HIV quasispecies and resampling. Science 273:415-416.
32. Major, M. E., K. Mihalik, A. A. Kolykhalov, D. Kleiner, C. M. Rice, and S. M. Feinstone. 1998. Long term follow-up of chimpanzees inoculated with the first HCV infectious clone: immune responses, disease progression, and sequence evolution, abstr. 27. Presented at the Fifth International Meeting on Hepatitis C Virus and Related Viruses: Molecular Virology and Pathogenesis, 25-28 June 1998, Venice, Italy.
33. Manzin, A., L. Solforosi, E. Petrelli, G. Macarri, G. Tosone, M. Piazza, and M. Clementi. 1998. Evolution of hypervariable region 1 of hepatitis C virus in primary infection. J. Virol. 72:6271-6276.
34. Martell, M., J. I. Esteban, J. Quer, J. Genesca, A. Weiner, R. Esteban, J. Guardia, and J. Gomez. 1992. Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution. J. Virol. 66:3225-3229.
35. Mattsson, L., A. Sonnerborg, and O. Weiland. 1993. Outcome of acute symptomatic non-A, non-B hepatitis: a 13-year follow-up study of hepatitis C virus markers. Liver 13:274-278.
36. McAllister, J., C. Casino, F. Davidson, J. Power, E. Lawlor, P. L. Yap, P. Simmonds, and D. B. Smith. 1998. Long-term evolution of the hypervariable region of hepatitis C virus in a common-source-infected cohort. J. Virol. 72:4893-4905.
37. Missale, G., R. Bertoni, V. Lamonaca, A. Valli, M. Massari, C. Mori, M. G. Rumi, M. Houghton, F. Fiaccadori, and C. Ferrari. 1996. Different clinical behaviors of acute hepatitis C virus infection are associated with different vigor of the anti-viral cell-mediated immune response. J. Clin. Investig. 98:706-714.
38. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
39. Neumann, A. U., N. P. Lam, H. Dahari, D. R. Gretch, T. E. Wiley, T. J. Layden, and A. S. Perelson. 1998. Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy. Science 282:103-107.
40. Odeberg, J., Z. B. Yun, A. Sönnerborg, K. Bjoro, M. Uhlén, and J. Lundeberg. 1997. Variation of hepatitis C virus hypervariable region 1 in immunocompromised patients. J. Infect. Dis. 175:938-943.
41. Ogata, N., H. J. Alter, R. H. Miller, and R. H. Purcell. 1991. Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. Proc. Natl. Acad. Sci. USA 88:3392-3396.
42. Okamoto, H., M. Kojima, S. Okada, H. Yoshizawa, H. Iizuka, T. Tanaka, E. E. Muchmore, D. A. Peterson, Y. Ito, and S. Mishiro. 1992. Genetic drift of hepatitis C virus during an 8.2-year infection in a chimpanzee: variability and stability. Virology 190:894-899.
43. Pawlotsky, J. M., G. Germanidis, A. U. Neumann, M. Pellerin, P. O. Frainais, and D. Dhumeaux. 1998. Interferon resistance of hepatitis C virus genotype 1b: relationship to nonstructural 5A gene quasispecies mutations. J. Virol. 72:2795-2805.
44. Rodrigo, A. G., and J. I. Mullins. 1996. Human immunodeficiency virus type 1 molecular evolution and the measure of selection. AIDS Res. Hum. Retroviruses 12:1681-1685.
45. Roth, W. K., J. H. Lee, B. Rüster, and S. Zeuzem. 1996. Comparison of two quantitative hepatitis C virus reverse transcriptase PCR assays. J. Clin. Microbiol. 34:261-264.
46. Shankarappa, R., P. Gupta, G. H. J. Learn, A. G. Rodrigo, C. R. J. Rinaldo, M. C. Gorry, J. I. Mullins, P. L. Nara, and G. D. Ehrlich. 1998. Evolution of human immunodeficiency virus type 1 envelope sequences in infected individuals with differing disease progression profiles. Virology 241:251-259.
47. Simmonds, P., P. Balfe, C. A. Ludlam, J. O. Bishop, and A. J. Brown. 1990. Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 3. J. Virol. 64:5840-5850.
48. Smith, D. B., J. McAllister, C. Casino, and P. Simmonds. 1997. Virus 'quasispecies': making a mountain out of a molehill? J. Gen. Virol. 78:1511-1519.
49. Smith, D. B., S. Pathirana, F. Davidson, E. Lawlor, J. Power, P. L. Yap, and P. Simmonds. 1997. The origin of hepatitis C virus genotypes. J. Gen. Virol. 78:321-328.
50. Smith, D. B., and P. Simmonds. 1997. Characteristics of nucleotide substitution in the hepatitis C virus genome: constraints on sequence change in coding regions at both ends of the genome. J. Mol. Evol. 45:238-246.
51. Steinhauer, D. A., and J. J. Holland. 1987. Rapid evolution of RNA viruses. Annu. Rev. Microbiol. 41:409-433.
52. Thomas, D. L., J. Z. Zenilman, H. J. Alter, J. W. Shih, N. Galai, and T. C. Quinn. 1995. Sexual transmission of hepatitis C virus among patients attending Baltimore sexually transmitted diseases clinics - an analysis of 309 sexual partnerships. J. Infect. Dis. 171:768-775.
53. Tong, M. J., N. S. El-Farra, A. R. Reikes, and R. L. Co. 1995. Clinical outcomes after transfusion-associated hepatitis C. N. Engl. J. Med. 332: 1463-1466.
54. van Doorn, L. J., I. Capriles, G. Maertens, R. DeLeys, K. Murray, T. Kos, H. Schellekens, and W. Quint. 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.
55. Villano, S. A., D. Vlahov, K. E. Nelson, S. Cohn, and D. L. Thomas. 1999. Persistence of viremia and the importance of long-term follow-up after acute hepatitis C infection. Hepatology 29:908-914.
56. Villano, S. A., D. Vlahov, K. E. Nelson, C. M. Lyles, S. Cohn, and D. L. Thomas. 1997. Incidence and risk factors for hepatitis C among injection drug users in Baltimore, Maryland. J. Clin. Microbiol. 35:3274-3277.
57. Vlahov, D., J. C. Anthony, A. Muñoz, J. Margolik, D. D. Celentano, L. Solomon, and B. F. Polk. 1991. The ALIVE Study: a longitudinal study of HIV-1 infection in intravenous drug users: description of methods. J. Drug Issues 21:759-776.
58. Wang, Y., S. C. Ray, O. Laeyendecker, J. R. Ticehurst, and D. L. Thomas. 1998. Assessment of hepatitis C virus sequence complexity by the electrophoretic mobility of both single- and double-stranded DNA. J. Clin. Microbiol. 36:2982-2989.
59. Weiner, A. J., H. M. Geysen, C. Christopherson, J. E. Hall, T. J. Mason, G. Saracco, F. Bonino, K. Crawford, C. D. Marion, K. A. Crawford, et al. 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.
60. Zhang, L., R. S. Diaz, D. D. Ho, J. W. Mosley, M. P. Busch, and A. Mayer. 1997. Host-specific driving force in human immunodeficiency virus type 1 evolution in vivo. J. Virol. 71:2555-2561.
61. Zibert, A., H. Meisel, W. Kraas, A. Schulz, G. Jung, and M. Roggendorf. 1997. Early antibody response against hypervariable region 1 is associated with acute self-limiting infections of hepatitis C virus. Hepatology 25:1245-1249.