Assessment of hepatitis C virus sequence complexity by electrophoretic mobilities of both single- and double-stranded DNAs

Journal of Clinical Microbiology

Volumn 36, Issue 10, 1998, Pages 2982-2989

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

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

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

^c Division of Infectious Diseases   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DOUBLE STRANDED DNA; VIRUS RNA;

ARTICLE; DNA SEQUENCE; ELECTROPHORETIC MOBILITY; GENOTYPE; HEPATITIS C; HEPATITIS C VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SINGLE STRAND CONFORMATION POLYMORPHISM; VIRUS HEPATITIS;

HEPATITIS C VIRUS; RNA VIRUSES;

EID: 0031689747     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/jcm.36.10.2982-2989.1998     Document Type: Article

References (47)

1. Axton, R. A., I. M. Hanson, J. Love, A. Seawright, J. Prosser, and V. van Heyningen. 1997. Combined SSCP/heteroduplex analysis in the screening for PAX6 mutations. Mol. Cell Probes 11:287-292.
2. Bukh, J., R. H. Miller, and R. H. Purcell. 1995. Genetic heterogeneity of hepatitis C virus: quasispecies and genotypes. Semin. Liver Dis. 15:41-63.
3. 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.
4. Calvo, P. L., J. Kansopon, K. Sra, S. Quan, R. Dinello, R. Guaschino, G. Calabrese, F. Danielle, M. R. Brunetto, F. Bonino, L. Massaro, A. Polito, M. Houghton, and A. J. Weiner. 1998. Hepatitis C virus heteroduplex tracking assay for genotype determination reveals diverging genotype 2 isolates in Italian hemodialysis patients. J. Clin. Microbiol. 36:227-233.
5. Carrington, M., T. Millter, M. White, B. Gerrard, C. Stewart, M. Dean, and D. Mann. 1992. Typing of HLA-DQA1 and DQB1 using DNA single-stranded conformational polymorphism. Hum. Immun. 33:208-212.
6. Cotton, R. G. 1993. Current methods of mutation detection. Mutat. Res. 285:125-144.
7. Delwart, E. L., H. Pan, H. W. Sheppard, D. Wolpert, A. U. Neumann, B. Korber, and J. I. Mullins. 1997. Slower evolution of human immunodeficiency virus type 1 quasispecies during progression to AIDS. J. Virol. 71: 7498-7508.
8. Delwart, E. L., E. G. Shpaer, J. Louwagie, F. E. McCutchan, M. Grez, W. H. Rubsamen, and J. I. Mullins. 1993. Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes. Science 262:1257-1261.
9. Delwart, E. L., E. G. Shpaer, and J. I. Mullins. 1995. Heteroduplex mobility assays for phylogenetic analysis, p. 154-160. In M. A. Innis, D. H. Gelfand, and J. J. Sninsky (ed.), PCR strategies. Academic Press, San Diego, Calif.
10. Domingo, E., E. Martinez-Salas, F. Sobrino, J. C. de la Torre, A. Portela, J. Ortin, C. Lopez-Galindez, P. Perez-Brena, N. Villanueva, and R. Najera. 1985. The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance - a review. Gene 40:1-8.
11. Eigen, M. 1971. Self organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58:465-523.
12. Feinstone, S. M., H. J. Alter, H. P. Dienes, Y. Shimizu, H. Popper, D. Blackmore, D. Sly, W. T. London, and R. H. Purcell. 1981. Non-A, non-B hepatitis in chimpanzees and marmosets. J. Infect. Dis. 144:588-598.
13. Gavier, B., M. A. Martinez-González, J. I. Riezu-Boj, J. J. Lasarte, N. Garcia, M. P. Civeira, and J. Prieto. 1997. Viremia after one month of interferon therapy predicts treatment outcome in patients with chronic hepatitis C. Gastroenterology 113:1647-1653.
14. Gretch, D. R., S. J. Polyak, J. J. Wilson, R. L. Carithers, Jr., J. D. Perkins, and L. Corey. 1996. Tracking hepatitis C virus quasispecies major and minor variants in symptomatic and asymptomatic liver transplant recipients. J. Virol. 70:7622-7631.
15. Higashi, Y., S. Kakumu, K. Yoshioka, T. Wakita, M. Mizokami, K. Ohba, Y. Ito, T. Ishikawa, M. Takayanagi, and Y. Nagai. 1993. Dynamics of genome change in the E2/NS1 region of hepatitis C virus in vivo. Virology 197:659-668.
16. Honda, M., S. Kaneko, A. Sakai, M. Unoura, S. Murakami, and K. Kobayashi. 1994. Degree of diversity of hepatitis C virus quasispecies and progression of liver disease. Hepatology 20:1144-1151.
17. 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.
18. Kato, N., Y. Ootsuyama, S. Ohkoshi, T. Nakazawa, H. Sekiya, M. Hijikata, and K. Shimotohno. 1992. Characterization of hypervariable regions in the putative envelope protein of hepatitis C virus. Biochem. Biophys. Res. Commun. 189:119-127.
19. 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.
20. Korber, B. T., K. J. Kunstman, B. K. Patterson, M. Furtado, M. M. McEvilly, R. Levy, and S. M. Wolinsky. 1994. Genetic differences between blood-and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients: evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences. J. Virol. 68:7467-7481.
21. Kreis, S., and T. Whistler. 1997. Rapid identification of measles virus strains by the heteroduplex mobility assay. Virus Res. 47:197-203.
22. 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.
23. Lee, J. H., T. Stripf, W. K. Roth, and S. Zeuzem. 1997. Non-isotopic detection of hepatitis C virus quasispecies by single strand conformation polymorphism. J. Med. Virol. 53:245-251.
24. Le Guen, B., G. Squadrito, B. Nalpas, P. Berthelot, S. Pol, and C. Brechot. 1997. Hepatitis C virus genome complexity correlates with response to interferon therapy: a study in French patients with chronic hepatitis C. Hepatology 25:1250-1254.
25. 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.
26. Navas, S., J. Martin, J. A. Quiroga, I. Castillo, and V. Carreno. 1998. Genetic diversity and tissue compartmentalization of the hepatitis C virus genome in blood mononuclear cells, liver, and serum from chronic hepatitis C patients. J. Virol. 72:1640-1646.
27. Nelson, J. A. E., S. A. Fiscus, and R. Swanstrom. 1997. Evolutionary variants of the human immunodeficiency virus type 1 V3 region characterized by using a heteroduplex tracking assay. J. Virol. 71:8750-8758.
28. Offermans, M. T., L. Struyk, B. de Geus, F. C. Breedveld, P. J. van den Elsen, and J. Rozing. 1996. Direct assessment of junctional diversity in rearranged T cell receptor beta chain encoding genes by combined heteroduplex and single strand conformation polymorphism (SSCP) analysis. J. Immunol. Methods 191:21-31.
29. 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.
30. 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.
31. 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.
32. Polyak, S. J., G. Faulkner, R. L. Carithers, Jr., L. Corey, and D. R. Gretch. 1997. Assessment of hepatitis C virus quasispecies heterogeneity by gel shift analysis: correlation with response to interferon therapy. J. Infect. Dis. 175: 1101-1107.
33. Pursall, M. C., T. M. Clay, and J. L. Bidwell. 1996. Combined PCR-heteroduplex and PCR-SSCP analysis for matching of HLA-A, -B and -C allotypes in marrow transplantation. Eur. J. Immunogenet. 23:41-53.
34. Shannon, C. E. 1948. A mathematical theory of communication. Bell Syst. Technol. J. 27:379-423.
35. Simmonds, P. 1995. Variability of hepatitis C virus. Hepatology 21:570-583.
36. Simmonds, P., E. C. Holmes, T.-A. Cha, S.-W. Chan, F. McOmish, B. Irvine, E. Beall, P. L. Yap, J. Kolberg, and M. S. Urdea. 1993. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J. Gen. Virol. 74:2391-2399.
37. Simmonds, P., D. B. Smith, F. McOmish, P. L. Yap, J. Kolberg, M. S. Urdea, and E. C. Holmes. 1994. Identification of genotypes of hepatitis C virus by sequence comparisons in the core, E1 and NS-5 regions. J. Gen. Virol. 75:1053-1061.
38. 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.
39. Spritz, R. A., S. A. Holmes, R. Ramesar, J. Greenberg, D. Curtis, and P. Beighton. 1992. Mutations of the KIT (mast/stem cell growth factor receptor) proto-oncogene account for a continuous range of phenotypes in human piebaldism. Am. J. Hum. Genet. 51:1058-1065. (Erratum, 52:654, 1993.)
40. Stewart, J. J., C. Y. Lee, S. Ibrahim, P. Watts, M. Shlomchik, M. Weigert, and S. Litwin. 1997. A Shannon entropy analysis of immunoglobulin and T cell receptor. Mol. Immunol. 34:1067-1082.
41. Strunnikova, N., S. C. Ray, R. A. Livingston, E. Rubalcaba, and R. P. Viscidi. 1995. Convergent evolution within the V3 loop domain of human immunodeficiency virus type 1 in association with disease progression. J. Virol. 69:7548-7558.
42. Sud, R., I. C. Talbot, and J. D. Delhanty. 1996. Infrequent alterations of the APC and MCC genes in gastric cancers from British patients. Br. J. Cancer 74:1104-1108.
43. Thomas, A. W., R. Morgan, M. Sweeney, A. Rees, and J. Alcolado. 1994. The detection of mitochondrial DNA mutations using single stranded conformation polymorphism (SSCP) analysis and heteroduplex analysis. Hum. Genet. 94:621-623.
44. Villano, S. A., D. Vlahov, K. E. Nelson, S. Cohn, and D. L. Thomas. Persistence of viremia and the importance of long-term follow-up after acute hepatitis C infection. Unpublished data.
45. 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.
46. Weiner, A. J., M. J. Brauer, J. Rosenblatt, K. H. Richman, J. Tung, K. Crawford, F. Bonino, G. Saracco, Q. L. Choo, M. Houghton, et al. 1991. Variable and hypervariable domains arc found in the regions of HCV corresponding to the flavivirus envelope and NS1 proteins and the pestivirus envelope glycoproteins. Virology 180:842-848.
47. Wilson, J. J., S. J. Polyak, T. D. Day, and D. R. Gretch. 1995. Characterization of simple and complex hepatitis C virus quasispecies by heteroduplex gel shift analysis: correlation with nucleotide sequencing. J. Gen. Virol. 76:1763-1771.