Divergent and convergent evolution after a common-source outbreak of hepatitis C virus

Journal of Experimental Medicine

Volumn 201, Issue 11, 2005, Pages 1753-1759

  Ray, Stuart C ^a   Fanning, Liam ^b   Wang, Xiao Hong ^a,c   Netski, Dale M ^a   Kenny Walsh, Elizabeth ^b   Thomas, David L ^a  

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

^b University College Cork and INFANT Centre   (Ireland)

^c THIRD MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE;

ALLELE; AMINO ACID SUBSTITUTION; ARTICLE; CELL SELECTION; CLINICAL ARTICLE; COHORT ANALYSIS; CONSENSUS; CONTROLLED STUDY; CONVERGENT EVOLUTION; EPIDEMIC; EVOLUTION; FEMALE; GENE SEQUENCE; GENETIC VARIABILITY; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; INOCULATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERTANT; VIRUS IMMUNITY;

ALLELES; AMINO ACID SUBSTITUTION; ANIMALS; CONSENSUS SEQUENCE; EPITOPES, T-LYMPHOCYTE; EVOLUTION, MOLECULAR; HEPACIVIRUS; HEPATITIS C; HEPATITIS C ANTIGENS; HLA ANTIGENS; MICE; SELECTION (GENETICS); VIRAL HEPATITIS VACCINES; VIRAL STRUCTURAL PROTEINS;

EID: 22344447485     PISSN: 00221007     EISSN: 00221007     Source Type: Journal    
DOI: 10.1084/jem.20050122     Document Type: Article

References (28)

1. 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.
2. Martell, M., J.I. Esteban, J. Quer, J. Genesca, A. Weiner, R. Esteban, 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.
3. Ray, S.C., Q. Mao, R.E. Lanford, S. Bassett, O. Laeyendecker, Y.M. Wang, and D.L. Thomas. 2000. Hypervariable region 1 sequence stability during hepatitis C virus replication in chimpanzees. J. Virol. 74:3058-3066.
4. 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.
5. Gaud, U., B. Langer, T. Petropoulou, H.C. Thomas, and P. Karayiannis. 2003. Changes in hypervariable region 1 of the envelope 2 glycoprotein of hepatitis C virus in children and adults with humoral immune defects. J. Med. Virol. 69:350-356.
6. Erickson, A.L., Y. Kimura, S. Igarashi, J. Eichelberger, M. Houghton, J. Sidney, D. McKinney, A. Sette, A.L. Hughes, and C.M. Walker. 2001. The outcome of hepatitis C virus infection is predicted by escape mutations in epitopes targeted by cytotoxic T lymphocytes. Immunity. 15:883-895.
7. Kenny-Walsh, 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.
8. 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.
9. Penin, F., C. Combet, G. Germanidis, P.O. Frainais, G. Deleage, and J.M. Pawlotsky. 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.
10. Allen, T.M., D.H. O'Connor, P. Jing, J.L. Dzuris, B.R. Mothe, T.U. Vogel, E. Dunphy, M.E. Liebl, C. Emerson, N. Wilson, et al. 2000. Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature. 407:386-390.
11. Cox, A.L., T. Mosbruger, Q. Mao, Z. Liu, X.-H. Wang, H.-C. Yang, J. Sidney, A. Sette, D. Pardoll, D.L. Thomas, and S.C. Ray. Cellular immune selection with hepatitis C virus persistence in humans. J. Exp. Med. 201:1741-1752.
12. Gandhi, R.T., A. Wurcel, E.S. Rosenberg, M.N. Johnston, N. Hellmann, M. Bates, M.S. Hirsch, and B.D. Walker. 2003. Progressive reversion of human immunodeficiency virus type 1 resistance mutations in vivo after transmission of a multiply drug-resistant virus. Clin. Infect. Dis. 37:1693-1698.
13. Friedrich, T.C., E.J. Dodds, L.J. Yant, L. Vojnov, R. Rudersdorf, C. Cullen, D.T. Evans, R.C. Desrosiers, B.R. Mothe, J. Sidney, et al. 2004. Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nat. Med. 10:275-281.
14. Leslie, A.J., K.J. Pfafferott, P. Chetty, R. Draenert, M.M. Addo, M. Feeney, Y. Tang, E.C. Holmes, T. Allen, J.G. Prado, et al. 2004. HIV evolution: CTL escape mutation and reversion after transmission. Nat. Med. 10:282-289.
15. Timm, J., G.M. Lauer, D.G. Kavanagh, I. Sheridan, A.Y. Kim, M. Lucas, T. Pillay, K. Ouchi, L.L. Reyor, J.S. Zur Wiesch, et al. 2004. CD8 epitope escape and reversion in acute HCV infection. J. Exp. Med. 200:1593-1604.
16. Moore, C.B., M. John, I.R. James, F.T. Christiansen, C.S. Witt, and S.A. Mallal. 2002. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science. 296:1439-1443.
17. Gaschen, B., J. Taylor, K. Yusim, B. Foley, F. Gao, D. Lang, V. Novitsky, B. Haynes, B.H. Hahn, T. Bhattacharya, and B. Korber. 2002. Diversity considerations in HIV-1 vaccine selection. Science. 296:2354-2360.
18. Nickle, D.C., M.A. Jensen, G.S. Gottlieb, D. Shriner, G.H. Learn, A.G. Rodrigo, and J.I. Mullins. 2003. Consensus and ancestral state HIV vaccines. Science. 299:1515-1518.
19. Fanning, L.J., E. Kenny-Walsh, and F. Shanahan. 2004. Persistence of hepatitis C virus in a white population: associations with human leukocyte antigen class 1. Hum. Immunol. 65:745-751.
20. Liu, Z., D.M. Netski, Q. Mao, O. Laeyendecker, J.R. Ticehurst, X.H. Wang, D.L. Thomas, and S.C. Ray. 2004. Accurate representation of the hepatitis C virus quasispecies in 5.2-kilobase amplicons. J. Clin. Microbiol. 42:4223-4229.
21. Jeanmougin, F., J.D. Thompson, M. Gouy, D.G. Higgins, and T.J. Gibson. 1998. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23:403-405.
22. Hall, T.A. 2001. BioEdit: Biological sequence alignment editor for Windows 95/98/NT version 5.0.7. software. http://www.mbio.ncsu. edu/RNaseP/info/programs/BIOEDIT/bioedit.html (accessed March 5, 2003).
23. Posada, D., and K.A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics. 14:817-818.
24. Ray, S.C., Y.M. Wang, O. Laeyendecker, J. Ticehurst, S.A. Villano, and D.L. Thomas. 1998. Acute hepatitis C virus structural gene sequences as predictors of persistent viremia: hypervariable region 1 as decoy. J. Virol. 73:2938-2946.
25. Schneider, T.D., and R.M. Stephens. 1990. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18:6097-6100.
26. Gorodkin, J., L.J. Heyer, S. Brunak, and G.D. Stormo. 1997. Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci. 13:583-586.
27. Chang, K.M., B. Rehermann, J.G. McHutchison, C. Pasquinelli, S. Southwood, A. Sette, and F.V. Chisari. 1997. Immunological significance of cytotoxic T lymphocyte epitope variants in patients chronically infected by the hepatitis C virus. J. Clin. Invest. 100:2376-2385.
28. Ward, S., G. Lauer, R. Isba, B. Walker, and P. Klenerman. 2002. Cellular immune responses against hepatitis C virus: the evidence base 2002. Clin. Exp. Immunol. 128:195-203.