Pyrosequencing reveals restricted patterns of CD8 + T cell escape-associated compensatory mutations in simian immunodeficiency virus

Journal of Virology

Volumn 85, Issue 24, 2011, Pages 13088-13096

  Burwitz, Benjamin J ^a   Sacha, Jonah B ^b,c   Reed, Jason S ^b,c   Newman, Laura P ^a   Norante, Francesca A ^a   Bimber, Benjamin N ^d   Wilson, Nancy A ^a   Watkins, David I ^a   O'Connor, David H ^a,d  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^c OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^d UNIVERSITY OF WISCONSIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; GAG PROTEIN;

AMINO ACID SUBSTITUTION; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CD8+ T LYMPHOCYTE; CONTROLLED STUDY; DISEASE ASSOCIATION; DNA FLANKING REGION; DOWN REGULATION; GENE FREQUENCY; GENETIC ASSOCIATION; MOLECULAR EVOLUTION; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; ONTOGENY; PRIORITY JOURNAL; PYROSEQUENCING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SIMIAN ACQUIRED IMMUNODEFICIENCY SYNDROME; SIMIAN IMMUNODEFICIENCY VIRUS; VIRUS CAPSID; VIRUS GENOME; VIRUS IMMUNITY; VIRUS MUTATION; VIRUS REPLICATION;

AMINO ACID SEQUENCE; ANIMALS; CD8-POSITIVE T-LYMPHOCYTES; EPITOPES; GENE PRODUCTS, GAG; IMMUNE EVASION; MACACA MULATTA; MOLECULAR SEQUENCE DATA; MUTATION, MISSENSE; SEQUENCE ANALYSIS, DNA; SIMIAN IMMUNODEFICIENCY VIRUS; TIME FACTORS;

HUMAN IMMUNODEFICIENCY VIRUS; SIMIAN IMMUNODEFICIENCY VIRUS;

EID: 84855846659     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.05650-11     Document Type: Article

References (26)

1. Allen, T. M., et al. 2000. Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature 407:386-390.
2. Allen, T. M., et al. 2000. Induction of AIDS virus-specific CTL activity in fresh, unstimulated peripheral blood lymphocytes from rhesus macaques vaccinated with a DNA prime/modified vaccinia virus Ankara boost regimen. J. Immunol. 164:4968-4978.
3. Bimber, B. N., et al. 2009. Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virusinfected macaques. J. Virol. 83:8247-8253.
4. Crawford, H., et al. 2007. Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLAB*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection. J. Virol. 81:8346-8351.
5. Dahirel, V., et al. 2011. Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proc. Natl. Acad. Sci. U. S. A. 108:11530-11535.
6. Dilernia, D. A., et al. 2008. HLA-driven convergence of HIV-1 viral subtypes B and F toward the adaptation to immune responses in human populations. PLoS One 3:e3429.
7. Friedrich, T. C., et al. 2004. Extraepitopic compensatory substitutions partially restore fitness to simian immunodeficiency virus variants that escape from an immunodominant cytotoxic-T-lymphocyte response. J. Virol. 78:2581-2585.
8. Honeyborne, I., et al. 2010. HLA-Cw*03-restricted CD8 T-cell responses targeting the HIV-1 gag major homology region drive virus immune escape and fitness constraints compensated for by intracodon variation. J. Virol. 84:11279-11288.
9. Kawashima, Y., et al. 2009. Adaptation of HIV-1 to human leukocyte antigen class I. Nature 458:641-645.
10. Kelleher, A. D., et al. 2001. Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T lymphocyte responses. J. Exp. Med. 193:375-386.
11. Lanman, J., et al. 2003. Identification of novel interactions in HIV-1 capsid protein assembly by high-resolution mass spectrometry. J. Mol. Biol. 325:759-772.
12. Li, S., C. P. Hill, W. I. Sundquist, and J. T. Finch. 2000. Image reconstructions of helical assemblies of the HIV-1 CA protein. Nature 407:409-413.
13. Matthews, P. C., et al. 2009. HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering. J. Virol. 83:4605-4615.
14. Ngandu, N. K., C. Seoighe, and K. Scheffler. 2009. Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission. Virol. J. 6:164.
15. Nietfield, W., et al. 1995. Sequence constraints and recognition by CTL of an HLA-B27-restricted HIV-1 gag epitope. J. Immunol. 154:2189-2197.
16. O'Connor, D. H., et al. 2004. A dominant role for CD8+-T-lymphocyte selection in simian immunodeficiency virus sequence variation. J. Virol. 78:14012-14022.
17. O'Connor, D. H., et al. 2003. Major histocompatibility complex class I alleles associated with slow simian immunodeficiency virus disease progression bind epitopes recognized by dominant acute-phase cytotoxic-T-lymphocyte responses. J. Virol. 77:9029-9040.
18. Overbaugh, J., and C. R. Bangham. 2001. Selection forces and constraints on retroviral sequence variation. Science 292:1106-1109.
19. Owens, C. M., et al. 2004. Binding and susceptibility to postentry restriction factors in monkey cells are specified by distinct regions of the human immunodeficiency virus type 1 capsid. J. Virol. 78:5423-5437.
20. Peyerl, F. W., et al. 2003. Simian-human immunodeficiency virus escape from cytotoxic T-lymphocyte recognition at a structurally constrained epitope. J. Virol. 77:12572-12578.
21. Peyerl, F. W., et al. 2004. Fitness costs limit viral escape from cytotoxic T lymphocytes at a structurally constrained epitope. J. Virol. 78:13901-13910.
22. Schneidewind, A., et al. 2008. Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLAB27-restricted epitope in human immunodeficiency virus type 1 capsid. J. Virol. 82:5594-5605.
23. Valentine, L. E., et al. 2009. Infection with "escaped" virus variants impairs control of simian immunodeficiency virus SIVmac239 replication in Mamu-B*08-positive macaques. J. Virol. 83:11514-11527.
24. Vogel, T. U., et al. 2003. Multispecific vaccine-induced mucosal cytotoxic T lymphocytes reduce acute-phase viral replication but fail in long-term control of simian immunodeficiency virus SIVmac239. J. Virol. 77:13348-13360.
25. Wilson, N. A., et al. 2006. Vaccine-induced cellular immune responses reduce plasma viral concentrations after repeated low-dose challenge with pathogenic simian immunodeficiency virus SIVmac239. J. Virol. 80:5875-5885.
26. Yeh, W. W., et al. 2006. Compensatory substitutions restore normal core assembly in simian immunodeficiency virus isolates with Gag epitope cytotoxic T-lymphocyte escape mutations. J. Virol. 80:8168-8177.