Vertical T cell immunodominance and epitope entropy determine HIV-1 escape.

@article{Liu2013VerticalTC,
  title={Vertical T cell immunodominance and epitope entropy determine HIV-1 escape.},
  author={Michael K P Liu and Natalie R. Hawkins and Adam John Ritchie and Vitaly V. Ganusov and Victoria E Whale and Simon Brackenridge and Hui Li and Jeffrey W. Pavlicek and Fangping Cai and Melissa Rose-Abrahams and Florette K Treurnicht and Peter T. Hraber and Catherine Riou and Clive M. Gray and Guido Ferrari and Rachel Tanner and Li‐hua Ping and Jeffrey A. Anderson and Ronald Swanstrom and Myron S. Cohen and Salim Abdool Karim and Barton F. Haynes and Persephone Borrow and Alan S. Perelson and George M. Shaw and Beatrice H. Hahn and Carolyn Williamson and Bette T. Korber and F. Gao and Steven G. Self and Andrew J. McMichael and Nilu Goonetilleke},
  journal={The Journal of clinical investigation},
  year={2013},
  volume={123 1},
  pages={
          380-93
        }
}
HIV-1 accumulates mutations in and around reactive epitopes to escape recognition and killing by CD8+ T cells. Measurements of HIV-1 time to escape should therefore provide information on which parameters are most important for T cell-mediated in vivo control of HIV-1. Primary HIV-1-specific T cell responses were fully mapped in 17 individuals, and the time to virus escape, which ranged from days to years, was measured for each epitope. While higher magnitude of an individual T cell response… 

Figures and Tables from this paper

The HIV-1 latent reservoir is largely sensitive to circulating T cells
TLDR
It is suggested that circulating T cells in PLWH on ART could contribute to control of rebound and could be targeted for boosting in curative strategies.
Recombination-mediated escape from primary CD8+ T cells in acute HIV-1 infection
TLDR
This study shows that recombination between multiple T/F viruses provide greater options for acute escape from CD8+ T cell responses than seen in cases of single T-F virus infection.
Kinetics of HIV-Specific CTL Responses Plays a Minimal Role in Determining HIV Escape Dynamics
TLDR
The results suggest that the current sparse measurements of temporal CTL dynamics in blood bear little quantitative information to improve predictions of HIV escape kinetics, and more frequent measurements using more sensitive techniques and sampling in secondary lymphoid tissues may allow to better understand whether and how CTL kinetics impacts viral escape.
Kinetics of HIV-Specific CTL Responses Plays a Minimal Role in Determining HIV Escape Dynamics
TLDR
The results suggest that the current sparse measurements of temporal CTL dynamics in blood bear little quantitative information to improve predictions of HIV escape kinetics, and more frequent measurements using more sensitive techniques and sampling in secondary lymphoid tissues may allow to better understand whether and how CTL kinetics impacts viral escape.
Epitope-Specific CD8+ T Cell Kinetics Rather than Viral Variability Determine the Timing of Immune Escape in Simian Immunodeficiency Virus Infection
TLDR
The results suggest that the conservation or variability of an epitope does not appear to affect the timing of immune escape in SIV, and that timing of escape is largely determined by the kinetics of epitope-specific CD8+ T cells.
Role of CD8+ T Cells in the Selection of HIV-1 Immune Escape Mutations.
TLDR
The selection of either escape mutations or compensatory mutations may negatively affect the course of the infection and are a major barrier for the development of new therapeutic strategies focused on reducing the impact of viral fitness.
Role of CD8+ T Cells in the Selection of HIV-1 Immune Escape Mutations.
TLDR
The selection of either escape mutations or compensatory mutations may negatively affect the course of the infection and are a major barrier for the development of new therapeutic strategies focused on the induction of specific CD8+ T cell responses.
Within-Epitope Interactions Can Bias CTL Escape Estimation in Early HIV Infection
TLDR
A previously developed simulation model of HIV is extended to include different distributions of fitness effects (DFEs) and inter-mutational genomic distances and it is found that across the DFEs analyzed, the aggregation procedure alters the detectability of escape mutations: large-effect mutations are overrepresented while small- effect mutations are concealed.
The Route of HIV Escape from Immune Response Targeting Multiple Sites Is Determined by the Cost-Benefit Tradeoff of Escape Mutations
TLDR
It is concluded that partial recognition loss is as important as fitness loss for predicting the order of escapes and, ultimately, for predicting conserved epitopes that can be targeted by vaccines.
Structured Observations Reveal Slow HIV-1 CTL Escape
TLDR
Sequence variation within CTL epitopes at the first time point was consistent with most mutations being transmitted in the infecting viral strain rather than with escape arising within the first few weeks of infection.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 76 REFERENCES
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection
TLDR
Kinetic analysis and mathematical modeling of virus immune escape showed that the contribution of CD8 T cell–mediated killing of productively infected cells was earlier and much greater than previously recognized and that it contributed to the initial decline of plasma virus in acute infection.
Variable Fitness Impact of HIV-1 Escape Mutations to Cytotoxic T Lymphocyte (CTL) Response
TLDR
CTL escape mutations in HIV-1 Gag p24 were associated with significant fitness costs, whereas most Escape mutations in the Env gene were fitness neutral, suggesting a balance between immunologic escape and replicative fitness costs.
Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response
TLDR
Evaluation of the extent and kinetics of HIV-1 escape from >40 different epitope-specific CD8 T cell responses enabled analysis of factors determining escape and suggested that escape is restricted by costs to intrinsic viral fitness and by broad, codominant distribution of CTL-mediated pressure on viral replication.
Antiviral pressure exerted by HIV-l-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus
TLDR
It is shown that in a patient whose early CTL response was focused on a highly immunodominant epitope in gp160, there was rapid elimination of the transmitted virus strain and selection for a virus population bearing amino acid changes at a single residue within this epitope, which conferred escape from recognition by epitope-specific CTL.
HIV evolution: CTL escape mutation and reversion after transmission
TLDR
Data show that the process of accumulation of escape mutations within HIV is not inevitable, and complex epitope- and residue-specific selection forces, including CTL-mediated positive selection pressure and virus-mediated purifying selection, operate in tandem to shape HIV evolution at the population level.
Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS
TLDR
Six donors who make a strong CTL response to an immunodominant HLA-B27-restricted epitope and two donors who progressed to AIDS, CTL escape to fixation by the same mutation was observed, but only after 9–12 years of epitope stability.
Relationship between Functional Profile of HIV-1 Specific CD8 T Cells and Epitope Variability with the Selection of Escape Mutants in Acute HIV-1 Infection
TLDR
Interestingly, only the magnitude of the total and not of the poly-functional T-cell responses was significantly associated with the selection of escape mutants, but the high contribution of MIP-1β-producing CD8+ T-cells to the total response suggests that mechanisms not limited to cytotoxicity could be exerting immune pressure during acute infection.
Escape from highly effective public CD8+ T-cell clonotypes by HIV.
TLDR
Detailed mechanistic insights are provided into the workings of an effective CD8(+) T-cell response against HIV, found to be preferentially selected in vivo and shared between individuals.
Kinetics of Expansion of Epitope-Specific T Cell Responses during Primary HIV-1 Infection1
TLDR
Observations document the preferential expansion of CD8+ T cells recognizing a subset of epitopes during the viral burst in acute HIV-1 infection and suggest that the nature of the initial, very rapidly expanded T cell response may influence the efficiency with which viral replication is contained in acute/early HIV infection.
Conflicting selective forces affect T cell receptor contacts in an immunodominant human immunodeficiency virus epitope
TLDR
The evolution in vivo of an immunodominant, HLA-A2–restricted CTL epitope is analyzed and two principal, diametrically opposed evolutionary pathways that exclusively affect T cell–receptor contact residues are found.
...
1
2
3
4
5
...