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Displaying record number 53899
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- PBMCs from HIV-1 infected Indian subjects were tested for HIV-1 Gag (with C clade peptides), Nef (with B clade peptides), and Env (clade B peptides) specific T-cell responses. 5 immunodominant regions conserved across clades were identified in Gag and Nef. 3 antigenic regions were found to be recognized by CTLs in the Indian subjects; these regions were not identified as immunodominant in studies from Africa.
- PBMCs from HIV-1 infected Indian subjects were tested for HIV-1 Gag (with C clade peptides), Nef (with B clade peptides), and Env (clade unspecified) specific T-cell responses. 5 immunodominant regions conserved across clades were identified in Gag and Nef. 3 antigenic regions were found to be recognized by CTLs in the Indian subjects; these regions were not identified as immunodominant in studies from Africa.
- 26 epitopes were predicted within reactive peptides, of which 90% were clustered in the conserved immunodominant regions of Gag and Nef.
- 3 of the epitopes were highly conserved across clades, and 7 novel epitopes were found.
- Epitope HSQRRQDIL showed some conservation to subtype B. It's HLA-restriction is predicted to be either to HLA-A*24, -B*37, Cw*0602 or Cw*0401.
References
Thakar2005
Madhuri R. Thakar, Leena S. Bhonge, Samir K. Lakhashe, U. Shankarkumar, Suvarna S. Sane, Smita S. Kulkarni, Bharati A. Mahajan, and Ramesh S. Paranjape. Cytolytic T Lymphocytes (CTLs) from HIV-1 Subtype C-Infected Indian Patients Recognize CTL Epitopes From a Conserved Immunodominant Region of HIV-1 Gag and Nef. J. Infect. Dis., 192(5):749-759, 1 Sep 2005. PubMed ID: 16088824.
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Displaying record number 56149
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- 3 phylogenetic correction methods---MLL (maximum likelihood character state analysis followed by likelihood ratio test), MLF (maximum likelihood character state analysis followed by Fisher test), and parsimony character state analysis were used to identify points in the HIV-1 subtype C proteome that conferred susceptibility or resistance to CTLs. Associations of HLA-epitope combinations that were inferred to be susceptible or resistant were organized into immunological sets that would help identify the best residues and genes as candidates for vaccines. While all proteins were interrogated, Gag, Pol, Env and Nef were focused upon. Amino acid changes were evaluated for association with plasma viral load.
- Proteome maps may be seen at http://www.hiv.lanl.gov/content/immunology/hlatem/study5/index.html with information showing single or multiple sites involving escape and reversion.
- HLA- B and -C alleles associated more with aa changes than HLA-A, suggesting that the former two are more important in driving viral evolution.
- The ratio of susceptible to resistant residues in HIV proteins was in descending order, Vpr>Gag>Rev>Pol>Nef>Vif>Tat>Env>Vpu, showing that epitopes from the earlier proteins are more conserved owing to viral fitness cost upon mutation.
- This Nef HLA-Cw*0404-restricted epitope, HSQRRQDIL, lies within a set of 6 immunological associations, experiencing conflicting selective pressures.
References
Rousseau2008
Christine M. Rousseau, Marcus G. Daniels, Jonathan M. Carlson, Carl Kadie, Hayley Crawford, Andrew Prendergast, Philippa Matthews, Rebecca Payne, Morgane Rolland, Dana N. Raugi, Brandon S. Maust, Gerald H. Learn, David C. Nickle, Hoosen Coovadia, Thumbi Ndung'u, Nicole Frahm, Christian Brander, Bruce D. Walker, Philip J. R. Goulder, Tanmoy Bhattacharya, David E. Heckerman, Bette T. Korber, and James I. Mullins. HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: Immune Escape and Viral Load. J. Virol., 82(13):6434-6446, Jul 2008. PubMed ID: 18434400.
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