Found 13 matching records:
Displaying record number 55736
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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. 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 previously described Gag p24 HLA B*81-restricted epitope, TPQDLNTML was susceptible at L5. Variants TPQDmNTML, TPQDyNTML, TPQDsNTML were resistant to CTL response, but associated with lower viral loads. This epitope is 1 of 7 that suggest a fitness cost to immune escape.
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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Displaying record number 56143
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Notes
- 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 previously described Gag p24 HLA B*57 or B*5801-restricted epitope, TSTLQEQIGW was susceptible at T3. Variants TSnLQEQIGW and TSsLQEQIGW were resistant to CTL response, but associated with lower viral loads. This epitope is 1 of 7 that suggest a fitness cost to immune escape.
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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Displaying record number 58681
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Notes
- 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 2 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 Gag p24 HLA C*08-restricted epitope, RALGPGATM was susceptible at P5. Variants RALGaGATM, RALGqGATM, RALGsGATM, RALGtGATM and RALGvGATM were resistant to CTL response, but associated with lower viral loads. This epitope is 1 of 7 that suggest a fitness cost to immune escape.
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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Displaying record number 56144
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Notes
- 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 2 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 Gag p24 HLA C*08-restricted epitope, RALGPGATL/M was susceptible at P5. Variants RALGaGATL/M, RALGqGATL/M, RALGsGATL/M, RALGtGATL/M and RALGvGATL/M were resistant to CTL response, but associated with lower viral loads. This epitope is 1 of 7 that suggest a fitness cost to immune escape.
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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Displaying record number 56151
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Notes
- 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 Pol HLA-B*42-restricted epitope, YPGIKVRQL, 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.
Show all entries for this paper.
Displaying record number 56145
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record as JSON.
Notes
- 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 previously described Pol HLA B*4403-restricted epitope, QEEHEKYHSNW was susceptible at E2. Variants QaEHEKYHSNW, QdEHEKYHSNW, QgEHEKYHSNW, and QvEHEKYHSNW were resistant to CTL response, but associated with lower viral loads. This epitope is 1 of 7 that suggest a fitness cost to immune escape.
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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Displaying record number 58683
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record as JSON.
Notes
- 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 previously described Vif HLA B*1503-restricted epitope, SKRASGWFF was susceptible at K2. Variants SgRASGWFF, SqRASGWFF and SrRASGWFF were resistant to CTL response, but associated with lower viral loads. This epitope is 1 of 7 that suggest a fitness cost to immune escape.
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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Displaying record number 56146
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record as JSON.
Notes
- 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 previously described Vif HLA B*1503-restricted epitope, SKRASGWFY was susceptible at K2. Variants SgRASGWFY, SqRASGWFY and SrRASGWFY were resistant to CTL response, but associated with lower viral loads. This epitope is 1 of 7 that suggest a fitness cost to immune escape.
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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Displaying record number 56150
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Notes
- 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 Tat HLA-B*42-restricted epitope, QPKTPCNKCY, 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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Displaying record number 58682
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record as JSON.
Notes
- 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 Rev HLA A*3001-restricted epitope, AVRIIKIL/M was susceptible at R3. Variants AVkIIKIM and AVqIIKIM were resistant to CTL response, but associated with lower viral loads. This epitope is 1 of 7 that suggest a fitness cost to immune escape.
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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Displaying record number 56147
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record as JSON.
Notes
- 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 Rev HLA A*3001-restricted epitope, AVRIIKIL was susceptible at R3. Variants AVkIIKIL and AVqIIKIL were resistant to CTL response, but associated with lower viral loads. This epitope is 1 of 7 that suggest a fitness cost to immune escape.
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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Displaying record number 56149
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Notes
- 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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Displaying record number 56148
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Notes
- 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-B*44-restricted epitope, KRQEILDLW, lies within a set of 7 immunological associations, experiencing the most 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.
Show all entries for this paper.
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