TABLE 3

Epitope-specific CD8+ T-cell targeting associated with HIV chronic progression

SequenceProteinNameCoordinatesaEffect sizebBootstrap frequencyc
StartStop
RPLVTIKIPol (Pr)RI88157.120.971
QELKNSAVSLEnv (gp41)QL102943035.700.893
KYCWNLLQYEnv (gp41)KQY92832913.940.855
RPMTYKAAVNefRV977856.710.836
IKLEPVHGVYPol (RT)IY103093184.410.759
KQNPDIVIYQYPol (RT)KY111731832.970.679
RAEQASQEVGag (p24)RV91731813.130.677
VPLRPMTYNefVY874813.670.666
SFEPIPIHYEnv (gp120)SY92092174.360.645
KAYETEVHNVWEnv (gp120)KW1159692.570.635
LVGKLNWASQIYPol (RT)LY122602713.270.614
LRSLFLFSYEnv(gp41)LY92492573.130.596
SLYNTVATLGag (p17)SL977852.370.588
THLEGKIILPol (Int)TL966744.140.564
IQQEFGIPYPol (Int)IY91351433.180.548
ILKEPVHGVPol (RT)IV93093171.630.539
GAETFYVDGAPol (RT)GA104364452.760.527
VPVWKEATTTLEnv (gp120)VL1142524.080.524
DTVLEEWNLPol (Pr)DWL930383.800.514
YTPGPGIRYNefYY91271350.740.511
RRQDILDLWVYNefRY111051152.040.505
  • a HXB2 coordinates with respect to protein domains (p24, RT, gp41, and gp120). See Table S1 in the supplemental material for coordinates with respect to polyproteins (Gag, Pol, Env).

  • b The natural logarithm of the odds ratio that an individual will be a progressor or not given that he or she targets this epitope. Parameters are estimated using a nonregularized logistic regression model including all HLAs and epitopes.

  • c The fraction of bootstrap samples in which the sequence is selected for inclusion in the predictive model.