TABLE 1

Identifying correlates of HLA allele-associated protective immunity

FeatureCategoryNo. of HLA alleles analyzedSpearman RP valueq valuea
Median OR of selection in GagStrength/constraint26−0.600.00120.04
No. of sites under selection (proteome-wide)Frequency/distribution53−0.410.00240.04
Proportion of selected sites occurring at HLA anchor residues (proteome-wide [%])Frequency/distribution34−0.470.00520.04
No. of sites under selection in GagFrequency/distribution53−0.380.00540.04
No. of sites under selection in accessory proteinsFrequency/distribution53−0.370.00580.04
No. of selected sites occurring at HLA anchor residues (proteome-wide)Frequency/distribution44−0.350.0180.10
No. of sites under selection within/near epitopes (proteome-wide)Frequency/distribution53−0.310.0250.11
No. of active epitopes in GagFrequency/distribution53−0.300.0270.11
Median no. of sites under selection per epitope in GagFrequency/distribution22−0.460.0320.12
Median OR of selection in PolStrength/constraint38−0.340.0390.13
No. of sites under selection in EnvFrequency/distribution53−0.280.0450.13
No. of sites under selection in PolFrequency/distribution53−0.280.0460.13
Median conservation of selected sites in NefStrength/constraint38−0.290.0790.20
Median conservation of selected sites in accessory proteinsStrength/constraint450.240.110.25
Median conservation of selected sites in EnvStrength/constraint320.280.130.28
No. of ites under selection within/near epitopes in GagFrequency/distribution28−0.270.160.33
No. of active epitopes (proteome-wide)Frequency/distribution53−0.170.230.41
Median no. of covarying codons per selected site (proteome-wide)Strength/constraint51−0.170.230.41
Median no. of sites under selection per epitope (proteome-wide)Frequency/distribution44−0.180.240.41
Median conservation of selected sites in NefStrength/constraint510.160.250.42
Proportion of sites under selection in Gag (%)Frequency/distribution51−0.140.330.50
Proportion of sites under selection in Env (%)Frequency/distribution51−0.130.350.50
Proportion of sites under selection in Nef (%)Frequency/distribution510.130.360.50
Proportion of sites under selection in accessory proteins (%)Frequency/distribution51−0.130.370.50
No. of sites under selection in NefFrequency/distribution53−0.120.390.50
Median OR of escape in NefStrength/constraint380.140.400.50
Median no. of covarying codons per site under selection (Gag only)Strength/constraint26−0.0840.680.81
Median OR of selection in accessory proteinsStrength/constraint450.0590.700.81
Median OR of selection in EnvStrength/constraint32−0.0670.720.81
Proportion of sites under selection in Pol (%)Frequency/distribution51−0.00690.960.99
Median conservation of selected sites in GagStrength/constraint26−0.00680.970.99
Median OR of selection (proteome-wide)Strength/constraint50−0.00240.990.99
Median conservation of selected sites in PolStrength/constraint390.00160.990.99
  • a Shown in boldface are q values of <0.2, indicating potential correlates of HLA-mediated protective immunity against disease progression.