HLA-associated viral polymorphisms in the +1 and +2 ARFs
| RF | Protein | Association | HLA | Pos HXB2 | aa | p-value | q-value | Dist |
| +1 | Gag | Adapted | C05 | 12 | T | 4.76 × 10−4 | 1.91 × 10−1 | 14 |
| +1 | Gag | Nonadapted | A03 | 45 | Q | 1.47 × 10−4 | 1.02 × 10−1 | 13 |
| +1 | Gag | Adapted | A29 | 86 | F | 1.07 × 10−4 | 7.94 × 10−2 | 5 |
| +1 | Gag | Adapted | B40 | 99 | R | 3.42 × 10−4 | 1.73 × 10−1 | 4 |
| +1 | Gag | Adapted | B08 | 132 | T | 3.84 × 10−4 | 1.73 × 10−1 | 5 |
| +1 | Gag | Nonadapted | A23 | 138 | S | 2.04 × 10−4 | 1.23 × 10−1 | 8 |
| +1 | Gag | Adapted | C06 | 168 | S | 8.89 × 10−5 | 6.79 × 10−2 | 20 |
| +1 | Gag | Adapted | B57 | 253 | T | 4.41 × 10−4 | 1.85 × 10−1 | 11 |
| +1 | Gag | Nonadapted | B57 | 253 | I | 4.43 × 10−4 | 1.85 × 10−1 | 11 |
| +1 | Gag | Adapted | B48 | 321 | Y | 3.08 × 10−4 | 1.64 × 10−1 | 9 |
| +1 | Gag | Nonadapted | B48 | 321 | C | 3.08 × 10−4 | 1.64 × 10−1 | 9 |
| +1 | Gag | Nonadapted | B52 | 499 | H | 4.07 × 10−4 | 1.76 × 10−1 | 17 |
| +1 | pol (pro) | Adapted | A01 | 73 | A | 4.26 × 10−6 | 3.55 × 10−3 | 10 |
| +1 | pol (RT) | Adapted | B07 | 25 | P | 2.87 × 10−4 | 1.18 × 10−1 | 10 |
| +1 | pol (RT) | Adapted | A01 | 53 | K | 2.17 × 10−4 | 9.2 × 10−2 | 18 |
| +1 | pol (RT) | Adapted | B46 | 151 | K | 1.49 × 10−4 | 7.66 × 10−2 | 7 |
| +1 | pol (RT) | Nonadapted | B46 | 151 | R | 1.53 × 10−4 | 7.66 × 10−2 | 7 |
| +1 | pol (RT) | Nonadapted | B40 | 258 | R | 5.1 × 10−4 | 1.74 × 10−1 | 13 |
| +1 | pol (RT) | Adapted | B40 | 258 | K | 5.1 × 10−4 | 1.74 × 10−1 | 13 |
| +1 | pol (RT) | Adapted | B58 | 271 | M | 8.2 × 10−5 | 4.93 × 10−2 | 6 |
| +1 | pol (RT) | Adapted | B14 | 305 | R | 5.63 × 10−4 | 1.84 × 10−1 | 8 |
| +1 | pol (RT) | Nonadapted | B14 | 305 | K | 5.63 × 10−4 | 1.84 × 10−1 | 8 |
| +1 | pol (RT) | Adapted | C06 | 326 | * | 5.75 × 10−4 | 1.86 × 10−1 | 3 |
| +1 | pol (RT) | Nonadapted | B27 | 356 | E | 4.39 × 10−4 | 1.58 × 10−1 | 11 |
| +1 | pol (int) | Adapted | B44 | 153 | L | 1.15 × 10−4 | 6.49 × 10−2 | 3 |
| +1 | pol (int) | Adapted | A03 | 240 | N | 2.4 × 10−4 | 10−1 | 6 |
| +1 | pol (int) | Nonadapted | A03 | 240 | S | 3.22 × 10−4 | 1.26 × 10−1 | 6 |
| +1 | pol (int) | Nonadapted | A03 | 241 | F | 1.78 × 10−8 | 3.55 × 10−5 | 7 |
| +1 | pol (int) | Adapted | A03 | 241 | S | 3.06 × 10−5 | 2.03 × 10−2 | 7 |
| +1 | pol (int) | Nonadapted | A23 | 241 | F | 3.56 × 10−4 | 1.33 × 10−1 | 7 |
| +1 | Nef | Nonadapted | B13 | 24 | S | 4.34 × 10−4 | 1.02 × 10−1 | 3 |
| +1 | Nef | Adapted | C05 | 28 | M | 6.29 × 10−4 | 1.3 × 10−1 | 4 |
| +1 | Nef | Adapted | A02 | 28 | P | 9.83 × 10−4 | 1.74 × 10−1 | 4 |
| +1 | Nef | Nonadapted | B18 | 58 | * | 4.28 × 10−4 | 1.02 × 10−1 | 4 |
| +1 | Nef | Nonadapted | B44 | 146 | Y | 8.49 × 10−4 | 1.6 × 10−1 | 3 |
| +1 | Nef | Adapted | C15 | 158 | K | 3.01 × 10−4 | 7.77 × 10−2 | 3 |
| +1 | Nef | Adapted | A24 | 177 | K | 1.41 × 10−4 | 3.98 × 10−2 | 3 |
| +2 | Gag | Adapted | C05 | 12 | L | 4.76 × 10−4 | 1.8 × 10−1 | 14 |
| +2 | Gag | Nonadapted | A03 | 45 | S | 5.19 × 10−5 | 4.08 × 10−2 | 13 |
| +2 | Gag | Nonadapted | C06 | 53 | S | 5.29 × 10−5 | 4.08 × 10−2 | 5 |
| +2 | Gag | Adapted | B40 | 99 | G | 3.42 × 10−4 | 1.51 × 10−1 | 4 |
| +2 | Gag | Adapted | A68 | 123 | R | 9.03 × 10−6 | 1.16 × 10−2 | 4 |
| +2 | Gag | Nonadapted | A23 | 138 | P | 1.82 × 10−4 | 1.04 × 10−1 | 8 |
| +2 | Gag | Adapted | C06 | 168 | H | 8.89 × 10−5 | 6.22 × 10−2 | 20 |
| +2 | Gag | Nonadapted | B49 | 183 | F | 1.47 × 10−4 | 9.18 × 10−2 | 28 |
| +2 | Gag | Adapted | B57 | 253 | P | 4.61 × 10−4 | 1.8 × 10−1 | 11 |
| +2 | Gag | Nonadapted | B57 | 253 | S | 4.61 × 10−4 | 1.8 × 10−1 | 11 |
| +2 | Gag | Adapted | C02 | 272 | S | 2.31 × 10−4 | 1.15 × 10−1 | 4 |
| +2 | Gag | Adapted | B48 | 298 | S | 5.09 × 10−4 | 1.9 × 10−1 | 4 |
| +2 | Gag | Adapted | B48 | 321 | I | 2.32 × 10−4 | 1.15 × 10−1 | 9 |
| +2 | Gag | Nonadapted | B53 | 465 | G | 1.18 × 10−5 | 1.29 × 10−2 | 12 |
| +2 | Gag | Adapted | B52 | 499 | A | 1.95 × 10−5 | 1.88 × 10−2 | 17 |
| +2 | Gag | Nonadapted | B51 | 499 | T | 7.49 × 10−5 | 5.41 × 10−2 | 17 |
| +2 | Gag | Nonadapted | B52 | 499 | T | 9.38 × 10−5 | 6.37 × 10−2 | 17 |
| +2 | pol (pro) | Adapted | A01 | 73 | H | 4.26 × 10−6 | 6.86 × 10−3 | 10 |
| +2 | pol (pro) | Nonadapted | A01 | 73 | Y | 2.61 × 10−4 | 1.63 × 10−1 | 10 |
| +2 | pol (RT) | Adapted | B07 | 25 | L | 2.87 × 10−4 | 1.75 × 10−1 | 10 |
| +2 | pol (RT) | Adapted | A01 | 53 | K | 2.18 × 10−4 | 1.49 × 10−1 | 18 |
| +2 | pol (RT) | Adapted | B58 | 271 | C | 6.64 × 10−5 | 6.5 × 10−2 | 6 |
| +2 | pol (int) | Adapted | A03 | 240 | T | 2.4 × 10−4 | 1.53 × 10−1 | 6 |
| +2 | pol (int) | Nonadapted | A03 | 240 | A | 2.41 × 10−4 | 1.53 × 10−1 | 6 |
| +2 | pol (int) | Nonadapted | A03 | 241 | S | 1.78 × 10−8 | 4.84 × 10−5 | 7 |
| +2 | pol (int) | Adapted | A03 | 241 | P | 3.08 × 10−5 | 3.24 × 10−2 | 7 |
| +2 | Nef | Adapted | B40 | 157 | * | 5.17 × 10−4 | 1.25 × 10−1 | 4 |
| RF | Protein | Association | HLA | Pos HXB2 | aa | p-value | q-value | Dist |
| +1 | Gag | Adapted | C05 | 12 | T | 4.76 × 10−4 | 1.91 × 10−1 | 14 |
| +1 | Gag | Nonadapted | A03 | 45 | Q | 1.47 × 10−4 | 1.02 × 10−1 | 13 |
| +1 | Gag | Adapted | A29 | 86 | F | 1.07 × 10−4 | 7.94 × 10−2 | 5 |
| +1 | Gag | Adapted | B40 | 99 | R | 3.42 × 10−4 | 1.73 × 10−1 | 4 |
| +1 | Gag | Adapted | B08 | 132 | T | 3.84 × 10−4 | 1.73 × 10−1 | 5 |
| +1 | Gag | Nonadapted | A23 | 138 | S | 2.04 × 10−4 | 1.23 × 10−1 | 8 |
| +1 | Gag | Adapted | C06 | 168 | S | 8.89 × 10−5 | 6.79 × 10−2 | 20 |
| +1 | Gag | Adapted | B57 | 253 | T | 4.41 × 10−4 | 1.85 × 10−1 | 11 |
| +1 | Gag | Nonadapted | B57 | 253 | I | 4.43 × 10−4 | 1.85 × 10−1 | 11 |
| +1 | Gag | Adapted | B48 | 321 | Y | 3.08 × 10−4 | 1.64 × 10−1 | 9 |
| +1 | Gag | Nonadapted | B48 | 321 | C | 3.08 × 10−4 | 1.64 × 10−1 | 9 |
| +1 | Gag | Nonadapted | B52 | 499 | H | 4.07 × 10−4 | 1.76 × 10−1 | 17 |
| +1 | pol (pro) | Adapted | A01 | 73 | A | 4.26 × 10−6 | 3.55 × 10−3 | 10 |
| +1 | pol (RT) | Adapted | B07 | 25 | P | 2.87 × 10−4 | 1.18 × 10−1 | 10 |
| +1 | pol (RT) | Adapted | A01 | 53 | K | 2.17 × 10−4 | 9.2 × 10−2 | 18 |
| +1 | pol (RT) | Adapted | B46 | 151 | K | 1.49 × 10−4 | 7.66 × 10−2 | 7 |
| +1 | pol (RT) | Nonadapted | B46 | 151 | R | 1.53 × 10−4 | 7.66 × 10−2 | 7 |
| +1 | pol (RT) | Nonadapted | B40 | 258 | R | 5.1 × 10−4 | 1.74 × 10−1 | 13 |
| +1 | pol (RT) | Adapted | B40 | 258 | K | 5.1 × 10−4 | 1.74 × 10−1 | 13 |
| +1 | pol (RT) | Adapted | B58 | 271 | M | 8.2 × 10−5 | 4.93 × 10−2 | 6 |
| +1 | pol (RT) | Adapted | B14 | 305 | R | 5.63 × 10−4 | 1.84 × 10−1 | 8 |
| +1 | pol (RT) | Nonadapted | B14 | 305 | K | 5.63 × 10−4 | 1.84 × 10−1 | 8 |
| +1 | pol (RT) | Adapted | C06 | 326 | * | 5.75 × 10−4 | 1.86 × 10−1 | 3 |
| +1 | pol (RT) | Nonadapted | B27 | 356 | E | 4.39 × 10−4 | 1.58 × 10−1 | 11 |
| +1 | pol (int) | Adapted | B44 | 153 | L | 1.15 × 10−4 | 6.49 × 10−2 | 3 |
| +1 | pol (int) | Adapted | A03 | 240 | N | 2.4 × 10−4 | 10−1 | 6 |
| +1 | pol (int) | Nonadapted | A03 | 240 | S | 3.22 × 10−4 | 1.26 × 10−1 | 6 |
| +1 | pol (int) | Nonadapted | A03 | 241 | F | 1.78 × 10−8 | 3.55 × 10−5 | 7 |
| +1 | pol (int) | Adapted | A03 | 241 | S | 3.06 × 10−5 | 2.03 × 10−2 | 7 |
| +1 | pol (int) | Nonadapted | A23 | 241 | F | 3.56 × 10−4 | 1.33 × 10−1 | 7 |
| +1 | Nef | Nonadapted | B13 | 24 | S | 4.34 × 10−4 | 1.02 × 10−1 | 3 |
| +1 | Nef | Adapted | C05 | 28 | M | 6.29 × 10−4 | 1.3 × 10−1 | 4 |
| +1 | Nef | Adapted | A02 | 28 | P | 9.83 × 10−4 | 1.74 × 10−1 | 4 |
| +1 | Nef | Nonadapted | B18 | 58 | * | 4.28 × 10−4 | 1.02 × 10−1 | 4 |
| +1 | Nef | Nonadapted | B44 | 146 | Y | 8.49 × 10−4 | 1.6 × 10−1 | 3 |
| +1 | Nef | Adapted | C15 | 158 | K | 3.01 × 10−4 | 7.77 × 10−2 | 3 |
| +1 | Nef | Adapted | A24 | 177 | K | 1.41 × 10−4 | 3.98 × 10−2 | 3 |
| +2 | Gag | Adapted | C05 | 12 | L | 4.76 × 10−4 | 1.8 × 10−1 | 14 |
| +2 | Gag | Nonadapted | A03 | 45 | S | 5.19 × 10−5 | 4.08 × 10−2 | 13 |
| +2 | Gag | Nonadapted | C06 | 53 | S | 5.29 × 10−5 | 4.08 × 10−2 | 5 |
| +2 | Gag | Adapted | B40 | 99 | G | 3.42 × 10−4 | 1.51 × 10−1 | 4 |
| +2 | Gag | Adapted | A68 | 123 | R | 9.03 × 10−6 | 1.16 × 10−2 | 4 |
| +2 | Gag | Nonadapted | A23 | 138 | P | 1.82 × 10−4 | 1.04 × 10−1 | 8 |
| +2 | Gag | Adapted | C06 | 168 | H | 8.89 × 10−5 | 6.22 × 10−2 | 20 |
| +2 | Gag | Nonadapted | B49 | 183 | F | 1.47 × 10−4 | 9.18 × 10−2 | 28 |
| +2 | Gag | Adapted | B57 | 253 | P | 4.61 × 10−4 | 1.8 × 10−1 | 11 |
| +2 | Gag | Nonadapted | B57 | 253 | S | 4.61 × 10−4 | 1.8 × 10−1 | 11 |
| +2 | Gag | Adapted | C02 | 272 | S | 2.31 × 10−4 | 1.15 × 10−1 | 4 |
| +2 | Gag | Adapted | B48 | 298 | S | 5.09 × 10−4 | 1.9 × 10−1 | 4 |
| +2 | Gag | Adapted | B48 | 321 | I | 2.32 × 10−4 | 1.15 × 10−1 | 9 |
| +2 | Gag | Nonadapted | B53 | 465 | G | 1.18 × 10−5 | 1.29 × 10−2 | 12 |
| +2 | Gag | Adapted | B52 | 499 | A | 1.95 × 10−5 | 1.88 × 10−2 | 17 |
| +2 | Gag | Nonadapted | B51 | 499 | T | 7.49 × 10−5 | 5.41 × 10−2 | 17 |
| +2 | Gag | Nonadapted | B52 | 499 | T | 9.38 × 10−5 | 6.37 × 10−2 | 17 |
| +2 | pol (pro) | Adapted | A01 | 73 | H | 4.26 × 10−6 | 6.86 × 10−3 | 10 |
| +2 | pol (pro) | Nonadapted | A01 | 73 | Y | 2.61 × 10−4 | 1.63 × 10−1 | 10 |
| +2 | pol (RT) | Adapted | B07 | 25 | L | 2.87 × 10−4 | 1.75 × 10−1 | 10 |
| +2 | pol (RT) | Adapted | A01 | 53 | K | 2.18 × 10−4 | 1.49 × 10−1 | 18 |
| +2 | pol (RT) | Adapted | B58 | 271 | C | 6.64 × 10−5 | 6.5 × 10−2 | 6 |
| +2 | pol (int) | Adapted | A03 | 240 | T | 2.4 × 10−4 | 1.53 × 10−1 | 6 |
| +2 | pol (int) | Nonadapted | A03 | 240 | A | 2.41 × 10−4 | 1.53 × 10−1 | 6 |
| +2 | pol (int) | Nonadapted | A03 | 241 | S | 1.78 × 10−8 | 4.84 × 10−5 | 7 |
| +2 | pol (int) | Adapted | A03 | 241 | P | 3.08 × 10−5 | 3.24 × 10−2 | 7 |
| +2 | Nef | Adapted | B40 | 157 | * | 5.17 × 10−4 | 1.25 × 10−1 | 4 |
RF indicates the reading frame relative to the regular coding frame of the respective protein. For associations, adapted forms are amino acids significantly enriched in the presence of the HLA allele in question (and vice versa), whereas nonadapted forms (also commonly called wild-type or susceptible forms) are amino acids significantly depleted in the presence of the HLA allele in question (and vice versa). HLA indicates the HLA allele for which the association was observed. Pos HXB2 indicates the amino acid position in the corresponding HXB2 primary reading frame sequence (Leitner et al., 2005). aa indicates the amino acid for which the HLA-associated polymorphism was observed. dist indicates the distance (in amino acids) to the next HLA-associated viral polymorphism (to any HLA allele) in the primary ORF. Asterisks indicate stop codons.