HLA imprints and regions tested
| RF | Protein | HLA | aa | Pos | Association | p-value | q-value | Dist | Region of imprint |
| +1 | gag | B52 | H | 499 | Nonadapted | 4.07 × 10−4 | 1.76 × 10−1 | 17 | *LPSDHSLATTPRH* |
| +1 | pol (RT) | B07 | P | 124 | Adapted | 2.87 × 10−4 | 1.18 × 10−1 | 10 | *SQEWMAQKLNNGH* |
| +1 | pol (RT) | A03 | F | 142 | Nonadapted | 1.78 × 10−8 | 3.55 × 10−5 | 7 | GTAEIHFGKDQQSFSGKVKGQ |
| +1 | pol (RT) | B46 | K | 149 | Adapted | 1.49 × 10−4 | 7.66 × 10−2 | 7 | RHQGLDISTMCFHRDGKDHQQYSKVA |
| +1 | pol (RT) | B40 | R | 258 | Nonadapted | 5.1 × 10−4 | 1.74 × 10−1 | 13 | *CCQKKTAGLSMTYRS* |
| +1 | pol (Int) | A03 | N | 240 | Adapted | 2.4 × 10−4 | 10−1 | 6 | TGTAEIHFGKDQQSFSGKVKGQ |
| +1 | pol (Int) | A03 | S | 240 | Nonadapted | 3.22 × 10−4 | 1.26 × 10−1 | 6 | TGTAEIHFGKDQQSFSGKVKGQ |
| +1 | nef | A24 | K | 177 | Adapted | 1.41 × 10−4 | 3.98 × 10−2 | 3 | *ASMGWMTRRKKC* |
| +1 | nef | C15 | K | 158 | Adapted | 3.01 × 10−4 | 7.77 × 10−2 | 3 | *KRPMQERTTACYTL* |
| +2 | gag | C05 | L | 12 | Nonadapted | 4.76 × 10−4 | 1.8 × 10−1 | 14 | GCESVSIKRGRIR* |
| +2 | gag | A03 | S | 45 | Nonadapted | 5.19 × 10−5 | 4.08 × 10−2 | 13 | TYSMGKQGARTIRS* |
| +2 | gag | C06 | S | 53 | Nonadapted | 5.29 × 10−5 | 4.08 × 10−2 | 5 | SWPVRNSRRL |
| +2 | gag | A68 | R | 123 | Adapted | 9.03 × 10−6 | 1.16 × 10−2 | 4 | *HRKQQPGQPKLPYSAE |
| +2 | gag | B49 | F | 183 | Nonadapted | 1.47 × 10−4 | 9.18 × 10−2 | 28 | HVFSIIRRSHPTRFKHHAKHSGGTSSS |
| +2 | gag | B51 | T | 499 | Nonadapted | 7.49 × 10−5 | 5.41 × 10−2 | 17 | SFPQITLWQRPLVT* |
| +2 | gag | B52 | T | 499 | Nonadapted | 9.38 × 10−5 | 6.37 × 10−2 | 17 | SFPQITLWQRPLVT* |
| +2 | gag | B53 | G | 465 | Nonadapted | 1.18 × 10−5 | 1.29 × 10−2 | 12 | TRANSPTRRELQVWGRDNNSLSEAGAD |
| +2 | pol (Pro) | A01 | H | 73 | Nonadapted | 4.26 × 10−6 | 6.86 × 10−3 | 10 | *SYRYSISRTYTCQHNWK |
| +2 | pol (RT) | B07 | L | 25 | Nonadapted | 2.87 × 10−4 | 1.75 × 10−1 | 10 | *TMAIDRRKNKSISRNLY |
| +2 | pol (Int) | A03 | S | 241 | Nonadapted | 1.78 × 10−8 | 4.84 × 10−5 | 7 | GQQRSTLERTSKASLER* |
| RF | Protein | HLA | aa | Pos | Association | p-value | q-value | Dist | Region of imprint |
| +1 | gag | B52 | H | 499 | Nonadapted | 4.07 × 10−4 | 1.76 × 10−1 | 17 | *LPSDHSLATTPRH* |
| +1 | pol (RT) | B07 | P | 124 | Adapted | 2.87 × 10−4 | 1.18 × 10−1 | 10 | *SQEWMAQKLNNGH* |
| +1 | pol (RT) | A03 | F | 142 | Nonadapted | 1.78 × 10−8 | 3.55 × 10−5 | 7 | GTAEIHFGKDQQSFSGKVKGQ |
| +1 | pol (RT) | B46 | K | 149 | Adapted | 1.49 × 10−4 | 7.66 × 10−2 | 7 | RHQGLDISTMCFHRDGKDHQQYSKVA |
| +1 | pol (RT) | B40 | R | 258 | Nonadapted | 5.1 × 10−4 | 1.74 × 10−1 | 13 | *CCQKKTAGLSMTYRS* |
| +1 | pol (Int) | A03 | N | 240 | Adapted | 2.4 × 10−4 | 10−1 | 6 | TGTAEIHFGKDQQSFSGKVKGQ |
| +1 | pol (Int) | A03 | S | 240 | Nonadapted | 3.22 × 10−4 | 1.26 × 10−1 | 6 | TGTAEIHFGKDQQSFSGKVKGQ |
| +1 | nef | A24 | K | 177 | Adapted | 1.41 × 10−4 | 3.98 × 10−2 | 3 | *ASMGWMTRRKKC* |
| +1 | nef | C15 | K | 158 | Adapted | 3.01 × 10−4 | 7.77 × 10−2 | 3 | *KRPMQERTTACYTL* |
| +2 | gag | C05 | L | 12 | Nonadapted | 4.76 × 10−4 | 1.8 × 10−1 | 14 | GCESVSIKRGRIR* |
| +2 | gag | A03 | S | 45 | Nonadapted | 5.19 × 10−5 | 4.08 × 10−2 | 13 | TYSMGKQGARTIRS* |
| +2 | gag | C06 | S | 53 | Nonadapted | 5.29 × 10−5 | 4.08 × 10−2 | 5 | SWPVRNSRRL |
| +2 | gag | A68 | R | 123 | Adapted | 9.03 × 10−6 | 1.16 × 10−2 | 4 | *HRKQQPGQPKLPYSAE |
| +2 | gag | B49 | F | 183 | Nonadapted | 1.47 × 10−4 | 9.18 × 10−2 | 28 | HVFSIIRRSHPTRFKHHAKHSGGTSSS |
| +2 | gag | B51 | T | 499 | Nonadapted | 7.49 × 10−5 | 5.41 × 10−2 | 17 | SFPQITLWQRPLVT* |
| +2 | gag | B52 | T | 499 | Nonadapted | 9.38 × 10−5 | 6.37 × 10−2 | 17 | SFPQITLWQRPLVT* |
| +2 | gag | B53 | G | 465 | Nonadapted | 1.18 × 10−5 | 1.29 × 10−2 | 12 | TRANSPTRRELQVWGRDNNSLSEAGAD |
| +2 | pol (Pro) | A01 | H | 73 | Nonadapted | 4.26 × 10−6 | 6.86 × 10−3 | 10 | *SYRYSISRTYTCQHNWK |
| +2 | pol (RT) | B07 | L | 25 | Nonadapted | 2.87 × 10−4 | 1.75 × 10−1 | 10 | *TMAIDRRKNKSISRNLY |
| +2 | pol (Int) | A03 | S | 241 | Nonadapted | 1.78 × 10−8 | 4.84 × 10−5 | 7 | GQQRSTLERTSKASLER* |
HLA indicates the HLA allele for which the association was observed. aa indicates the amino acid for which the HLA-associated polymorphism was observed. Pos indicates the amino acid position in the corresponding HXB2 primary reading frame sequence (Leitner et al., 2005). For associations, adapted forms are amino acids significantly enriched in the presence of the HLA allele in question (and vice versa), whereas nonadapted forms are amino acids significantly depleted in the presence of the HLA allele in question (and vice versa). Dist indicates the distance (in amino acids) to the next HLA-associated viral polymorphism (to any HLA allele) in the primary ORF. Region of imprint shows the sequences surrounding the imprint (bold). In cases where predicted epitopes were tested, the respective sequence is underlined. *, stop codon.