Supplemental figure 1. Allelic frequency of HLA alleles in this cohort and Vietnam.
HLA-A, HLA-B and HLA-C allele frequencies in our Vietnamese cohort (Blue bar) are shown alongside their corresponding frequencies in Vietnam from the open database (Red bar).
A*01:01 A*02:01
A*02:03 A*02:06
A*02:07 A*02:11
A*02:16 A*03:01
A*03:02 A*11:01
A*11:02 A*11:04
A*24:02 A*24:03
A*24:07 A*24:10
A*26:01 A*29:01
A*30:01 A*31:01
A*32:01 A*33:03
A*34:01 A*68:01
A*68:02 0
5 10 15 20 25 30
Vietnamese cohort Vietnamese database
HLA-A allelic frequency (%)
C*01:02 C*02:02
C*03:02 C*03:03
C*03:04 C*03:17
C*04:01 C*04:03
C*04:06 C*06:02
C*07:01 C*07:02
C*07:04 C*08:01
C*12:02 C*12:03
C*14:02 C*15:02
C*15:05 C*16:02 0
2 4 6 8 10 12 14 16 18
HLA-C allelic frequency (%)
B*07:02 B*07:05
B*08:01 B*13:01
B*13:02 B*15:01
B*15:02 B*15:10
B*15:11 B*15:12
B*15:13 B*15:18
B*15:21 B*15:25
B*15:27 B*15:35
B*18:01 B*18:02
B*27:04 B*27:05
B*27:06 B*35:01
B*35:03 B*35:05
B*37:01 B*38:01
B*38:02 B*39:01
B*39:09 B*40:01
B*40:02 B*40:03
B*40:06 B*44:03
B*46:01 B*48:01
B*48:03 B*50:01
B*51:01 B*51:02
B*52:01 B*54:01
B*55:01 B*55:02
B*55:04 B*56:01
B*56:02 B*56:04
B*57:01 B*58:01
B*71:37 B*73:01 0
2 4 6 8 10 12 14 16
HLA-B allelic frequency (%)
Supplemental figure 2. Correlation between HLA-associated substitutions in Gag, Pol, and Nef with clinical parameters.
The total number of HLA-associated substitutions in each individual’s Gag, Pol, and Nef amino acid sequence was
counted (see methods). Correlations between the HLA-associated substitutions in Gag, Pol or Nef and pVL or
CD4 count were analyzed using Spearman’s correlation. Trend lines are included to help visualize the relationship.
Protein Codon HLA allele Amino Acid Consensus TT TF FT FF N Direction PValue QValue
Gag 7 A0206 I V 1 37 58 273 369 NonAdapted 0.0001 0.05
Gag 7 A0206 V V 37 1 273 58 369 Adapted 0.0001 0.05
Gag 9 B1301 S S 21 13 299 35 368 NonAdapted 1.018E-05 0.008
Gag 9 B1301 T S 11 23 29 305 368 Adapted 2.123E-05 0.01
Gag 26 B1525 K K 22 21 304 22 369 NonAdapted 2.078E-11 5.064E-08
Gag 26 B1525 R K 21 22 18 308 369 Adapted 1.979E-12 5.786E-09
Gag 30 A1102 R R 21 0 234 69 324 Adapted 0.0001 0.05
Gag 30 A2402 K R 1 56 64 248 369 NonAdapted 2.652E-05 0.02
Gag 30 B1502 R R 67 29 218 55 369 NonAdapted 0.0004 0.13
Gag 31 A2601 M M 14 1 197 157 369 Adapted 0.0005 0.16
Gag 42 B5701 D E 0 16 29 324 369 NonAdapted 0.0006 0.16
Gag 42 B5701 E E 16 0 321 32 369 Adapted 0.0006 0.16
Gag 46 A0203 L L 34 16 285 34 369 NonAdapted 2.069E-05 0.02
Gag 46 A0203 I L 13 37 27 292 369 Adapted 0.0004 0.13
Gag 46 A1102 L L 17 5 284 44 350 NonAdapted 0.0006 0.15
Gag 46 C0801 L L 99 6 202 43 350 Adapted 0.0008 0.18
Gag 49 B3802 G G 39 5 319 6 369 NonAdapted 0.0005 0.15
Gag 54 A0203 A A 24 26 284 35 369 NonAdapted 6.228E-10 1.138E-06
Gag 54 A0203 G A 9 41 12 307 369 Adapted 8.973E-06 0.01
Gag 54 A0203 T A 9 41 10 309 369 Adapted 2.786E-05 0.02
Gag 60 A1101 I I 89 83 123 74 369 NonAdapted 0.0003 0.13
Gag 60 A1101 L I 80 92 69 128 369 Adapted 1.569E-05 0.01
Gag 75 B5801 L L 38 24 269 38 369 NonAdapted 1.167E-06 0.001
Gag 75 B5801 V L 12 50 13 294 369 Adapted 0.0006 0.16
Gag 75 C0302 I L 12 48 21 288 369 Adapted 0.0002 0.08
Gag 76 B1502 R K 15 81 65 208 369 NonAdapted 0.0004 0.14
Gag 79 A3101 F F 4 10 254 101 369 NonAdapted 0.0004 0.13
Gag 79 A3101 Y F 10 4 98 257 369 Adapted 0.0004 0.13
Gag 82 A3303 I I 27 60 126 156 369 NonAdapted 9.243E-05 0.05
Gag 82 B5801 L I 12 50 20 287 369 Adapted 0.0002 0.07
Gag 83 A1101 A A 122 50 171 26 369 NonAdapted 0.0005 0.15
Gag 83 A1101 V A 48 124 24 173 369 Adapted 0.0004 0.13
Gag 83 B4601 V A 11 63 54 196 324 NonAdapted 6.186E-05 0.03
Gag 86 C0302 W W 35 25 267 42 369 NonAdapted 0.0002 0.08
Gag 91 A1101 R R 129 43 162 35 369 NonAdapted 0.0007 0.17
Gag 91 B4001 R R 25 17 266 61 369 NonAdapted 0.0006 0.15
Gag 93 B4001 E E 23 19 273 54 369 NonAdapted 0.0001 0.05
Gag 93 B5701 E E 8 8 288 65 369 NonAdapted 0.0005 0.14
Gag 107 B1502 E V 0 96 20 253 369 NonAdapted 0.0003 0.09
Gag 110 B5801 E K 6 55 9 296 366 Adapted 0.0002 0.09
Gag 113 B4403 Q Q 15 5 328 15 363 NonAdapted 0.0008 0.19
Gag 122 B4403 T P 8 10 71 272 361 Adapted 6.24E-05 0.03
Gag 125 A0206 S S 38 0 268 47 353 Adapted 0.0007 0.17
Gag 143 B1525 V V 32 11 315 11 369 NonAdapted 1.087E-06 0.001
Gag 146 C0602 P P 7 19 285 58 369 NonAdapted 3.161E-09 4.621E-06
Gag 146 C0602 A P 8 18 13 330 369 Adapted 0.0002 0.08
Gag 146 C0602 S P 14 12 42 301 369 Adapted 4.25E-08 5.648E-05
Gag 228 B1301 L M 6 28 13 322 369 Adapted 9.276E-05 0.04
Gag 242 B5701 T T 0 16 281 72 369 NonAdapted 7.023E-17 3.423E-13
Gag 242 B5701 N T 15 1 72 281 369 Adapted 2.302E-14 8.415E-11
Gag 242 B5801 T T 4 58 277 30 369 NonAdapted 4.437E-38 3.244E-34
Gag 242 B5801 N T 58 4 29 278 369 Adapted 2.111E-38 3.086E-34
Gag 248 B5801 A G 9 48 18 279 354 Adapted 0.0002 0.07
Gag 255 B5401 P P 8 5 301 55 369 NonAdapted 0.0002 0.07
Gag 255 B5401 S P 3 10 25 331 369 Adapted 0.0006 0.15
Gag 255 C0702 P P 106 13 203 47 369 Adapted 0.0008 0.19
Gag 280 C0102 V V 81 25 246 17 369 NonAdapted 2.916E-05 0.02
Gag 280 C0102 T V 19 87 8 255 369 Adapted 0.0001 0.05
Gag 281 C0102 S S 86 20 254 9 369 NonAdapted 2.394E-05 0.02
Gag 281 C0102 G S 19 87 9 254 369 Adapted 6.122E-05 0.03
Gag 315 C0302 N N 48 12 304 5 369 NonAdapted 2.242E-07 0.0003
Gag 342 A0206 T T 23 15 300 31 369 NonAdapted 9.906E-07 0.001
Gag 342 A0206 S T 15 23 31 300 369 Adapted 9.906E-07 0.001
Gag 369 B3802 N H 10 34 54 271 369 Adapted 0.0005 0.14
Gag 371 A1102 Q Q 20 3 335 11 369 NonAdapted 0.0008 0.19
Gag 375 B3802 N N 28 16 264 61 369 NonAdapted 0.0005 0.15
Gag 386 C0303 Q Q 18 16 278 57 369 NonAdapted 0.0007 0.16
Gag 386 C0303 P Q 14 20 50 285 369 Adapted 7.335E-05 0.04
Gag 397 A3101 K K 5 9 343 12 369 NonAdapted 1.16E-09 1.884E-06
Gag 397 A3101 R K 9 5 10 345 369 Adapted 3.455E-10 7.216E-07
Gag 403 A3101 R R 9 5 342 13 369 NonAdapted 0.0005 0.14
Gag 403 A3101 K R 5 9 13 342 369 Adapted 0.0005 0.14
Gag 437 C0801 I I 63 49 198 59 369 NonAdapted 0.0005 0.15
Gag 441 A2407 S N 2 19 9 281 311 Adapted 0.0008 0.19
Gag 462 B1525 D N 0 43 67 259 369 NonAdapted 2.398E-05 0.02
Gag 466 A1102 R G 5 18 9 332 364 Adapted 0.0007 0.17
Gag 481 B4001 E E 23 13 283 27 346 NonAdapted 1.211E-05 0.01
Gag 481 B4001 G E 7 29 8 302 346 Adapted 0.0002 0.08
Gag 483 A1101 S P 8 142 2 176 328 Adapted 0.0007 0.16
Pol 14 B0705 K K 38 15 276 30 359 NonAdapted 4.763E-05 0.02
Pol 14 B0705 R K 14 39 30 276 359 Adapted 0.0002 0.05
Pol 19 C0602 L L 21 4 315 19 359 NonAdapted 0.0009 0.17
Pol 41 C0702 K K 106 11 237 5 359 NonAdapted 0.0001 0.04
Pol 41 C0702 R K 10 107 5 237 359 Adapted 0.0005 0.12
Pol 60 C0401 D D 23 3 314 19 359 NonAdapted 0.001 0.19
Pol 63 A0203 L L 23 27 213 96 359 NonAdapted 0.0005 0.12
Pol 82 B4601 V V 64 17 245 33 359 NonAdapted 0.0004 0.12
Pol 82 B4601 I V 17 64 33 245 359 Adapted 0.0004 0.12
Pol 93 B1512 I I 3 16 233 107 359 NonAdapted 0.0001 0.04
Pol 93 B1512 L I 16 3 101 239 359 Adapted 0.0002 0.08
Pol 110 B0705 K T 34 19 89 217 359 Adapted 0.0004 0.12
Pol 138 B1502 T K 16 71 38 233 358 Adapted 0.0007 0.15
Supplemental table 1. HLA-associated polymorphisms in HIV-1 Gag, Pol, and Nef in Hanoi cohort (q<0.2).
Pol 138 C0303 K K 7 27 164 161 359 NonAdapted 0.0003 0.09
Pol 138 C0303 A K 4 30 11 314 359 Adapted 0.0003 0.11
Pol 159 C0302 I V 2 60 40 253 355 NonAdapted 9.389E-05 0.04
Pol 159 C0302 V V 60 2 253 40 355 Adapted 9.391E-05 0.04
Pol 201 C1502 K K 11 5 328 15 359 NonAdapted 0.0008 0.16
Pol 210 B1502 V V 76 11 262 10 359 NonAdapted 1.261E-05 0.01
Pol 210 B1502 I V 11 76 10 262 359 Adapted 1.261E-05 0.01
Pol 222 A1102 S S 22 1 240 96 359 Adapted 0.0009 0.17
Pol 222 B4001 S S 36 4 226 93 359 Adapted 0.001 0.19
Pol 234 A0206 T I 11 25 32 290 358 Adapted 6.721E-05 0.04
Pol 234 B1525 T I 2 38 41 277 358 NonAdapted 0.0009 0.18
Pol 234 B5101 I I 4 11 286 57 358 NonAdapted 0.0003 0.09
Pol 234 C1402 I I 2 10 288 58 358 NonAdapted 1.852E-06 0.002
Pol 234 C1402 T I 8 4 35 311 358 Adapted 0.0004 0.12
Pol 261 C0702 Y C 13 104 13 229 359 Adapted 0.0006 0.132
Pol 261 C1505 Y C 10 37 16 296 359 Adapted 0.0001 0.042
Pol 272 A1101 I I 116 47 110 86 359 Adapted 0.0009 0.18
Pol 272 B0705 I I 21 32 205 101 359 NonAdapted 0.0007 0.17
Pol 293 A1101 E E 154 9 192 3 358 NonAdapted 0.0007 0.14
Pol 299 C1203 I T 5 9 31 314 359 Adapted 0.001 0.19
Pol 301 B1502 V I 0 86 20 252 358 NonAdapted 0.001 0.19
Pol 301 B1502 I I 86 0 251 21 358 Adapted 0.0006 0.14
Pol 306 A3303 S S 38 49 155 117 359 NonAdapted 0.0001 0.05
Pol 306 B4001 N S 17 23 46 273 359 Adapted 2.477E-05 0.02
Pol 306 C0302 G S 9 54 11 285 359 Adapted 0.0005 0.12
Pol 306 C0701 N S 10 10 53 286 359 Adapted 1.878E-06 0.0022
Pol 310 B4601 S S 76 4 245 30 355 Adapted 0.0006 0.132
Pol 310 B5801 N S 5 59 13 278 355 Adapted 0.001 0.192
Pol 313 A3303 L F 1 86 19 253 359 NonAdapted 0.001 0.17
Pol 313 A3303 F F 86 1 253 19 359 Adapted 0.001 0.17
Pol 344 B4403 E E 7 11 328 13 359 NonAdapted 5.442E-11 2.001E-07
Pol 344 B4403 K E 7 11 6 335 359 Adapted 1.91E-07 0.0003
Pol 348 B4403 K K 10 8 325 16 359 NonAdapted 4.252E-06 0.003
Pol 348 B4403 R K 8 10 12 329 359 Adapted 5.527E-07 0.0007
Pol 374 A0206 R K 7 29 8 315 359 Adapted 0.0001 0.04
Pol 385 B5401 T A 5 9 114 231 359 Adapted 0.0006 0.13
Pol 410 A0203 K K 31 19 287 22 359 NonAdapted 0.001 0.19
Pol 411 B3802 T T 28 16 255 60 359 NonAdapted 0.0001 0.05
Pol 444 A1101 P P 145 18 193 3 359 NonAdapted 0.0001 0.04
Pol 468 A0201 T T 17 4 318 20 359 NonAdapted 0.0006 0.13
Pol 470 B5101 V V 13 2 333 11 359 NonAdapted 0.0002 0.08
Pol 474 B1301 I I 21 10 307 21 359 NonAdapted 7.442E-05 0.03
Pol 474 B1301 V I 10 21 20 308 359 Adapted 0.001 0.19
Pol 474 C1202 I I 14 5 314 26 359 NonAdapted 0.0006 0.13
Pol 475 C1203 A A 6 8 321 24 359 NonAdapted 2.889E-06 0.003
Pol 475 C1203 S A 7 7 14 331 359 Adapted 3.054E-06 0.003
Pol 478 C0302 S S 54 9 290 6 359 NonAdapted 0.0001 0.043
Pol 478 C0302 G S 8 55 3 293 359 Adapted 2.525E-05 0.02
Pol 480 C0302 V V 40 23 286 10 359 NonAdapted 2.296E-14 1.688E-10
Pol 480 C0302 I V 23 40 9 287 359 Adapted 1.098E-14 1.615E-10
Pol 498 A2402 E E 53 6 294 6 359 NonAdapted 0.0008 0.16
Pol 498 A2402 D E 6 53 6 294 359 Adapted 0.0008 0.16
Pol 531 A1101 D D 150 13 192 4 359 NonAdapted 0.001 0.19
Pol 531 A1101 E D 13 150 4 192 359 Adapted 0.001 0.19
Pol 551 A2601 I L 5 10 17 327 359 Adapted 0.0004 0.12
Pol 582 A3303 H H 53 34 175 97 359 NonAdapted 0.0005 0.12
Pol 582 C0403 Y H 0 36 79 244 359 NonAdapted 3.968E-05 0.02
Pol 590 B5801 S S 58 7 280 14 359 NonAdapted 0.0003 0.09
Pol 626 B3505 K K 17 0 318 24 359 Adapted 0.0004 0.12
Pol 628 A3101 E E 8 7 310 34 359 NonAdapted 0.0005 0.12
Pol 628 A3101 D E 7 8 33 311 359 Adapted 0.0004 0.12
Pol 629 A0203 K K 50 0 283 25 358 Adapted 0.001 0.19
Pol 629 B1525 K K 40 1 293 24 358 Adapted 0.001 0.19
Pol 653 A2901 L S 8 39 10 302 359 Adapted 0.0002 0.07
Pol 653 B0705 A S 16 37 20 286 359 Adapted 0.0009 0.17
Pol 653 C0801 A S 3 100 33 223 359 NonAdapted 0.001 0.19
Pol 653 C1505 S S 7 40 204 108 359 NonAdapted 1.619E-13 7.937E-10
Pol 653 C1505 A S 16 31 20 292 359 Adapted 8.587E-05 0.03
Pol 653 C1505 N S 6 41 23 289 359 Adapted 0.0005 0.12
Pol 653 C1505 T S 8 39 16 296 359 Adapted 0.0008 0.18
Pol 655 C1505 I I 23 24 288 24 359 NonAdapted 1.308E-08 1.924E-05
Pol 655 C1505 V I 24 23 22 290 359 Adapted 4.716E-09 7.707E-06
Pol 657 C1505 K K 29 18 276 36 359 NonAdapted 1.097E-05 0.008
Pol 657 C1505 R K 18 29 33 279 359 Adapted 5.095E-06 0.005
Pol 670 B4403 E E 2 16 280 61 359 NonAdapted 1.154E-09 2.122E-06
Pol 670 B4403 D E 16 2 56 285 359 Adapted 3.423E-10 1.007E-06
Pol 673 B1525 R R 40 1 279 39 359 Adapted 0.001 0.18
Pol 673 C0702 K R 18 99 19 223 359 Adapted 0.0008 0.16
Pol 680 C0702 A T 28 89 32 210 359 Adapted 0.0004 0.12
Pol 690 B5101 I I 4 11 287 57 359 NonAdapted 7.011E-05 0.04
Pol 690 B5101 V I 11 4 55 289 359 Adapted 5.128E-05 0.03
Pol 691 C1402 V V 4 8 324 23 359 NonAdapted 3.147E-06 0.003
Pol 691 C1402 I V 8 4 19 328 359 Adapted 8.478E-07 0.0013
Pol 704 C1402 L L 8 4 334 13 359 NonAdapted 0.0010073 0.18
Pol 731 A0206 V V 23 13 291 32 359 NonAdapted 8.181E-06 0.007
Pol 731 A0206 I V 13 23 31 292 359 Adapted 6.052E-06 0.005
Pol 743 C0702 V I 0 117 11 231 359 NonAdapted 0.001 0.19
Pol 743 C0702 I I 117 0 227 15 359 Adapted 0.0001 0.04
Pol 783 C0302 N A 7 56 12 284 359 Adapted 0.0008 0.16
Pol 783 C0602 A A 12 13 277 57 359 NonAdapted 7.371E-05 0.04
Pol 785 B5801 V V 51 14 264 30 359 NonAdapted 0.0005 0.12
Pol 785 B5801 L V 10 55 9 285 359 Adapted 0.0002 0.08
Pol 786 B5701 K K 5 11 317 26 359 NonAdapted 8.473E-10 1.78E-06
Pol 786 B5701 R K 11 5 26 317 359 Adapted 8.473E-10 1.78E-06
Pol 795 A2601 Q R 1 14 87 257 359 NonAdapted 0.001 0.19
Pol 795 B1502 R R 71 16 176 96 359 Adapted 0.0004 0.12
Pol 795 B1525 Q R 1 40 87 231 359 NonAdapted 0.00005 0.03
Pol 795 B1525 R R 37 4 210 108 359 Adapted 0.0006 0.13
Pol 795 C0801 Q R 12 91 76 180 359 NonAdapted 0.0001 0.05
Pol 824 A0203 V V 31 19 253 56 359 NonAdapted 0.0008 0.16
Pol 824 A0203 I V 19 31 54 255 359 Adapted 0.0005 0.12
Nef 7 B5701 K K 12 5 344 6 367 NonAdapted 2.808E-05 0.01
Nef 8 A1101 S S 158 7 156 30 351 Adapted 0.0003 0.07
Nef 8 B5701 S S 6 6 277 22 311 NonAdapted 0.0008 0.11
Nef 8 B5701 G S 2 10 6 297 315 Adapted 0.0004 0.08
Nef 10 B4601 L I 9 66 6 249 330 Adapted 0.0002 0.05
Nef 10 B5701 I I 3 9 268 49 329 NonAdapted 9.55E-05 0.03
Nef 10 B5701 L I 4 8 10 307 329 Adapted 0.002 0.16
Nef 11 B5701 V V 7 7 295 24 333 NonAdapted 5.639E-05 0.02
Nef 16 A3303 V V 51 38 158 125 372 NonAdapted 0.002 0.16
Nef 16 A3303 I V 38 51 125 158 372 Adapted 0.002 0.16
Nef 21 C0303 Q R 4 29 9 329 371 Adapted 0.002 0.16
Nef 27 A0207 T A 7 54 100 209 370 NonAdapted 0.0003 0.07
Nef 27 A0207 A A 54 7 208 101 370 Adapted 0.0003 0.07
Nef 48 A0203 M M 38 13 196 125 372 Adapted 0.001 0.15
Nef 48 B1512 M M 7 11 227 127 372 NonAdapted 0.001 0.12
Nef 48 B1512 I M 11 7 112 242 372 Adapted 0.0003 0.07
Nef 48 C0602 I M 2 27 121 222 372 NonAdapted 0.0003 0.08
Nef 48 C0602 M M 25 4 209 134 372 Adapted 0.002 0.16
Nef 51 B1502 A A 69 24 242 36 371 NonAdapted 0.0009 0.12
Nef 51 C0303 A A 31 2 280 58 371 Adapted 0.0002 0.06
Nef 51 C0304 A A 31 11 280 49 371 NonAdapted 0.0005 0.09
Nef 52 C1203 D D 11 3 332 13 359 NonAdapted 0.0007 0.11
Nef 53 C0302 S S 45 19 273 32 369 NonAdapted 0.0002 0.07
Nef 54 B1502 V V 56 35 227 51 369 NonAdapted 0.0007 0.1
Nef 54 B4403 I V 6 14 50 299 369 Adapted 0.002 0.18
Nef 54 B5502 T V 3 14 15 337 369 Adapted 0.001 0.16
Nef 54 C0801 I V 30 78 26 235 369 Adapted 0.0004 0.08
Nef 59 B5401 Q Q 8 5 297 37 347 NonAdapted 0.001 0.15
Nef 63 A3303 D D 49 33 179 87 348 NonAdapted 0.0009 0.12
Nef 65 A1101 E G 28 135 87 101 351 NonAdapted 2.017E-07 0.0001
Nef 65 A1101 G G 134 29 100 88 351 Adapted 2.339E-07 0.0001
Nef 65 A3303 E G 34 46 80 188 348 Adapted 0.0004 0.08
Nef 65 B4403 G G 6 10 218 97 331 NonAdapted 0.001 0.15
Nef 71 B0705 R R 32 21 284 35 372 NonAdapted 8.151E-06 0.003
Nef 71 B0705 K R 18 35 35 284 372 Adapted 0.001 0.14
Nef 71 B1512 R R 7 11 309 45 372 NonAdapted 1.216E-08 1.734E-05
Nef 71 B1512 K R 11 7 42 312 372 Adapted 5.296E-09 1.133E-05
Nef 71 C0702 R R 80 37 236 19 372 NonAdapted 2.324E-07 0.0001
Nef 71 C0702 K R 36 81 17 238 372 Adapted 2.209E-08 1.91E-05
Nef 81 C0303 Y Y 8 25 174 165 372 NonAdapted 0.0004 0.08
Nef 81 C0303 F Y 25 8 165 174 372 Adapted 0.0004 0.08
Nef 81 C0702 Y Y 33 84 149 106 372 NonAdapted 2.091E-08 1.91E-05
Nef 81 C0702 F Y 84 33 106 149 372 Adapted 2.091E-08 1.91E-05
Nef 81 C1402 Y Y 5 8 177 182 372 NonAdapted 0.002 0.16
Nef 81 C1402 F Y 8 5 182 177 372 Adapted 0.002 0.16
Nef 83 A1101 E G 28 145 12 187 372 Adapted 0.0005 0.09
Nef 83 B4001 E G 1 38 39 293 371 NonAdapted 0.001 0.12
Nef 83 B5801 G G 62 4 231 73 370 Adapted 0.0008 0.11
Nef 92 A1101 K K 142 28 188 4 362 NonAdapted 5.18E-07 0.0003
Nef 92 A1101 R K 28 142 4 188 362 Adapted 5.18E-07 0.0003
Nef 98 A0207 D D 44 17 280 31 372 NonAdapted 0.0004 0.08
Nef 98 A0207 E D 17 44 31 280 372 Adapted 0.0004 0.08
Nef 98 C0303 E D 7 24 39 282 352 Adapted 0.002 0.16
Nef 98 C0303 D D 24 7 282 39 352 NonAdapted 0.002 0.16
Nef 101 A0207 I I 35 26 279 32 372 NonAdapted 3.512E-09 1.002E-05
Nef 101 A0207 V I 22 39 28 283 372 Adapted 9.464E-07 0.0004
Nef 101 A1102 V I 1 23 46 284 354 NonAdapted 0.0007 0.1
Nef 101 B4001 I I 37 2 277 56 372 Adapted 0.0007 0.11
Nef 102 B4403 Y Y 10 11 331 20 372 NonAdapted 1.255E-06 0.0006
Nef 102 B4403 H Y 11 10 14 337 372 Adapted 1.509E-07 0.0001
Nef 105 C0701 K K 11 12 326 22 371 NonAdapted 7.067E-05 0.02
Nef 105 C0701 R K 11 12 21 327 371 Adapted 0.0006 0.1
Nef 108 B4403 E E 9 12 332 18 371 NonAdapted 1.076E-06 0.0005
Nef 108 B4403 D E 12 9 18 332 371 Adapted 1.076E-06 0.0005
Nef 133 A2407 T I 6 17 38 311 372 Adapted 0.001 0.14
Nef 135 A2402 Y Y 21 38 257 56 372 NonAdapted 2.232E-08 1.91E-05
Nef 135 A2402 F Y 38 21 54 259 372 Adapted 6.619E-09 1.133E-05
Nef 148 C1502 I V 3 13 11 345 372 Adapted 0.0001 0.04
Nef 150 A0203 P P 37 14 270 48 369 NonAdapted 0.001 0.13
Nef 151 C0702 K R 13 104 57 195 369 NonAdapted 0.002 0.17
Nef 152 A0203 E E 37 10 259 21 327 NonAdapted 0.002 0.17
Nef 152 C0403 D E 8 26 21 313 368 Adapted 0.0005 0.09
Nef 156 A3303 E D 2 85 32 244 363 NonAdapted 0.002 0.17
Nef 156 B0705 N D 6 46 100 212 364 NonAdapted 0.001 0.17
Nef 156 C0702 A D 1 113 12 237 363 NonAdapted 0.001 0.15
Nef 157 A1102 N T 4 19 31 307 361 Adapted 0.0009 0.12
Nef 158 A3303 K K 72 16 246 27 361 NonAdapted 0.0009 0.12
Nef 158 B3505 K K 17 0 297 41 355 Adapted 0.0007 0.1
Nef 158 C0403 K K 24 12 293 31 360 NonAdapted 0.0003 0.07
Nef 158 C1203 K K 10 4 308 39 361 NonAdapted 0.0003 0.07
Nef 159 B4001 G G 25 14 297 26 362 NonAdapted 3.459E-05 0.01
Nef 159 B4001 E G 11 28 22 301 362 Adapted 0.0006 0.1
Nef 161 B4001 D N 1 38 35 295 369 NonAdapted 0.001 0.16
Nef 162 B4601 T N 0 85 23 261 369 NonAdapted 0.002 0.19
Nef 169 C1505 N N 23 24 178 138 363 NonAdapted 0.0005 0.09
Nef 169 C1505 S N 24 23 136 180 363 Adapted 0.0004 0.08
Nef 173 A2901 F F 12 35 130 193 370 NonAdapted 0.001 0.12
Nef 173 C0702 I F 9 107 28 222 366 NonAdapted 0.001 0.13
Nef 173 C1505 I F 12 36 26 298 372 Adapted 0.0005 0.08
Nef 174 B1301 E E 22 9 263 67 361 NonAdapted 0.0004 0.08
Nef 174 B4001 E E 12 27 284 49 372 NonAdapted 9.173E-11 3.925E-07
Nef 174 B4001 D E 19 20 40 293 372 Adapted 2.558E-05 0.01
Nef 174 B4001 G E 9 30 10 323 372 Adapted 1.214E-05 0.005
Nef 176 B1301 G E 4 28 10 329 371 Adapted 0.002 0.16
Nef 176 B4403 E E 2 19 313 37 371 NonAdapted 1.301E-11 1.113E-07
Nef 176 B4403 D E 8 13 9 341 371 Adapted 8.784E-07 0.0004
Nef 182 B4001 I M 8 31 28 305 372 Adapted 0.0006 0.09
Nef 188 A1101 A A 159 14 156 42 371 Adapted 0.0002 0.07
Nef 192 B4601 K K 41 45 205 81 372 NonAdapted 0.0006 0.1
Nef 194 A3101 L I 5 10 13 344 372 Adapted 0.0001 0.04
Nef 194 C0102 V I 7 103 6 256 372 Adapted 0.002 0.18
Nef 194 C0302 I I 49 15 265 38 367 NonAdapted 0.002 0.17
Nef 198 A0101 R L 7 16 23 326 372 Adapted 0.001 0.18
Nef 198 B5701 L L 6 13 281 72 372 NonAdapted 6.245E-06 0.003
Nef 198 C0602 M L 5 24 9 334 372 Adapted 0.002 0.16
Nef 199 B1525 H H 31 10 291 40 372 NonAdapted 0.0008 0.11
Nef 199 B1525 R H 9 32 35 296 372 Adapted 0.0006 0.09
Nef 199 C0302 H H 44 20 278 30 372 NonAdapted 0.0003 0.07
Nef 199 C0302 R H 19 45 25 283 372 Adapted 0.0003 0.07
Nef 201 B3505 D E 13 5 149 205 372 Adapted 0.001 0.14
* Specific condons, consencus amino acids and substitutions listed here are consistent with immune escape map of each gene. The adapted and nondapted
form of each HLA-AP is differentiated in red and blue, respectively. Amino acid substitutions are addressed using same color with the direction of the
association. P-values and q-values represent the minimum values observed using a phylogenetically corrected logistical-regression model. The columns
TT-FF denote the 2x2 contingency table (TT=number of patient with both HLA allele and the target amino acid. TF=number of patients with HLA allele
and without the target amino acid. FT=number of patients without HLA alleles and with the target amino acid. FF=number of patients without both HLA
allele and the target amino acid). N represents number of sequences available for each codon.
HLA allele Number of HLA-associated polymorphisms
Total
Gag Pol Nef
A0101 1 1
A0201 1 1
A0203 5 5 3 13
A0206 5 4 9
A0207 6 6
A1101 6 5 7 18
A1102 4 1 2 7
A2402 1 2 2 3
A2407 1 1 2
A2601 1 2 3
A2901 1 1 2
A3101 6 2 1 9
A3303 1 4 6 11
B0705 5 3 8
B1301 3 2 2 7
B1502 3 6 2 11
B1512 2 4 6
B1525 4 5 2 11
B3505 1 2 3
B3802 3 1 4
B4001 4 2 9 15
B4403 2 6 8 16
B4601 1 3 3 7
B5101 4 4
B5401 2 1 1 4
B5502 1 1
B5701 5 2 7 14
B5801 7 4 1 12
C0102 4 1 5
C0302 3 8 4 15
C0303 2 2 6 10
C0304 1 1
C0401 1 1
C0403 1 2 3
C0602 3 2 3 8
C0701 1 2 3
C0702 1 7 7 15
C0801 2 2 1 5
C1202 1 1
C1203 3 2 5
C1402 5 2 7
C1502 1 1 2
C1505 9 3 12
Supplemental table 2. Number of the HLA-APs in Gag, Pol, and Nef restricted by particular HLA alleles.
* The total of HLA-APs for each HLA allele is counted throughout immune escape maps of Gag, Pol,