Table 2.
HIV-1 genetic polymorphisms identified in this study, which have previously been associated with disease progression and/or impaired replicative fitness
| Positiona | Viremic non-progressors (VNP) | Typical progressors (TP) | Rapid progressor (RP) | ||||
|---|---|---|---|---|---|---|---|
| VNP-1 | VNP-2 | VNP-3 | TP-1 | TP-2 | TP-3 | RP | |
| LTR | |||||||
| 287–292 | A219G (18%) | A292ins (1%) | C290T (2%) | A219G (3%) A219ins (3%) |
T287C (11%) T292A (99%) |
||
| 319–324 | T319A (99%) | T319A (100%) A324G (100%) |
T319A (99%) A324G (27%) |
T319A (99%) A324G (99%) |
T319A (99%) 320ins (11–57%) A324G (72%) |
T319A (99%) | T319A (100%) |
| 325–333 | 329ins (39%) C333T (11%) |
332del (3%) | 328ins (1%) | G331A (1%) | |||
| 346–356 | G350A (1%) | A348T (11%) 355del (2%) |
G350A (3%) | ||||
| 361–371 | G363A (6%) G364A (7%) |
G366A (1%) | T32C (9%) G363A (10%) |
||||
| 374–385 | A374G (74%) A378G (1%) G379A (1%) G385A (97%) |
G377A (3%) 381ins (1%) |
A374G (7%) | 381ins (1%) | A378G (2%) 380ins (1%) C381T (99%) G384A (1%) |
374ins (91%) G384A (100%) G385A (100%) |
A374G (9%) 374ins (52%) G384A (99%) |
| 386–397 | C386T (97%) C387G (2%) G389A (30%) |
G395A (2%) | 380del (1%) | G389A (2%) | 396ins (99%) | 387G (3%) G393A (2%) | |
| 398–409 | G399A (7%) | 398ins (2%) | 403ins (1%) 405ins (3%) |
T398A (90%) | G409A (8%) | G400A (18%) | |
| 427–431 | 430del (1%), 431del (1%) | 430del (2%) | 430del (9%), 431del (1%) | 430del (2%) | 431del (2%) | ||
| 455–515 | 11SNPs (>1%), 13 indels (>1%) | 8 SNPS, 11 indels | 3 SNPs (>1%), 12 indels (>1%) | 3 SNPs (>1%), 5 indels (>1%) | 2 SNPs (>1%), 6 indels (>1%) | 4 SNPs (>1%), 2 indels (>1%) | 5 SNPs (>1%), 3 indels (>1%) |
| gag | |||||||
| 823–825 | E12Q (99%) | ||||||
| 988–990 | S67A (16%) | S67A (3%) | S67A (100%) | ||||
| 1093–1095 | D102E (98%) | D102E (9%) | D102E (73%) | D102E (100%) | |||
| 1225–1227 | A146P (86%) | ||||||
| 1513–1515 | T242N (99%) | ||||||
| 1531–1533 | G284A (99%) | G284A (99%) | G284A (99%) | ||||
| 1954–1956 | T389I (99%) | T389I (100%) | |||||
| 2233–2235 | E482D (99%) | ||||||
| vif | |||||||
| 5434–5436 | R132S (92%) | ||||||
| vpr | |||||||
| 5773–5775 | F72S (4%) | ||||||
| 5788–5790 | R77Q (99%) | R77Q (99%) | R77Q (99%) | R77Q (99%) | R77Q (99%) | R77Q (99%) | |
| 5806–5826 | Ins (7%) | ||||||
| rev | |||||||
| 8522–8524 | Q74H (99%) | Q74P (99%) | Q74P (75%) | ||||
| 8612–8614 | V104G (99%) | V104L (33%) | |||||
| nef | |||||||
| 9208–9210 | T138C (99%) | ||||||
| 8839–8841 | T15A (99%) | T15A (98%) | T15N (100%) | ||||
| 8950–8952 | |||||||
| 9100–9102 | H102Y (99%) | H102Y (99%) | H102W (99%) | H102W (99%) | H102Y (99%) | H102Y (99%) | H102Y (100%) |
| 9340–9342 | E182Q (99%) | E182V (99%) | E182V (99%) | ||||
a Positions in the HIV-1 genome relative to the HIV-1HXB2 (GenBank: K03455) strain reference. Single-nucleotide polymorphisms (SNPs) in the LTR or amino substitutions in the HIV-1 coding regions are indicated, including their frequency in the virus population (%) quantified by deep sequencing. For example: A219G (18%) in the LTR of the VNP-1 HIV-1 isolate or R77Q (99%) in the vpr gene of the VNP-2 HIV-1 isolate. Indels, insertions and/or deletions