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Table 2 HIV-1 genetic polymorphisms identified in this study, which have previously been associated with disease progression and/or impaired replicative fitness

From: Impaired human immunodeficiency virus type 1 replicative fitness in atypical viremic non-progressor individuals

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%)    
  1. 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