Table 1.
Sequence analysis of the CCR5 locus in HIV controllers.
| CCR5 reference haplotypes (a) | −2733 | −2554 | −2459 | −2135 | −2132 | −2086 | −1835 | D32 551-582 | ||
|---|---|---|---|---|---|---|---|---|---|---|
| HHA | A | G | G | T | C | A | C | - | ||
| HHB | A | T | G | T | C | A | C | - | ||
| HHC | A | T | G | T | C | G | C | - | ||
| HHD | A | T | G | T | T | A | C | - | ||
| HHE | A | G | A | C | C | A | C | - | ||
| HHF | A | G | A | C | C | A | T | - | ||
| HHG*1 | G | G | A | C | C | A | C | - | ||
| HHG*2 | G | G | A | C | C | A | C | D32 |
| HIV controller CCR5 genotype (b) | −2733 | −2554 | −2459 | −2135 | −2132 | −2086 | −1835 | D32 551-582 | other ORF mutations | CCR5 promoter haplotypes |
|---|---|---|---|---|---|---|---|---|---|---|
| HIC01 | AA | GG | AA | CC | CC | AA | TT | - | - | HHF/HHF |
| HIC02 | AA | GT | AG | CT | CC | AG | CT | - | - | HHC/HHF |
| HIC03 | AA | TT | GG | TT | CC | GG | CC | - | - | HHC/HHC |
| HIC04 | AA | GT | GG | TT | CT | AA | CC | - | - | HHA/HHD |
| HIC05 | AA | GG | AA | CC | CC | AA | CC | - | - | HHE/HHE |
| HIC06 | AA | GG | AA | CC | CC | AA | CC | - | - | HHE/HHE |
| HIC07 | AA | GT | AG | CT | CT | AA | CC | - | A335V | HHD/HHE |
| HIC08 | AA | TT | GG | TT | CC | GG | CC | - | - | HHC/HHC |
| HIC09 | AA | GT | AG | CT | CC | AG | CC | - | - | HHC/HHE |
| HIC10 | AA | GG | AA | CC | CC | AA | CT | - | A335V | HHE/HHF |
| HIC11 | AG | GG | AA | CC | CC | AA | CT | D32 | Q280P | HHF/HHG*2 |
| HIC12 | AA | GT | AG | CT | CC | AG | CT | - | - | HHC/HHF |
| HIV controller CCR5 genotype (c) | −2733 | −2554 | −2459 | −2135 | −2132 | −2086 | −1835 | D32 551-582 | other ORF mutations | CCR5 promoter haplotypes |
|---|---|---|---|---|---|---|---|---|---|---|
| HIC-D32-1 | AG | GT | AG | CT | CC | AG | CC | D32 | - | HHC/HHG*2 |
| HIC-D32-2 | AG | GT | AG | CT | CC | AG | CC | D32 | F118L | HHC/HHG*2 |
| HIC-D32-3 | AG | GT | AG | CT | CC | AG | CC | D32 | - | HHC/HHG*2 |
(a) List of CCR5 promoter haplotypes as defined by Mummidi et al. (J Biol Chem 275:18946, 2000).
Nucleotide changes compared to the reference haplotype HHA are in bold.
The names of deleterious haplotypes associated with high CCR5 expression are in bold italics.
(b) The whole CCR5 locus (9 kb) was sequenced by PacBio long-read technology for the 12 HIV controllers included in the MHCII tetramer study, except for HIC09, for whom the CCR5 locus was sequenced by the Sanger method except for HIC09, for whom the CCR5 locus was sequenced by the Sanger method.
CCR5 promoter haplotypes were imputed according to Mummidi et al.
Genotypes with at least one deleterious CCR5 promoter haplotype are in bold italics.
(c) Analysis of the CCR5 locus in 3 HIV controllers carrying the D32 mutation and showing low CCR5 expression.