Table 1.
HLA-associated polymorphisms detectable at the population level in early HIV-1 infection
| Protein | HLA | HIV polymorphism a | Early infection | Chronic infection | CD8+ epitope * | p-value (early vs. chronic) d | ||
|---|---|---|---|---|---|---|---|---|
| Odds Ratio b | p-value c | Odds Ratio b | p-value c | (HIV codon coordinates) | ||||
| Gag | B*57:01 | T242N | 33 | 3 × 10−9 | 151 | 6 × 10−17 | TSTLQEQIGW (240–248) | 0.3 |
| C*07:04 | M378x | 3.6 | 0.006 | 3.5 | 0.0002 | IMMQRGNF (377–383)* | 0.7 | |
| A*31:01 | K397R | 6.2 | 1 × 10−7 | 83 | 8 × 10−10 | CGKEGHIAR (395–403) | 0.5 | |
| A*31:01 | I401L | 5.1 | 0.005 | 1.98 | 0.01 | CGKEGHIAR (395–403) | 0.2 | |
| A*31:01 | R403K | 1.5 | 0.007 | ~41 | 1 × 10−7 | CGKEGHIAR (395–403) | 0.002 | |
| Pol (RT) | B*51:01 | I135x | 2.1 | 0.004 | 25 | 5 × 10−11 | TAFTIPSI (128–135) | 0.0001 |
| Pol (Int) | B*51:01 | L28I | 16 | 0.009 | 5 | 7 × 10−5 | LPPIVAKEI (28–36) | 0.2 |
| Nef | B*37:01 | E38 D | 13 | 0.006 | ~24 | 0.002 | LEKHGAIT (37–45)* | 0.2 |
| C*03:04 | V85L | 2.4 | 0.002 | 4 | 0.0002 | AALDLSHFL (83–91) | 0.6 | |
| A*11:01 | K92R | 5.3 | 0.009 | 8.4 | 4 × 10−6 | AVDLSHFLK (84–92) | 0.2 | |
| C*03:04 | H102x | 3.2 | 0.001 | ~1 | 0.25 | none | 0.1 | |
| A*23:01 | F143Y | 8.4 | 0.01 | 852 | 5 × 10−8 | RYPLTFGWCF (134–143) | 0.1 | |
| B*57:01 | x133I | 6 | 0.004 | 1.4 | 0.29 | YTPGPGIRY (127–135) | 0.2 | |
| A*24:02 | Y135F | 2.3 | 0.004 | 15 | 2 × 10−21 | RYPLTFGW (134–141) | 0.0005 | |
aA total of 24 associations, occurring at 14 unique HIV-1 codons, are listed. The total 24 is reached because HLA-associated nonadapted and adapted forms are counted individually (e.g. B*57:01-Gag-T242N comprises two associations– the nonadapted T and the adapted N). Cases where a specific non-adapted or adapted form was not detected in early infection are denoted by a lowercase “x” (e.g. B*51:01-RT-I135x). Polymorphisms in bold represent associations detectable in both early and chronic infection at p ≤ 0.01; those italicized represent associations detectable in only the early cohort with p < 0.01.
bWhere both nonadapted and adapted forms for a given HLA are identified, the maximum absolute Odds Ratio is shown.
cWhere both nonadapted and adapted forms for a given HLA are identified, the lowest p-value is shown. Note the chronic p-value for B*37:01-Nef-E38D refers to its nonadapted (E38x) form; the p-value for the adapted (x38D) form at this stage is 0.07.
*Bioinformatically predicted CTL epitopes are denoted by asterisks (*); the remainder are published (http://www.hiv.lanl.gov/content/immunology/tables/tables.html). Bold letters indicate the position within the epitope where the HLA-associated polymorphism occurs. Note the C*03-restricted AALDLSHFL epitope has been published in its C*03-adapted form.
dFor each HLA-associated polymorphism in the table, its strength association in early versus chronic infection was compared using a previously-described phylogenetically-corrected interaction test (see Methods and [12,27]). The p-values of these comparisons are listed in this column.