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Table 1 HLA-associated polymorphisms detectable at the population level in early HIV-1 infection

From: Early immune adaptation in HIV-1 revealed by population-level approaches

Protein HLA HIV polymorphisma Early infection Chronic infection CD8+ epitope* p-value (early vs. chronic)d
Odds Ratiob p-valuec Odds Ratiob p-valuec (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
  1. 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.
  2. bWhere both nonadapted and adapted forms for a given HLA are identified, the maximum absolute Odds Ratio is shown.
  3. 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.
  4. *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.
  5. 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.
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Retrovirology

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