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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

ISSN: 1742-4690

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