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Table 3 Amino acids associated with intra-subtype Nef HLA-I downregulation function

From: Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes

Subtype Codona AAb Cons.c Functiond No. of samplese p-value q-value
+ AA - AA + AA -AA
A 3 G G 82.3 87.1 71 23 0.007 0.4
  9 R S 94.5 83.1 5 84 0.02 0.4
  11 V V 81.5 87.9 74 16 0.007 0.4
  83 G G 80.6 87.0 63 31 0.01 0.4
  89 F H 90.8 82.4 15 79 0.01 0.4
  105 R K 78.4 85.0 22 72 0.02 0.4
  120 Y Y 82.4 86.7 56 38 0.02 0.4
  168 M I 87.1 81.9 23 71 0.02 0.4
  191 L L 81.0 87.1 57 37 0.005 0.4
  196 Q R 80.2 86.2 34 60 0.008 0.4
B 8 R S 98.2 94.6 28 56 0.006 0.2
  8 S S 94.3 98.0 38 46 0.0009 0.2
  14 P P 94.4 97.7 58 34 0.01 0.2
  28 A D 101.5 95.0 7 85 0.004 0.2
  65 D E 89.7 96.4 8 84 0.02 0.3
  65 E E 96.4 87.3 83 9 0.009 0.2
  89 F H 63.7 95.6 5 87 0.03 0.4
  89 H H 95.7 60.8 86 6 0.007 0.2
  98 D E 99.7 95.1 6 86 0.02 0.3
  98 E E 95.0 100.6 85 7 0.007 0.2
  105 Q K 91.0 96.5 18 74 0.03 0.4
  153 I V 90.5 96.7 16 75 0.007 0.2
  153 V V 96.7 90.0 74 17 0.003 0.2
  198 K L 98.8 94.7 19 73 0.01 0.2
  202 F Y 99.4 95.0 9 83 0.01 0.2
  202 Y Y 95.0 99.4 83 9 0.01 0.2
C 9 S S 78.1 96.6 66 5 0.01 0.3
  40 H H 84.0 72.3 38 36 0.005 0.3
  40 Y H 72.3 84.0 34 40 0.003 0.3
  102 H Y 56.2 81.8 12 62 0.02 0.4
  105 K K 83.5 71.1 53 21 0.005 0.3
  105 R K 57.8 82.5 15 59 0.01 0.3
  108 D E 71.1 83.7 37 37 0.01 0.3
  108 E E 83.7 71.1 37 37 0.01 0.3
  182 Q K 49.6 80.7 8 66 0.01 0.3
  1. aNumbered according to HXB2.
  2. b Amino acid variants associated with differences in HLA-I downregulation function. Only common amino acid variants (present at n ≥ 5 in each subtype) were investigated.
  3. cConsensus amino acid for the codon and subtype indicated.
  4. dMedian HLA-I downregulation function (expressed as a percentage relative to SF2) of Nef sequences with (+AA) and without (-AA) the amino acid variant.
  5. eNumber of sequences with (+AA) and without (-AA) the amino acid variant. Amino acid totals vary, as gaps in the alignment are considered missing data.
  6. A similar intra-subtype analysis was performed to identify Nef amino acids associated with CD4 downregulation function; no associations q < 0.4 were identified using this approach.