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Table 4 Codon-by-codon analysis of Gag-protease polymorphisms and viral replication capacity (VRC) for CRF 02_AG

From: Subtype-specific differences in Gag-protease replication capacity of HIV-1 isolates from East and West Africa

aConsensus AA/Codon bAA Signal Median VRC with AA Median VRC without AA No. of patients with AA No. of patients without AA p-value q-value A-list epitope
L34 L 0.91 0.95 83 27 0.022 0.525 KW9 (HLA A*24:02), HL9, LF11 (HLA A*30)
L34 I 0.95 0.91 27 83 0.022 0.525
A83 A 0.93 0.73 109 6 0.015 0.525 RY11 (HLA B*08:01), SL9 (HLA A*02:01, HLA A*02:02, HLA A*02:05), SY10 (HLA A*02:01), LY9 (HLA A*29:02, HLA B*44:03)
A83 V 0.73 0.93 6 109 0.015 0.525
S125 S 0.91 0.95 69 40 0.029 0.525 NY9 (HLA B*35:01)
A146 N 1.00 0.91 13 101 0.006 0.514 GI8 (HLA B*13:02), HL9 (HLA B*15:10), QW11 (HLA A*25:01), IW9 (HLA B*57:01, HLA B*63)
E260 D 0.97 0.91 19 96 0.011 0.525 NY10, PY9 (HLA B*35:01),EI8 (HLA B*08:01)
E260 E 0.91 0.97 94 21 0.017 0.525
V267 V 0.91 0.94 58 56 0.032 0.525 EI10(HLA B*08:01), RK10 (HLA B*27:03), KK10 (HLA B*27:05)
V267 I 0.94 0.91 56 58 0.032 0.525
S332 A 1.04 0.92 5 110 0.005 0.514 DL9 (HLA B*08:01)
R335 R 0.91 0.95 73 40 0.025 0.525 DL9 (HLA B*08:01)
R335 K 0.95 0.91 40 73 0.025 0.525
  1. aThis column represents the consensus amino acid at specified at that locus; bThis column represents the amino acid variant being reported by the codon analysis; cA-list epitope as available from http://www.lanl.com