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

Retrovirology

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

^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 A24:02), HL9, LF11 (HLA A30)
L34	I	0.95	0.91	27	83	0.022	0.525	KW9 (HLA A24:02), HL9, LF11 (HLA A30)
A83	A	0.93	0.73	109	6	0.015	0.525	RY11 (HLA B08:01), SL9 (HLA A02:01, HLA A02:02, HLA A02:05), SY10 (HLA A02:01), LY9 (HLA A29:02, 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 B13:02), HL9 (HLA B15:10), QW11 (HLA A25:01), IW9 (HLA B57:01, HLA B*63)
E260	D	0.97	0.91	19	96	0.011	0.525	NY10, PY9 (HLA B35:01),EI8 (HLA B08:01)
E260	E	0.91	0.97	94	21	0.017	0.525	NY10, PY9 (HLA B35:01),EI8 (HLA B08:01)
V267	V	0.91	0.94	58	56	0.032	0.525	EI10(HLA B08:01), RK10 (HLA B27:03), KK10 (HLA B*27:05)
V267	I	0.94	0.91	56	58	0.032	0.525	EI10(HLA B08:01), RK10 (HLA B27:03), KK10 (HLA B*27:05)
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	DL9 (HLA B*08:01)

^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

ISSN: 1742-4690