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

Retrovirology

Table 5 Codon-by-codon analysis of Gag-protease polymorphisms and viral replication capacity (VRC) for A1

Consensus AA/Codon	AA 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
K12	K	0.68	0.23	52	8	0.045	0.862	GI9 (HLA B*40:02)
K28	K	0.69	0.47	45	13	0.008	0.862	RK9 and RY10 (HLA A*03:01)
A67	A	0.63	0.82	57	5	0.023	0.862	–
K69	Q	0.77	0.63	8	52	0.048	0.862	–
S125	N	0.76	0.63	8	52	0.042	0.862	NY9 (HLA B*35:01)
L147	I	0.79	0.63	5	55	0.039	0.862	GI8 (HLA B13:02), HL9 (HLA B15:10), QW11 (HLA A25:01), IW9 (HLA B57:01, B*63)
V158	V	0.63	0.75	54	9	0.038	0.862	VF (HLA B*15:03)
V158	A	0.75	0.63	9	54	0.038	0.862	VF (HLA B*15:03)
I223	I	0.63	0.73	49	14	0.028	0.862	HA9 (HLA B*35:01, B7)
R380	K	0.75	0.63	9	53	0.036	0.862	–
P497	L	0.54	0.68	16	42	0.021	0.862	–

^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