TABLE 2.

Autologous variants of known and predicted HIV-1 Env epitopes that evolved throughout infection

Epitope locationa	Amino acid sequenceb	Subjectc	Autologous variant sequenced	Time of evolution (YPS)e	Predicted MHC class I affinity (nM)f
Env gp12052–61	LFCASDAKAY	S2	LFCASDAKAY	0.2	29,256.5
		S3	LFCASDAKAY	0.2	29,256.5
		S8	LFCASDARAY	0.5	27,869.6
			LFCASDAKAY	5.0	29,256.5
Env gp120158–165	SFNISTSI	S2	TFNITTSI	0.2	1,515.1
			TFNITTNI	9.6	1,382.9
		S3	SFNITTNI	0.2	1,321.7
			SFNITTDI	5.3	3,088.4
		S8	SFNVTTSI	0.5	1,862.3
Env gp120168–176	KVQKEYAFF	S2	KMQKEYALF	0.2	17.9
			KVQKEYALF	3.4	139.7
		S3	KVQKEYALF	0.2	139.7
			KVRQEYALF	5.3	768.5
		S8	KMKREYAFF	0.5	132.5
			KIKREYATF	5.0	1,256.3
			KRRREYATF	6.6	9,284.2
Env gp120311–320	RGPGRAFVTI	S2	MGPGGAFYAT	0.2	26,383.6
			IGPGRAFYAT	3.4	27,231.5
		S3	IGPGRAFYAT	0.2	27,231.5
			IGPGRAFYAA	6.4	19,176.8
		S8	IGPGRAFYTT	0.5	21,484.4
Env gp120383–391	FYCNSTQLF	S2	FYCNTTQLF	0.2	8.9
		S3	FYCNSTQLF	0.2	11.5
			FYCNTTQLF	1.5	8.9
			FYCNTTRLF	8.3	28.5
		S8	FYCNTAQLF	0.5	11.9
			FYCNTSQLF	2.4	9.4
Env gp120434–443	MYAPPISGQI	S2	MYAPPIRGQI	0.2	89.0
			MYAPPIKGLI	3.4	52.9
		S3	MYAPPISGLI	0.2	21.4
			MYAPPIKGLI	8.3	52.9
			MYAPPNKGLI	8.3	82.5
		S8	MYAPPIRGEI	0.5	99.5
			MYAPPISGVI	5.0	46.8
Env gp120483–491	LYKYKVVKI	S2	LYKYKVVKI	0.2	301.8
		S3	LYKYKVVKI	0.2	301.8
			LYKYKVVEI	8.3	237.6
		S8	LYKYKVVKI	0.5	301.8

^aHXB2 location of each HIV-1 epitope within the Env protein.

^bHXB2 consensus amino acid sequences for known and predicted HLA A*24-restricted HIV-1 Gag and Env epitopes. Known epitopes are in boldface type, and the HXB2 sequences of predicted CTL epitopes are in lightface type.

^cSubjects S2, S3, and S8 were chosen from the Multicenter AIDS Cohort study for analysis.

^dAutologous epitope variants were identified by single-genome gag p17-p6 and env gp120 sequencing of autologous plasma-derived HIV-1. Underlined variants were the dominant form of the epitope (>55% of the variant pool) that was observed at the last time point sequenced.

^eThe time at which the epitope variant was detected by single-genome sequencing. YPS, years postseroconversion.

^fPredicted affinity for HLA A*2402, as determined by using netMHCpan. A lower value indicates a higher predicted affinity.