TABLE 1.

Autologous variants of known and predicted HIV-1 Gag 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
Gag p1728–36	KYKLKHIVW	S2	KYKLKHIVW	0.2	954.7
			KYRLKHIVW	1.2	1,164.5
		S3	KYKLKHIVW	0.2	954.7
			QYKLKHIVW	0.2	1,616.7
		S8	RYRLKHLVW	0.5	233.0
Gag p1743–51	RFAVNPGLL	S2	RFAVNPGLL	0.2	626.9
			RFAVNPSLL	3.4	245.9
		S3	RFAVNPGLL	0.2	626.9
			RFALNPGLL	6.4	650.0
		S8	RFAVNPGLI	0.5	293.8
			RFAVNPGLL	2.4	626.9
Gag p17131–132/p241–6	NYPIVQNI	S2	NYPIVQNI	0.2	74.0
			NYPIVQNL	9.6	214.7
		S3	NYPIVQNL	0.2	214.7
		S8	NYPIVQNL	0.5	214.7
Gag p2431–40	AFSPEVIPMF	S2	AFSPEVIPMF	0.2	274.3
		S3	AFSPEVIPMF	0.2	274.3
		S8	AFSPEVIPMF	0.5	274.3
Gag p24129–138	IYKRWIILGL	S2	IYKGWIILGL	0.2	107.3
			IYKRWIILGL	0.2	78.9
		S3	IYKRWIILGL	0.2	78.9
		S8	IYKRWIILGL	0.5	78.9
Gag p24163–171	DYVDRFYKT	S2	DYVDRFYKT	0.2	19,856.1
		S3	DYVDRFYKT	0.2	19,856.1
		S8	DYVDRFYKT	0.5	19,856.1

^aHXB2 location of each HIV-1 epitope within Gag p17 and p24.

^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.