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Systematic Identification of Optimal HIV-1 CTL Epitopes

Christian Brander1 and Bruce D. Walker2

1AIDS Research Center, Massachusetts General Hospital, 149 13th Street, Room 5234,
2Charlestown, MA 02129, USA, and Harvard Medical School Boston, MA USA

Updated October 1997

Over the last ten years, the efforts of many laboratories have led to the identification of numerous HLA class I restricted CTL epitopes in most of the HIV-1 proteins. With the help of many other scientists, who generously contributed their unpublished data, we have created this list which includes only epitopes for which the restricting HLA class I molecule has been defined and for which peptide titration with truncated peptides have been performed. Since the last update of this CTL epitope list in 1997, four new epitopes have been included while two epitopes have been removed due to conflicting data regarding HLA restriction and definition of the minimal epitope, respectively. We consistently try to verify data regarding newly described CTL epitopes before their inclusion in this database. In order to keep this list as flawless and updated as possible it would be very helpful for us to receive information about newly identified epitopes as they become available. Also conflicting data, when brought to our attention, will be addressed to keep the database as accurate as possible. For comments and/or contributions to the CTL epitope list (C.B. or B.W.) or the database (B.K.) please call, write, or mail us at:

Bette Korber		Christian Brander		Bruce D. Walker
phone:  505 665 4453    phone:  617 724 5789		phone:  617 724 8332
FAX:    505 665 3493    FAX:    617 726 5411		FAX:    617 726 4691	Brander@Helix.MGH.Harvard.Edu	BWalker@Helix.MGH.Harvard.Edu

Table-1 Best Defined HIV CTL Epitopes

HLA	Protein		AA	Isolate	 	Sequence 	Reference

HLA-A2						2      C	Falk91
 						L      V
						I      L 
	p17	      77-85	 LAI		SLYNTVATL	Johnson91,Parker92,Parker94
	RT	      33-41	 LAI		ALVEICTEM	Haas98
	RT	      346-354	 LAI		VIYQYMDDL	Harrer96
	RT	      476-484	 LAI		ILKEPVHGV	Walker89,Tsomides91
A*0201	gp120	      311-320	 III-B		RGPGRAFVTI	Alexander-Miller96
	gp41	      818-827	 LAI		SLLNATDIAV	Dupuis95
	nef	      136-145	 LAI		PLTFGWCYKL	Haas96, B. Maier and B. Autran, Per.comm.
	nef	      180-189	 LAI		VLEWRFDSRL	Haas96, B. Maier and B. Autran, Per.comm.

HLA-A3.1					 23     C	DiBrino93
						 IF     K	
						 L      Y	
	p17	      18-26 	 LAI		KIRLRPGGK	Harrer96b
	p17	      20-28	 LAI		RLRPGGKKK	B. Culmann, D. Lewinsohn, D. Ruhl, S. Riddell, B. Wilkes, Per.comm.
	p17	      20-29	 LAI		RLRPGGKKKY	B. Wilkes, D. Ruhl, Per.comm.
	RT	      33-43	 LAI		ALVEICTEMEK	Haas98
	RT	      325-333	 LAI		AIFQSSMTK	Threlkeld97
	gp120	      37-46	 LAI		TVYYGVPVWK	Johnson94
	gp41	      775-785	 LAI		RLRDLLLIVTR	Takahashi91
	nef	      73-82 	 LAI		QVPLRPMTYK	Koenig90,Culmann91

HLA-A11						 2      C	Zhang93
						 I      K
	p17	      84-92	 LAI	        TLYCVHQRI	T. Harrer, Per.comm.
	p24	      349-359	 III-B		ACQGVGGPGGHK	Sipsas97
	RT	      325-333	 LAI		AIFQSSMTK	Johnson94b,Zhang93,Threlkeld97
	RT	      508-517	 LAI		IYQEPFKNLK	B. Culmann, Per.comm.
	nef	      75-82	 LAI		PLRPMTYK	Culmann91
	nef	      84-92	 LAI		AVDLSHFLK	Culmann91

A*7401	RT	      71-79	Clade A/B/D	ITLWQRPLV	S. Rowland-Jones, Per.comm.

	p17	      28-36	LAI		KYKLKHIVW	D. Lewinsohn, Per.comm.
	p24	      296-306	HIV-1 Clade A	RDYVDRFFKTL	S. Rowland-Jones, Per.comm.
	gp120	      53-62	LAI		LFCASDAKAY	Lieberman92,Shankar96 
	gp41	      591-598	LAI		YLKDQQLL	Dai92
	Nef	      138-147	LAI		RYPLTFGW	Goulder97e

	p24	      145-155	LAI		QAISPRTLNAW	I. Kurane, K. West, Per.comm.
	p24	      203-212	LAI		ETINEEAAEW	Klenerman96,vanBaalen96

	p24	      167-175	LAI		EVIPMFSAL	Goulder96b
	RT	      593-603	LAI		ETFYVDGAANR	B. Wilkes, D. Ruhl, Per.comm.

A*6802	RT	      71-79	Clade A/B/D	ITLWQRPLV	S. Rowland-Jones, Per.comm.
A*6802	RT	      85-93	Clade D		DTVLEEMNL	S. Rowland-Jones, Per.comm.

	gp120	      376-384	LAI		FNCGGEFFY	Wilson97

	gp41	      775-785	LAI		RLRDLLLIVTR	Safrit94a,Safrit94b

	RT	      559-568	LAI		PIQKETWETW	Harrer96b
	gp120	      419-427	HXB2		RIKQIINMW	Harrer96b

HLA-B7						123      C	Englehard93
						APR      L	
	p24	      148-156	LAI		SPRTLNAWV	D. Lewinsohn, Per.comm.
	p24	      179-187	LAI		ATPQDLNTM	B. Wilkes, D. Ruhl, Per.comm.
	RT	      323-332	LAI		SPAIFQSSMT	C. Hey and D. Ruhl, Per.comm.
	gp120	      303-312	LAI		RPNNNTRKSI	Safrit94b
	gp41	      843-851	LAI		IPRRIRQGL	B. Wilkes and D. Ruhl, Per.comm.
	nef	      68-77	LAI		FPVTPQVPLR	Haas96, B. Maier and B. Autran, Per.comm.
	nef	      77-85	LAI		RPMTYKAAL	Bauer97
	nef	      128-137	LAI		TPGPGVRYPL	CulmannPenciolelli94,Haas96, B. Maier and B. Autran, Per.comm.

HLA-B8						  23 5  C	Hill92b,Sutton93
						  P  R  L
						  LK K  I
	p17	      24-31	LAI		GGKKKYKL	RowlandJones93a,Goulder97
	p17	      74-82	LAI		ELRSLYNTV	Goulder97c
	p24	      260-267	LAI		EIYKRWII	Sutton93,Goulder97c
	gp120	      2-10	III-B		RVKEKYQHL	Sipsas97
	gp41	      591-598	LAI		YLKDQQLL		Johnson92,Shankar96
	nef	      13-20	LAI		WPTVRERM	Goulder97c
	nef	      90-97	LAI		FLKEKGGL	CulmannPenciolelli94,Price97

HLA-B14						 23 56  C	DiBrino94b
						 RL RI  L
						    KY HL
	p24	     298-306	LAI		DRFYKTLRA	Harrer96b
	gp41	     589-597	LAI		ERYLKDQQL	Johnson92

	gp120	     375-383	LAI		SFNCGGEFF	Wilson97

	p24	     293-302	HIV-1 clade B/D	FRDYVDRFYK	Ogg98b
	nef	     135-143	LAI		YPLTFGWCY	Culmann91,CulmannPenciolelli94

HLA-B27						 2       C	Jardetzky91
						 R       K	
	p17	     18-27	LAI		KIRLRPGGKK	D. Lewinsohn, Per.comm.
	p17	     19-27	LAI		IRLRPGGKK	D. Lewinsohn, Per.comm.
	p24	     263-272	LAI		KRWIILGLNK	Nixon88,Buseyne93
	gp41	     590-597	LAI		RYLKDQQL	Shankar96
	gp41	     791-799	LAI		GRRGWEALKY	Lieberman92, J. Lieberman, Per.comm.
HLA-B*2703p24	     265-274	HIV-2		RRWIQLGLQK	RowlandJones98b

B*2705	nef	     105-114	LAI		RRQDILDLWI	Goulder97d
	nef	     73-82	LAI		QVPLRPMTYK	B. Culmann, Per.comm.
	nef	     134-141	LAI		RYPLTFGW	B. Culmann, Per.comm.

HLA-B35						 2      C	Hill92b
						 P      Y	
	p17	     124-132	JH31		NSSKVSQNY	RowlandJones95
	p17	     36-44	LAI		WASRELERF	Goulder97a
	p24	     254-262	U455		PPIPVGDIY	RowlandJones95
	RT	     262-270	LAI		TVLDVGDAY	B. Wilkes, D. Ruhl, Per.comm.
	RT	     273-282	III-B		VPLDEDFRKY	Sipsas97,Shiga96
	RT	     328-336	III-B		NPDIVIYQY	Sipsas97,Shiga96
	RT	     342-350	LAI		HPDIVIYQY	RowlandJones95
	gp120	     42-52	LAI		VPVWKEATTTL	B. Wilkes, D. Ruhl, Per.comm.
	gp41	     611-619	LAI		TAVPWNASW	Johnson94
	nef	     74-81	LAI		VPLRPMTY	Culmann91,CulmannPenciolelli94
	gag	     245-253	HIV-2		NPVPVGNIY	RowlandJones95

	nef	     120-128	LAI		YFPDWQNYT	Culmann91 and Per.comm.

	p24	     193-201	LAI		GHQAAMQML	I. Kurane, K. West, Per.comm.

	p17	     20-29	LAI		RLRPGGKKKY	B. Wilkes, D. Ruhl, Per.comm.
	RT	     438-446	LAI		YPGIKVRQL	B. Wilkes, D. Ruhl, Per.comm.

	p24	     306-316	SF2		AEQASQDVKNW	Lewinsohn, Per.comm.
	gp120	     30-38	SF33		AENLWVTVY	Borrow97

 HLA-B*4402&p24	     294-304	HIV-1 Clade B	RDYVDRFYKTL	Ogg98b

	RT	     591-600	LAI		GAETFYVDGA	B. Wilkes, D. Ruhl, Per.comm.
	p24	     325-333	LAI		NANPDCKTI	B. Wilkes, D. Ruhl, Per.comm.
	RT	     42-50	LAI		EKEGKISKI	Haas98
	RT	     295-302	III-B		TAFTIPSI	Sipsas97
	gp41	     557-565	III-B		RAIEAQQHL	Sipsas97

	p24	     275-282	LAI		RMYSPTSI	B. Wilkes, D. Ruhl, Per.comm.

HLA-B53						 2      C	Hill92b
						 P      Y
	HIV-2 gag    173-181	HIV-2		TPYDINQML	Gotch93

	gp120	     42-51	LAI		VPVWKEATTT	Shankar96

	p24	     147-155	III-B		ISPRTLNAW	Johnson91,Goulder96
	p24	     140-149	LAI		TSTLQEQIGW	Goulder96
	p24	     162-172	LAI		KAFSPEVIPMF	Goulder96
	p24	     240-249	LAI		TSTLQEQIGW	Goulder96
	p24	     311-319	LAI		QASQEVKNW	Goulder96
	p24	     311-319	LAI		QASQDVKNW	Goulder96
	nef 	     116-125	LAI		HTQGYFPDWQ	Culmann91
	nef 	     120-128	LAI		YFPDWQNYT	Culmann91

	p24	     240-249	LAI		TSTLQEQIGW	Goulder96

HLA-B60	p17	     92-101	LAI		IEIKDTKEAL	A. Trocha and S. Kalams, Per.comm.

	p17	     20-29	LAI		RLRPGGKKKY	Johnson91, B. Wilkes, D. Ruhl, Per.comm.
	p24	     268-277	LAI		LGLNKIVRMY	Johnson91
	RT	     415-426	III-B		LVGKLNWASQIY	P. Johnson, Per.comm.
	RT	     476-485	LAI		ILKEPVHGVY	Johnson91, P. Johnson, Per.comm.
	nef	     84-91	LAI		AVDLSHFL	CulmannPenciolelli94
	nef	     117-127	LAI		TQGYFPDWQNY	B. Culmann, Per.comm.

	p24	     168-175	LAI		VIPMFSAL	P. Goulder in press 
HLA-Cw4						 2      C	Falk94
						 Y      F
						 P      L
						 F      M
	gp120	     380-388	LAI		SFNCGGEFF	Johnson93,Wilson97
C*0401	p24	     308-316	LAI		QASQEVKNW	Buseyne97


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