Table II. Comparison of amino acid... | Rockefeller University Press

Table II.

Comparison of amino acid sequences of known CD8⁺ T cell epitopes between SIVmac239Δnef, SIVsmE660, and circulating virus during the chronic phase of infection in the vaccinated animals

Sequence origin	Epitope sequence
*Mamu-A01**	Gag_149-157LW9	Gag_181-189CM9	Gag_254-262QI9	Gag_372-379LF8	Pol_147-156LV10	Pol_363-372GM10	Pol_592-600QV9	Pol_625-633SV9
SIVmac239Δnef	LSPRTLNAW	CTPYDINQM	QNPIPVGNI	LAPVPIPF	LGPHYTPKIV	GSPAIFQYTM	QVPKFHLPV	STPPLVRLV
SIVsmE660	.........	.........	.........	.R.DQL..	...N....V.	..........	E........	.........
02092	.........	.A.......	.........	.R.DQL..	...N....V.	..........	E.....V..	.........
88085	.........	.........	.........	........	..........	..........	.........	.........
*Mamu-A01**	Env_233-241CL9	Env_622-630TL9	Env_729-738ST10	Tat_28-35SL8	Vif_144-152QA9	Vpx_8-18II11
SIVmac239Δnef	CAPPGYALL	TVPWPNASL	SSPPSYFQQT	STPESANL	QVPSLQYLA	IPPGNSGEETI
SIVsmE660	.........	......ET.	....A.V..I	P.......	.........	...........
02092	.........	......GT.	....A.V..I	P.......	.........	...........
88085	.........	......ET.	....A.V..I	....L...	.........
*Mamu-A02**	Gag_71-79GY9	Pol_324-332FF9	Pol_518-526LY9	Env_296-304RY9	Env_317-325KM9	Env_359-367QY9	Env_519-528GF10	Env_760-768SY9
SIVmac239Δnef	GSENLKSLY	FSIPLDEEF	LSQEQEGCY	RTIISLNKY	KTVLPVTIM	QTIVKHPRY	GTSRNKRGVF	SSWPWQIEY
SIVsmE660	.........	.........	.........	.........	.........	E.L......	.A........	R........
01022	.........		.........
rhAO84	.........	.........	.........	.........	...f.....	E.L......	.A........	R........
*Mamu-A02**	Env_788-795RY8	Nef_20-28LY9	Vif_89-97IW9	Vif_97-104WY8	Vpr_63-71RM9
SIVmac239Δnef	RTLLSRVY	LLRARGETY	ITWYSKNFW	WTDVTPNY	RILQRALFM
SIVsmE660	.DW.L.T.	..Q......	.....R...	......D.	........I
01022		.........
rhAO84	.DW.L.T.	..Q......	.....R...	......D.	K.......I
*Mamu-A11**	Gag_178-186SI9	Pol_92-100AL9	Pol_457-465RI9	Pol_507-517AI11	Env_495-502GI8	Vpr_13-21RV9
SIVmac239Δnef	SEGCTPYDI	AERKQREAL	RETWTVNDI	AEAEYEENKII	GDYKLVEI	REPWDEWVV
SIVsmE660	.........	G.–...T.	.........	...........	........	.........
01009	.........	RK–...T.	.........	...........	........	.........
rh2000	.........	G.–...T.	.........	...........	........
*Mamu-B08**	Gag_263-272YL9	Env_524-532KF9	Env_573-581KL9	Env_717-725LF9	Env_868-876RL9	Rev_12-20KL9	Rev_44-51RL8	Nef_8-16RL9
SIVmac239Δnef	YRRWIQLGL	KRGVFVLGF	KRQQELLRL	LRQGYRPVF	RRIRQGLEL	KRLRLIHLL	RRRWQQLL	RRSRPSGDL
SIVsmE660	.........	.........	...H.....	.........	.........	.......F.	.Q....I.	KQC.RG.N.
02132	.........	...G..R..	...H.....	.........	..V......	.......F.	.Q....I.	KQCRRR.N.
01048	.........	.........		.S.......		.........	........	.........
*Mamu-B08**	Vif_123-131RL9	Vif_172-179RL8
SIVmac239Δnef	RRAIRGEQL	RRDNRRGL
SIVsmE660	.......K.	G.N...s.
02132
01048	.........	.....G..
*Mamu-B17**	Pol_372-379MF8	Pol_435-443FW9	Pol_604-613VW10	Env_241-251LF11	Env_816-825LY10	Env_830-838FW9	Vif_44-52HW9	Vif_66-73HW8
SIVmac239Δnef	MRHVLEPF	FQWMGYELW	VWEQWWTDYW	LRCNDTNYSGF	LRTELTYLQY	FHEAVQAVW	HFKVGWAWW	HLEVQGYW
SIVsmE660	..N.....	.........	I.........	.....S.....	I..GIA....	.Q.....W.	.H.......	........
01003	........	.........	..........	.....S.....	..........	.Y.......	.H.......	Q.......
01079	..N.....	.........	I.........	.....S.....	..........	.Y.......	.H.......	........
*Mamu-B17**	Vif_135-143CY9	cryptic RW9
SIVmac239Δnef	CRFPRAHKY	RHLAFKCLW
SIVsmE660	.K..K...N	.A..S..FR
01003	.K..K...N	.A..S..FR
01079	.K..K...N	.A..S..FR

Sequence origin	Epitope sequence
Mamu-A*01	Gag_149-157LW9	Gag_181-189CM9	Gag_254-262QI9	Gag_372-379LF8	Pol_147-156LV10	Pol_363-372GM10	Pol_592-600QV9	Pol_625-633SV9
SIVmac239Δnef	LSPRTLNAW	CTPYDINQM	QNPIPVGNI	LAPVPIPF	LGPHYTPKIV	GSPAIFQYTM	QVPKFHLPV	STPPLVRLV
SIVsmE660	.........	.........	.........	.R.DQL..	...N....V.	..........	E........	.........
02092	.........	.A.......	.........	.R.DQL..	...N....V.	..........	E.....V..	.........
88085	.........	.........	.........	........	..........	..........	.........	.........
Mamu-A*01	Env_233-241CL9	Env_622-630TL9	Env_729-738ST10	Tat_28-35SL8	Vif_144-152QA9	Vpx_8-18II11
SIVmac239Δnef	CAPPGYALL	TVPWPNASL	SSPPSYFQQT	STPESANL	QVPSLQYLA	IPPGNSGEETI
SIVsmE660	.........	......ET.	....A.V..I	P.......	.........	...........
02092	.........	......GT.	....A.V..I	P.......	.........	...........
88085	.........	......ET.	....A.V..I	....L...	.........
Mamu-A*02	Gag_71-79GY9	Pol_324-332FF9	Pol_518-526LY9	Env_296-304RY9	Env_317-325KM9	Env_359-367QY9	Env_519-528GF10	Env_760-768SY9
SIVmac239Δnef	GSENLKSLY	FSIPLDEEF	LSQEQEGCY	RTIISLNKY	KTVLPVTIM	QTIVKHPRY	GTSRNKRGVF	SSWPWQIEY
SIVsmE660	.........	.........	.........	.........	.........	E.L......	.A........	R........
01022	.........		.........
rhAO84	.........	.........	.........	.........	...f.....	E.L......	.A........	R........
Mamu-A*02	Env_788-795RY8	Nef_20-28LY9	Vif_89-97IW9	Vif_97-104WY8	Vpr_63-71RM9
SIVmac239Δnef	RTLLSRVY	LLRARGETY	ITWYSKNFW	WTDVTPNY	RILQRALFM
SIVsmE660	.DW.L.T.	..Q......	.....R...	......D.	........I
01022		.........
rhAO84	.DW.L.T.	..Q......	.....R...	......D.	K.......I
Mamu-A*11	Gag_178-186SI9	Pol_92-100AL9	Pol_457-465RI9	Pol_507-517AI11	Env_495-502GI8	Vpr_13-21RV9
SIVmac239Δnef	SEGCTPYDI	AERKQREAL	RETWTVNDI	AEAEYEENKII	GDYKLVEI	REPWDEWVV
SIVsmE660	.........	G.–...T.	.........	...........	........	.........
01009	.........	RK–...T.	.........	...........	........	.........
rh2000	.........	G.–...T.	.........	...........	........
Mamu-B*08	Gag_263-272YL9	Env_524-532KF9	Env_573-581KL9	Env_717-725LF9	Env_868-876RL9	Rev_12-20KL9	Rev_44-51RL8	Nef_8-16RL9
SIVmac239Δnef	YRRWIQLGL	KRGVFVLGF	KRQQELLRL	LRQGYRPVF	RRIRQGLEL	KRLRLIHLL	RRRWQQLL	RRSRPSGDL
SIVsmE660	.........	.........	...H.....	.........	.........	.......F.	.Q....I.	KQC.RG.N.
02132	.........	...G..R..	...H.....	.........	..V......	.......F.	.Q....I.	KQCRRR.N.
01048	.........	.........		.S.......		.........	........	.........
Mamu-B*08	Vif_123-131RL9	Vif_172-179RL8
SIVmac239Δnef	RRAIRGEQL	RRDNRRGL
SIVsmE660	.......K.	G.N...s.
02132
01048	.........	.....G..
Mamu-B*17	Pol_372-379MF8	Pol_435-443FW9	Pol_604-613VW10	Env_241-251LF11	Env_816-825LY10	Env_830-838FW9	Vif_44-52HW9	Vif_66-73HW8
SIVmac239Δnef	MRHVLEPF	FQWMGYELW	VWEQWWTDYW	LRCNDTNYSGF	LRTELTYLQY	FHEAVQAVW	HFKVGWAWW	HLEVQGYW
SIVsmE660	..N.....	.........	I.........	.....S.....	I..GIA....	.Q.....W.	.H.......	........
01003	........	.........	..........	.....S.....	..........	.Y.......	.H.......	Q.......
01079	..N.....	.........	I.........	.....S.....	..........	.Y.......	.H.......	........
Mamu-B*17	Vif_135-143CY9	cryptic RW9
SIVmac239Δnef	CRFPRAHKY	RHLAFKCLW
SIVsmE660	.K..K...N	.A..S..FR
01003	.K..K...N	.A..S..FR
01079	.K..K...N	.A..S..FR

Periods represent conserved amino acids in comparison to SIVmac239Δnef. The aa sequence for each epitope corresponds to the vaccine strain SIVmac237Δnef. Any aa substitutions in these epitopes present in our stock of SIVsmE660 or in the plasma virus of our vaccinated animals during the chronic phase of infection are identified with capital letters or lowercase letters for mixed populations. Periods represent conserved aa in comparison to SIVmac239Δnef.

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