Table V.

Putative HLA-A*7401–restricted epitopes predicted using motif inference (32) combined with analysis of HLA-A*7401 associations with sequence polymorphisms

Protein	HXB2 Position of Polymorphism	Durban Consensus Sequencea	Reversion	p Value	q Value	Predicted HLA-A*7401 Epitope
		A*7401 Polymorphism ▼				P2	C Terminus	Epitope Designation
p17 Gag	12	G A R A S I L R G E K L D K W E K I R L R	R	2.71E-14	0.00	S I L R G E K L D	K	(Gag-SK10)
p17 Gag	20	G E K L D K W E K I R L R P G G K K H Y M	R	6.47E-10	0.00	K L D K W E K I	R	(Gag-KR9)
Protease	9	F F R E N L A F P Q G E A R E F P S E		4.83E-05	0.02	N L A F P Q G E A	R	(Prot-NR10)
RT	277	A S Q I Y P G I K V R Q L C K L L R G A K		3.13E-04	0.13	Q I Y P G I K V S Q I Y P G I K V	R R	(RT-QR9) (RT-SR10)
RT	476	I V S L T E T T N Q K T E L Q A I Q L A L		6.03E-04	0.15	S L T E T T N Q	K	(RT-SK9)
Nef	192	K W K F D S S L A R R H L A R E L H P E Y	R	4.95E-05	0.00	S L A R R H L A	R	(Nef-SR9)

Six sites of HLA-A*7401–associated polymorphism identified from lineage-corrected analysis of sequences from a total of 710 Durban subjects (q < 0.2), as previously published (3). The position of the polymorphism is marked ▼, with consensus sequence 10 aa upstream and downstream of the site of polymorphism. Arrows indicate anchor positions (shown in bold and underlined) as in Table IV. R indicates polymorphisms that are predicted to revert to wild-type after transmission to an HLA-mismatched recipient [methods as previously described (17, 57)].

^aSequences based on Durban consensus sequence from Gag (n = 446) and Nef (n = 436) subjects.