. 2012 Nov 19;7(11):e49562. doi: 10.1371/journal.pone.0049562

Table 1. Comparison of peptide clade-B consensus sequence and autologous sequence (WT and mutants) corresponding to the Nef-specific CD8 T-cell responses detected in study subjects.

Clade B Nef Consensus		#039 Nef Autologous (High Viremic)				#016 Nef Autologous (Low Viremic)
Primary & Chronic Phases		Primary Phase day 92 (WT)		Chronic Phase day 448 (Mutants)		Primary Phase day 155 (WT)		Chronic Phase day 372 (Mutants)
Name	Peptide Sequence	Name	Peptide Sequence	Name	Peptide Sequence	Name	Peptide Sequence	Name	Peptide Sequence
`5140`	`WSKRSVVGWPTVRER`					`5140c`	`WSKRSVPGWNTIRER`	`5140q`	`WSKRGVPGWNTIRER`
						`5140d`	`WSKRSVPGWNIIRER`
						`5140f`	`WSKRSVPGWNAIRER`
						`5140h`	`WSKRSVPGWNVIRER`
`5141`	`SVVGWPTVRERMRRA`					`5141c`	`SVPGWNTIRERIRRA`	`5141q`	`GVPGWNTIRERIRRA`
						`5141d`	`SVPGWNIIRERIRRA`
						`5141h`	`SVPGWNVIRERIRRA`
`5145`	`PAADGVGAVSRDLEK`	`5145a`	`PAADGVGAASQDLAK`
`5149`	`GAITSSNTAANNADC`	`5149a`	`GAITSSNTAATNADC`	`5149b`	`GAITSSNTAATNDDC`
`5151`	`AANNADCAWLEAQEE`	`5151a`	`AATNADCAWLEAHEE`	`5151b`	`AATNDDCAWLEAHEE`
`5152`	`ADCAWLEAQEEEEVG`	`5152a`	`ADCAWLEAHEEEEVG`	`5152b`	`DDCAWLEAHEEEEVG`
`5153`	`WLEAQEEEEVGFPVR`					`5153c`	`WLEAQEEEEVGFPVK`
`5156`	`PVRPQVPLRPMTYKA`					`5156c`	`PVKPQVPLRPMTYKG`
`5157`	`QVPLRPMTYKAAVDL`					`5157c`	`QVPLRPMTYKGALDL`
`5158`	`RPMTYKAAVDLSHFL`	`5158a`	`RPMTYKGAVDLSHFL`
`5159`	`YKAAVDLSHFLKEKG`	`5159a`	`YKGAVDLSHFLKEEG`			`5159c`	`YKGALDLSHFLKEKG`
`5160`	`VDLSHFLKEKGGLEG`	`5160a`	`VDLSHFLKEEGGLEG`
`5161`	`HFLKEKGGLEGLIYS`	`5161a`	`HFLKEEGGLEGLVWS`
`5162`	`EKGGLEGLIYSQKRQ`					`5162c`	`EKGGLEGLIYSQQRQ`
`5167`	`WVYHTQGYFPDWQNY`	`5167` ^*	`WVYHTQGYFPDWQNY`			`5167` ^*	`WVYHTQGYFPDWQNY`	`5167q`	`WVYHTEGYFPDWQNY`
`5169`	`FPDWQNYTPGPGIRY`	`5169a`	`FPDWQNYTPGPGVRY`
`5170`	`QNYTPGPGIRYPLTF`	`5170a`	`QNYTPGPGVRYPLTF`
`5171`	`PGPGIRYPLTFGWCF`	`5171a`	`PGPGVRYPLTFGWCF`	`5171b`	`PGPGVRYPLTFGWCY`
`5172`	`IRYPLTFGWCFKLVP`	`5172a`	`VRYPLTFGWCFKLVP`	`5172b`	`VRYPLTFGWCYKLVP`
`5173`	`LTFGWCFKLVPVEPE`	`5173a`	`LTFGWCFKLVPMEED`	`5173b`	`LTFGWCYKLVPMEED`
`5178`	`NEGENNSLLHPMSLH`	`5178a`	`NAGENNSLLHPICQH`
`5179`	`NNSLLHPMSLHGMDD`	`5179a`	`NNSLLHPICQHGIDD`

shows that the consensus and the autologous peptides had similar a. a. sequences, and a.a differences between consensus and autologous sequences are shown in bold.