Table 1.
Epitopes recognized by anamnestic SIVmac239-specific CD4+ T-cell responses in vaccinated animalsa
| SIV Proteinb | Peptide Pool & aa positionc | Epitope & aa position (abbreviation)d | Epitope Sequencee | MHC-II restricting allelef | Animal(s) targeting the epitopeg | |
|---|---|---|---|---|---|---|
| Gag | Matrix (p15) | A1-51 | EL17-31 (EL15) | EKIRLRPNGKKKYML | DRB1*0303 | r02089 |
| KA27-37 (KA11) | KKYMLKHVVWA | DRB1*1007 | r02089 | |||
| LL41-51 (LL11) | LDRFGLAESLL | DQB1*1708 | r01099 | |||
| DQA1*2402 | ||||||
| B41-91 | SL49-67 (SL19) | SLLENKEGCQKILSVLAPL | - | r97112 | ||
| KP59-69 (KP11) | KILSVLAPLVP | DPB1*06 | r02089 | |||
| SE77-91 (SE15) | SLYNTVCVIWCIHAE | - | r97112 | |||
| C81-131 | KH93-107 (KH15) | KVKHTEEAKQIVQRH | - | r02089 | ||
| Capsid (p27) | D121-171 | TE153-163 (TL11) | TLNAWVKLIEE | DPB1*04 | r02114 | |
| E161-211 | CA181-199 (CA19) | CTPYDINQMLNCVGDHQAA | DRB1*0309 | r97112 | ||
| DI185-203 (DI19) | DINQMLNCVGDHQAAMQII | DQB1*1801 | r02089 | |||
| DQA1*2601 | ||||||
| VA193-211 (VA19) | VGDHQAAMQIIRDIINEEA | - | r02089 & r01099 | |||
| F201-251 | AY237-251 (AY15) | AGTTSSVDEQIQWMY | - | r02089 | ||
| G241-291 | WP249-258 (WP10) | WMYRQQNPIP | DQB1*1801 | r02089 | ||
| DQA1*2601 | ||||||
| EV245-259 (EV15) | EQIQWMYRQQNPIPV | - | r01099 | |||
| IL257-271 (IL15) | IPVGNIYRRWIQLGL | DPB1*02 | r01099 | |||
| IV257-275 (IV19) | IPVGNIYRRWIQLGLQKCV | DRB*w303 | r02114 | |||
| NN261-279 (NN19) | NIYRRWIQLGLQKCVRMYN | DQB1*1801 | r02089 | |||
| DQA1*2601 | ||||||
| LK269-287 (LK19) | LGLQKCVRMYNPTNILDVK | - | r02089 | |||
| KK273-291 (KK19) | KCVRMYNPTNILDVKQGPK | DRBw*201 | r97112, r02103 & r02114 | |||
| H281-331 | RT300-310 (RT11) | RFYKSLRAEQT | DRB1*0303 | r02089 | ||
| QA309-327 (QA19) | QTDAAVKNWMTQTLLIQNA | - | r02103 | |||
| WC317-331 (WC15) | WMTQTLLIQNANPDC | DRB1*1007 | r02089 & r97112 | |||
| (p2) & (p8) | J361-411 | PI376-391 (PI16) | PIPFAAAQQRGPRKPI | DQB1*1801 | r02089 | |
| DQA1*2601 | ||||||
| RA385-403 (RA19) | RGPRKPIKCWNCGKEGHSA | - | r01099 | |||
| K401-451 | KD419-429 (KD11) | KMDHVMAKCPD | DPB1*06 | r02089 | ||
| (p1) & (p6) | L451-491 | KV443-452 (KV10) | KPRNFPMAQV | DQB1*1801 | r02089 | |
| DQA1*2601 | ||||||
| LK469-483 (LK15) | LLKNYMQLGKQQREK | - | r02089 | |||
| Pol | RT (p51) | G199-250 | AP200-218 (AP19) | ALREICEKMEKDGQLEEAP | - | r97112 |
| MP208-226 (MP19) | MEKDGQLEEAPPTNPYNTP | - | r02114 | |||
| FI228-442 (FI15) | FAIKKKDKNKWRMLI | DRB1*0303 | r02089 | |||
| KV231-250 KV19) | KKDKNKWRMLIDFRELNRV | - | r97112 | |||
| I280-330 | DY280-294 (DY15) | DAYFSIPLDEEFRQY | - | r02089 | ||
| M440-490 | GE440-458 (GE19) | GIKTKHLCRLIRGKMTLTE | DPB1*06 | r02089 | ||
| EY471-486 (EY15) | ENKIILSQEQEGCYY | - | r02089 | |||
| (p15) | S676-726 | IK688-706 (IK19) | IEEMIKKSEIYVAWVPAHK | - | r02089 | |
| Integrase (p31) | V796-846 | GQ808-822 (GQ19) | GFIEAEVIPQETGRQ | DRBw*201 | r97112 | |
| PH816-838 (PH23) | PQETGRQTALFLLKLAGRWPITH | - | r97112 | |||
| X880-934 | TR900-914 (TR15) | TIVLMAVHCMNFKRR | - | r02113 | ||
| Y924-978 | EK924-942 (EK19) | ERLINMITTEQEIQFQQSK | - | r02089 | ||
| Vif | A1-51 | MI1-15 (MI15) | MEEEKRWIAVPTWRI | - | r02114 | |
| EY17-31 (EY15) | ERLERWHSLIKYLKY | - | r02089 | |||
| C81-131 | AA105-119 (AA15) | ADILLHSTYFPCFTA | - | r02089 | ||
| Rev | A1-51 | EL9-20 (EL12) | ELRKRLRLIHLL | DRB1*0318 | r01099 | |
| RT13-23 (RT11) | RLRLIHLLHQT | DPB1*06 | r02089 & r97112 | |||
| B40-90 | KY40-58 (KY19) | KRRWRRRWQQLLALADRIY | - | r02089 | ||
| AD72-86 (AD15) | AIQQLQNLAIESIPD | - | r02089 & r97112 | |||
| Nef | E166-216 | EY209-223 (EY15) | EVLAWKFDPTLAYTY | DRB1*0309 | r02103 | |
We mapped the SIV-specific CD4+ T-cell responses from five vaccinated animals (r01099, r02103, r02114, r02089, r97112), and generated 23 CD4+ T-cell clones specific for 23 different epitopes to determine MHC-II restriction.
Only the proteins that elicited an anamnestic SIV-specific CD4+ T-cell response were included in the table.
Peptide-pools were comprised of ten peptides of 15 amino acids in length that overlapped by 11 amino acids. We used peptide-pools that span the entire SIVmac239 proteome to detect anamnestic SIV-specific CD4+ T-cell immune responses. The amino acid (aa) position for each peptide-pool in SIVmac239 is written in subscript next to each letter.
Epitopes are named after their two flanking amino acids (aa) and their position in the SIVmac239 protein.
Epitopes highlighted in gray denote epitopes that were mapped to a core epitope.
The alpha chain is only denoted for the DQ alpha alleles. A dash (−) indicates that the restricting MHC-II allele for the targeted epitope was not determined.
Animals with SIV-specific CD4+ T-cell responses targeting the same epitope are in bold.