Table 1. .
Examples of viral vatches within the HIV-1 envelope protein, for viruses where vaccines are available.
| Viruses and Alignments with the HIV-1 env protein All are within a predicted B cell epitope region (or within an experimentally described IEDB epitope) | ||||
|---|---|---|---|---|
| Chicken pox (Human Herpesvirus 3) 73: A +PTDP+ 108: IIS W+ 121: KLTP LC TL 142: SSSGR 214: PIHY APA 252: RP V +LL 276: NFT NA 305: KR R IG 307: KRIH and KR RI 313: P RAF+ PGRA 413: TITLP 500: KAKRRV 502: KRRVV 573: GI QLQ 574: IK QLQA 690: GGLVG |
Hepatitis A 38: VYYGV 477: +NWRS+ +KI 492: EPLGV 575: QL VLA 608: VP NAS |
Hepatitis B 39: Y VPV WK 74: CVPTD 75: VPTDP P 108: IS W SL and IISL 141: NSSSG 142: SSSGR 214: PIH CA 218: CAPA F 237: GPCT+ 252: RP V QL 253: PIVST 255: ST+LL 293: B +INCT 307: KR H PGRA 314: GR AFYT 359: QSS GD 362: KQSSG 441: GQ RCS S I 494: LGVAP 495: GVAPT 575: QL ARV 583: VE YLKD ++L LG GC KL+C 584: E YLKD 607: AV WNA and AV WN S 678: W LW +I IF 685: FI++V 690: GGL GL 708: VRQ YS LS 712: YSPLS 802: YW QEL 803: W QELK |
Influenza A virus ( many different strains) 32: DT+VHN 42: VPVW 108: I SLWDQ and IISLW 110: SLWDQ 121: K T PLCV L 124: PLCV L 125: LCVTL 131: CTDLK 139: NTNSS 142: SSSGR 167: GKVQK 205: CPKVS 207: KI FEP IP and KI SFE IP 214: P+HYC 234: NGTGP 252: R IVSTQ and RPIV Q 254: IVSTQ 263: GSLAE+ 294: INCTR 298: RPNNN 302: NNTRK and NYNK KRI I and NYNKR 303: YNK KR 304: TRKRI 305: KRIRI and KR R+ I PG and KRKR 312: GPGR F+ and GPG F+ 349: LREQF 350: REQFG 356: NKTII 357: KTIIF 358: TIIFK 362: KQSSG 364: SSGGD 369: PEIVT 370: EIVTH 371: IVTHS 372: VTHSF 373: THSFN 405: SNNTE 407: NTEGS 412: DTITL 445: CSSNI 490: KIEPL 493: PLGVA 571: VWGI AR 573: QL ARV 576: L+ARVL 605: TTAVP 608: +PW NASW 679: LWYI K F and LW IKI 685: FI+ IV GLV 686: IMIV 687: MIV G V L and MI+GG 710: QG YS LSFQ 711: GYS LSF 725: RGPDR 730: PEG+EE 744: RDRSI 805: +ELKN 806: ELKNS and ELK+ AV 807: LKNS V 825: G DRVI 828: RV E LQR and RV E+LQR 830: IEVLQ |
Japanese encephalitis virus 59: K YDTE 110: SLWD 240: T++STV 241: NVSTV 306: RKRI+ 497: APTKA 526: AGST+G A S TL R 576: L ARV Y LK 688: IVGGL L I 690: GGLV 742: RDRSI 829: VIEVL R and VIE VLQR 830: IEVLQR |
| Measles virus (repeat motifs in Bold) 55: ASDAKA 109: ISL WD SL 110: SLWD 252: RPI S QL 253: PI S QL 263: GSLA EE 304: NKRK 308: RIH IGPG 312: GPGRA 314: GRAF T 401: STEGS 493: PLGVA 573: IKQL QA V 581: LAVE LK 647: E SQ+QQ+ 685: F+M LVGL 688: IVGG V 706: NRVRQ 707: RVRQG 715: L F+ LPTPR 716: NRVRQ 719: THLPT 721: LPTPR 732: GI EE+G + R DRDR 801: +Y SQEL 828: R EVVQ |
Mumps virus 112: W DQSL 135: N NT SSS 140: NT SSS 254: I STQL 305: KRI IG 443: QI CS NI 493: PLGVA 573: IK QLQA 577: QAR LA 688: IV GLV 823:AEG RVI |
Papillomavirus(several strains) 35: WV V YGV 36: VTV PV 58: AYDT+ 60: AY+T HN+ 70: ATHAC 74: CVPTD P P 77: TDPNP 82: QE+VLV 142: SSSGR 208: ISF+P 218: CAPA F 234: NGTGP 238: PCTNV 239: CT N STVQC 240: TNVST 253: PI STQ 264: SLAEE 300: NNNTR 301: NNTRK 302: NTRKR 305: KR RI I and KRKR+ 349: LREQF 363: QSSGG 364: SSGGD 401: STEGS 406: NNTEG 407: NTEGS 410: GSDTI 413: TITLP 440: SGQIR 493: PLGVA 497: APTKA 500: KAKRR 502: KRRVV 570: VWGIK L+ 574: KQLQ 576: LQ VLA 605: TTAVP 633: REIN Y S 635: I+NYTS 644: SLIEES 658: QELLE 688: IVGG 690: GG+VG 721: LPTP GP 730: PEG ++EGG 731: EG+EEE 734: EEEG E +R D S R 799: LL W QEL 806: ELKNS V 807: LKNSA 820: IAVAE D IE 828: R IEVL |
Poliovirus (1,2 and 3) 36: V VYYG 252: RP + TQ 255: VSTQ 314: GRA YT 336: AKW++ and AK NN 529: TMGAA 531: GAAS+ 836: AC I IP IRQG |
Human Rotavirus A 63: TEVHN 121: KL LCV 133: DLKND 208: ISF P +Y 252: A R I VSTQ 303: YNKR 307: KRIH and KR RI 308: A RIHI 313: PG AF+ 337: KW +TL 369: PEIVT 413: TITLP 576: LQ V L VE YLK 583: VER L D QLL I G and VE YLK and VE Y+K 686: IM V GL V L 691: GLVG+ 822: VAEGT+ 829: VIEVL 831: EV LQRA |
| Rabies virus 122: L LC+TL 218: CAPA F 220: PAG AI 337: KWNN 354: GNNKT 584: ER+LK 687: MI GGL L 800: LQ WSQ 805: QELKN |
Rubella 70: AT ACV PTD 738: GGE DR 825: G DRV+ V Q |
Vaccinia virus or Vaccinia virus Tian Tan 34: K W+TV 35: LW YYGV 36: VT+ Y GVPV 37: T+YYG 55: V LNAT IA 57: DAKAY 82: Q VVLV 108: II LW+ |
Yellow fever virus 108: IIS DQ 131: KC L D SSS 231: KTF GTG CT 259: LLLN E+ SV T N T I + S E NC PN R 276: N D KTI V L T P 354: GNNKT 417: PCRI I+ 484: YK KVVK+ L AP KA V+ R+ R G 632: + EI NY S H |
|
| |
|
112: W DQSL 122: LTPL V 143: SSGRM 153: EIKNC 267: EEEVV 276: NFTD A 312: GPGR 313: A PG AF+ 355: NNKTI 359: IIFKQ 360: IFKQS 524: GAAGST 577: QARV AV 579: RVLA+ R and RV AVE and RVL AV RY 587: L +QQ LL 635: I NYTS 645: LI EE +QE E Q L+E 646: +EE N+++ K EQELL 712: YSPLS 714: P SFQT 719: TH P T + PE I 720: HL TP GP 741: DR+R IR 804: SQELK 807: LK+SA+ |
687: M VGG V L 691: GLVG 826: TDR IE V+G 842: H RIR GL+ |
|
| Viruses that modulate HIV-1 infection (for measles see above) | ||||
| Dengue virus (1, 2 or 3) 36: VT Y+GV H and VT Y GV V WK 108: IIS DQ 208: I EPIP 242: VSTVQ 252: RP V LL 254: IVST LL 256: STQLL 264: SL EE+ 264: SLAEE 265: LAE EV 302: NTRKR 302: NKRKR 313: PGR TT 335: RAK NT 348: ESQ +QE 363: QSSGG 402: TEGSN 523: LG GSTM 570: VWGI AR 580: VLAVE 606: TA PWN 685: F +VGG VG 686: IM V GLV L 691: VGGL 722: PTPRG |
|
GB virus C 70: ATHAC D P+++ 122: LTPL CV 140: T SSSG EK 209: SFE IP 213: IPI AG A 252: RP+VS 253: PIVS 306: RKR + PG 468: FR GGG D W 521: FLG T A LT L G V 523: LGAAG TM A M 531: GA S+T T QA 574: K L ARVL 581: LAVE LK 582: AVE LK 610: VPW AS 686: IMI GL 689: VG LVG and VG L GL 729: R G GER DR 738: GER IRLV 807: LK VSLLNA 828: RVIE 830: IE QRA 831: EVL RA |
|
|
| Position within env protein |
Epitope from IEDB |
Type |
||
| 33 | KLWVTVYYGV | MHC binding | ||
| 36 | VTVYYGVPVWK | T cell/MHC binding | ||
| 108 | IISLWDQSL | MHC binding | ||
| 121 | KLTPLCVTL | T cell/MHC binding | ||
| 206 | PKISFEPIPIHYCAPAGFA | MHC binding | ||
| 252 | RPIVSTQLL | MHC binding | ||
| 302 | NYNKRKRIHIGPGRAFYTTKNII | B cell | ||
| 311 | IGPGRAFHT | T cell | ||
| 312 | GPGRAFYTT | MHC binding | ||
| 335 | RAKWNNTLK | MHC binding | ||
| 570 | VWGIKQLQARVLAVERYLKD | MHC binding | ||
| 606 | TAVPWNASW | MHC binding | ||
| 678 | WLWYIKIFI | MHC binding | ||
| 685 | FIMIVGGLV | MHC binding | ||
| 686 | IMIVGGLVGL | MHC binding | ||
| 799 | LLQYWSQEL | MHC binding | ||
| 828 | RVIEVLQRA | MHC binding | ||
Their start position (within the env protein of 856 amino acids) is marked as is their position with respect to predicted B-cell epitopes within the env protein (these are all within regions with an antigenicity index of greater than the server-set threshold of 0.35: see supplementary Table 1). Spaces within the sequences indicate nonidentical amino acids and + signs an amino acid with similar physicochemical properties. The gray shaded sequences are within sequences that have been described as epitopes in experimental studies (B cell, T cell, or MHC binding from IEDB: The amino acid sequences of these experimentally verified epitopes are appended at the bottom of the table). Note that these sequences often overlap within consecutive regions of the env protein. In the majority of cases shown, contiguous sequences were of pentapeptides, although longer gapped sequences are also illustrated.