title: Sequence analysis of HIV-1 isolates from Guinea-Bissau: selection of vaccine epitopes relevant in both West African and European countries.
abstract: For a CD8 epitope-based vaccine to match different geographic locations, the targeted epitopes for cytotoxic T-lymphocytes (CTLs) must be present in the local circulating HIV-1 strains. Secondly, the vaccine epitopes should match the host population HLA types. We characterized two new HIV-1 isolates from Guinea-Bissau. Also, we have identified 15 subdominant CD8 epitopes representing common HLA super-types theoretically covering most HLA alleles in any population. Herein we demonstrate that the selected vaccine epitopes are well conserved and simultaneously present in sequences from West Africa and Denmark. Use of the selected epitopes will likely ensure ≥10 immune targets in the majority of candidates for experimental therapeutic vaccination in both geographic regions. Our results warrant testing of the selected vaccine epitopes in both geographic locations.
authors.affiliation: Virus Research and Development, Statens Serum Institut, Copenhagen, Denmark. lvi@ssi.dk
authors.forename: Lasse
authors.initials: L
authors.lastname: Vinner
authors.forename: Birgitta
authors.initials: B
authors.lastname: Holmgren
authors.forename: Kristoffer J
authors.initials: KJ
authors.lastname: Jensen
authors.forename: Joakim
authors.initials: J
authors.lastname: Esbjornsson
authors.forename: Marie
authors.initials: M
authors.lastname: Borggren
authors.forename: Julie L
authors.initials: JL
authors.lastname: Hentze
authors.forename: Ingrid
authors.initials: I
authors.lastname: Karlsson
authors.forename: Betina S
authors.initials: BS
authors.lastname: Andresen
authors.forename: Gregers J
authors.initials: GJ
authors.lastname: Gram
authors.forename: Henrik
authors.initials: H
authors.lastname: Kloverpris
authors.forename: Peter
authors.initials: P
authors.lastname: Aaby
authors.forename: Zacarias José
authors.initials: ZJ
authors.lastname: Da Silva
authors.forename: Eva-Maria
authors.initials: EM
authors.lastname: Fenyö
authors.forename: Anders
authors.initials: A
authors.lastname: Fomsgaard
mesh_terms: D016915:AIDS Vaccines / Q000235:genetics / Q000276:immunology*; D001483:Base Sequence; D003718:Denmark; D018984:Epitopes, T-Lymphocyte / Q000276:immunology*; D006169:Guinea-Bissau; D015658:HIV Infections / Q000276:immunology / Q000517:prevention & control / Q000821:virology*; D015497:HIV-1 / Q000235:genetics* / Q000276:immunology*; D006680:HLA Antigens / Q000235:genetics / Q000276:immunology; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology*
chemical_list: D016915:AIDS Vaccines; D018984:Epitopes, T-Lymphocyte; D006680:HLA Antigens; D012367:RNA, Viral