title: Characterization of near full-length genomes of HIV type 1 strains in Denmark: basis for a universal therapeutic vaccine.
abstract: We report here the near full-length sequence characterization of 17 Danish clinical HIV-1 strains isolated from HLA-A02 patients not in need of ART, with relatively low viral loads and normal CD4 cell counts. Sequencing was performed directly on DNA extracted from short-term cocultures of PBMCs. The near full-length genomes did not contain any major insertions, deletions, or rearrangements. Sixteen of the isolates were characterized as nonrecombinant subtype B and one isolate as nonrecombinant subtype C. Phylogenetic analysis did not reveal any founder effect among the sequences. Also, we investigated the presence of infrequently targeted subdominant HLA-A02-binding CTL epitopes. The epitopes were conserved in the Danish strains as well as globally in reference sequences of all subtypes. Thus, the selected epitopes were not subtype-specific or region-specific. This lends support for the concept of a universal immunotherapeutic vaccine construct based on these epitopes.
authors.affiliation: Department of Virology, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Betina S
authors.initials: BS
authors.lastname: Andresen
authors.forename: Lasse
authors.initials: L
authors.lastname: Vinner
authors.forename: Sheila
authors.initials: S
authors.lastname: Tang
authors.forename: Karoline
authors.initials: K
authors.lastname: Bragstad
authors.forename: Gitte
authors.initials: G
authors.lastname: Kronborg
authors.forename: Jan
authors.initials: J
authors.lastname: Gerstoft
authors.forename: Sylvie
authors.initials: S
authors.lastname: Corbet
authors.forename: Anders
authors.initials: A
authors.lastname: Fomsgaard
mesh_terms: D000328:Adult; D000368:Aged; D018791:CD4 Lymphocyte Count; D004279:DNA, Viral / Q000235:genetics; D003718:Denmark; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D015234:HLA-A Antigens / Q000235:genetics; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D019562:Viral Load
chemical_list: D004279:DNA, Viral; D015234:HLA-A Antigens