title: Generation of a consensus sequence from prevalent and incident HIV-1 infections in West Africa to guide AIDS vaccine development.
abstract: We considered several key issues regarding the development of a DNA-based human immunodeficiency virus type 1 (HIV-1) vaccine: (1) should the candidate vaccine construct be derived from incident or prevalent HIV-1 strains; and (2) should circulating plasma virus, archived HIV-1 provirus recovered from peripheral blood mononuclear cells, or both be included? To address these questions, we collected circulating HIV-1 strains from infected individuals residing in Abidjan, Côte d'Ivoire. From a panel of 23 strains, 22 were HIV-1 subtype A in gag, 19 of which phylogenetically clustered with the recombinant HIV-1, CRF02-AG strains from West Africa. The mosaic genome of CRF02-AG was confirmed by sequencing the protease gene. A consensus gag p24 protein sequence was generated and 147 of 148 codons were identical to CRF02-AG (IbNG). Regardless of the sequence origin (RNA, provirus, incident, or prevalent), the gag p24 consensus sequences were highly representative of these distinct virologic compartments. These data suggest that the consensus sequence generated from incident and prevalent infections may provide an appropriate sequence for a DNA vaccine and is largely representative of the major circulating viral strain.
authors.affiliation: HIV and Retrovirology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA. dellenberger@cdc.gov
authors.forename: Dennis L
authors.initials: DL
authors.lastname: Ellenberger
authors.forename: Bin
authors.initials: B
authors.lastname: Li
authors.forename: L Davis
authors.initials: LD
authors.lastname: Lupo
authors.forename: S Michele
authors.initials: SM
authors.lastname: Owen
authors.forename: John
authors.initials: J
authors.lastname: Nkengasong
authors.forename: Madeleine Sassan
authors.initials: MS
authors.lastname: Kadio-Morokro
authors.forename: James
authors.initials: J
authors.lastname: Smith
authors.forename: Harriet
authors.initials: H
authors.lastname: Robinson
authors.forename: Marta
authors.initials: M
authors.lastname: Ackers
authors.forename: Alan
authors.initials: A
authors.lastname: Greenberg
authors.forename: Thomas
authors.initials: T
authors.lastname: Folks
authors.forename: Salvatore
authors.initials: S
authors.lastname: Butera
mesh_terms: D000354:Africa, Western; D000595:Amino Acid Sequence; D016384:Consensus Sequence; D007560:Cote d'Ivoire / Q000453:epidemiology; D016655:HIV Core Protein p24 / Q000235:genetics*; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D016333:HIV Protease / Q000235:genetics*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D015994:Incidence; D008969:Molecular Sequence Data; D010802:Phylogeny; D015995:Prevalence; D014176:Protein Biosynthesis
chemical_list: D016655:HIV Core Protein p24; D016333:HIV Protease