title: Among 46 near full length HIV type 1 genome sequences from Rakai District, Uganda, subtype D and AD recombinants predominate.
abstract: The impact of HIV-1 genetic diversity on candidate vaccines is uncertain. To minimize genetic diversity in the evaluation of HIV-1 vaccines, vaccine products must be matched to the predominant subtype in a vaccine cohort. To that end, full genome sequencing was used to detect and characterize HIV-1 subtypes and recombinant strains from individuals in Rakai District, Uganda. DNA extracted from peripheral blood mononuclear cells (PMBC) was PCR amplified using primers in the long terminal repeats (LTRs) to generate nearly full length genomes. Amplicons were directly sequenced with dye terminators and automated sequencers. Sequences were phylogenetically analyzed and recombinants were detected and mapped with distance scan and bootscan. Among 46 sequences, 54% were subtype D, 15% were subtype A, and 30% were recombinant. All recombinants were individually unique, and most combined subtypes A and D. Subtype D comprised more than 70% of all the HIV-1 genomes in Rakai when both pure subtypes and recombinants were considered. Candidate vaccines based on HIV-1 subtype D would be appropriate for evaluation in Rakai District, Uganda.
authors.affiliation: Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA. Harris@hivresearch.org
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Harris
authors.forename: David
authors.initials: D
authors.lastname: Serwadda
authors.forename: Nelson
authors.initials: N
authors.lastname: Sewankambo
authors.forename: Bohye
authors.initials: B
authors.lastname: Kim
authors.forename: Godfrey
authors.initials: G
authors.lastname: Kigozi
authors.forename: Noah
authors.initials: N
authors.lastname: Kiwanuka
authors.forename: James B
authors.initials: JB
authors.lastname: Phillips
authors.forename: Fred
authors.initials: F
authors.lastname: Wabwire
authors.forename: Mary
authors.initials: M
authors.lastname: Meehen
authors.forename: Tom
authors.initials: T
authors.lastname: Lutalo
authors.forename: James R
authors.initials: JR
authors.lastname: Lane
authors.forename: Randall
authors.initials: R
authors.lastname: Merling
authors.forename: Ron
authors.initials: R
authors.lastname: Gray
authors.forename: Maria
authors.initials: M
authors.lastname: Wawer
authors.forename: Deborah L
authors.initials: DL
authors.lastname: Birx
authors.forename: Merlin L
authors.initials: ML
authors.lastname: Robb
authors.forename: Francine E
authors.initials: FE
authors.lastname: McCutchan
mesh_terms: D000293:Adolescent; D000328:Adult; D001483:Base Sequence; D004279:DNA, Viral / Q000737:chemistry*; D005260:Female; D016679:Genome, Viral; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D014454:Uganda
chemical_list: D004279:DNA, Viral