title: Forty-one near full-length HIV-1 sequences from Kenya reveal an epidemic of subtype A and A-containing recombinants.
abstract: OBJECTIVE
  To further define the genetic diversity of HIV-1 in Kenya using approaches that clearly distinguish subtypes from inter-subtype recombinants.
  
  
  METHODS
  Near full genome sequencing and analysis were used, including sensitive new tools for detection and mapping of recombinants.
  
  
  METHODS
  Purified peripheral blood mononuclear cell DNA from 41 HIV-1 positive blood donations collected from six hospitals across southern Kenya was used to amplify near full-length genomes by nested PCR. These were sequenced on an ABI 3100 automated sequencer and analyzed phylogenetically.
  
  
  RESULTS
  Among 41 near full-length genomes, 25 were non-recombinant (61%) and 16 were recombinant (39%). Of the 25 pure subtypes, 23 were subtype A, one was subtype C and one was subtype D. Most recombinants consisted of subtype A and either subtype C or subtype D; a few contained A2, a recently identified sub-subtype. Two A2/D recombinants had identical breakpoints and may represent a circulating recombinant form. A third A2/D recombinant had the same structure as a previously described Korean isolate, and these may constitute a second A2-containing circulating recombinant form.
  
  
  CONCLUSIONS
  In Kenya, 93% of HIV-1 genomes were subtype A or A-containing recombinant strains. Almost 40% of all strains were recombinant. Vaccine candidates tested in Kenya should be based on subtype A strains, but the methods used for evaluation of breakthrough infections during future vaccine trials should be capable of identifying non-A subtypes, the A2 sub-subtype, and recombinants.
authors.affiliation: Walter Reed Army Institute of Research, Washington, DC, USA.
authors.forename: William E
authors.initials: WE
authors.lastname: Dowling
authors.forename: Bohye
authors.initials: B
authors.lastname: Kim
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Mason
authors.forename: K Monique
authors.initials: KM
authors.lastname: Wasunna
authors.forename: Uzma
authors.initials: U
authors.lastname: Alam
authors.forename: Lynne
authors.initials: L
authors.lastname: Elson
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
authors.forename: Jean K
authors.initials: JK
authors.lastname: Carr
mesh_terms: D004196:Disease Outbreaks; D016679:Genome, Viral; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D007630:Kenya / Q000453:epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA