title: Recombination following superinfection by HIV-1.
abstract: BACKGROUND
  There is increasing recognition of recombinant HIV-1 strains globally, but it has been unclear whether recombination results from superinfection during untreated, chronic infection.
  
  
  OBJECTIVE
  To search for evidence of recombination and superinfection in Africa, where multiple HIV-1 subtypes facilitate identification of strains.
  
  
  METHODS
  Serial blood samples from highly exposed, chronically infected women in Nairobi's Pumwani sex workers cohort were examined. Serial, complete HIV-1 RNA sequence analyses were performed for seven untreated long-term survivors. Sequences were subjected to computational analysis.
  
  
  RESULTS
  One woman had evidence of both superinfection and recombination. Complete HIV-1 RNA sequences were first derived from plasma obtained in 1986, when the woman had been HIV seropositive for at least 21 months; this sequence was entirely subtype A. The sequences obtained from plasma in 1995 and 1997, however, were subtype A/C recombinants with a SimPlot demonstrating that the subtype A fragment in 1995 and 1997 was derived from the original 1986 A sequence. Heteroduplex tracking assays demonstrated that the subtype C sequences were not detectable as minor species in 1986.
  
  
  CONCLUSIONS
  Intersubtype recombination took place between the original non-recombinant subtype A strain and the superinfecting subtype C strain in an untreated, chronically infected woman. This finding helps to explain the rising prevalence of recombinant HIV-1 worldwide. Recombination resulting from superinfection with diverse strains may pose problems for eliciting broad immune responses necessary for an effective vaccine.
authors.affiliation: Wadsworth Center, NY State Department of Health, Albany, 12208, USA.
authors.forename: Guowei
authors.initials: G
authors.lastname: Fang
authors.forename: Barbara
authors.initials: B
authors.lastname: Weiser
authors.forename: Carla
authors.initials: C
authors.lastname: Kuiken
authors.forename: Sean M
authors.initials: SM
authors.lastname: Philpott
authors.forename: Sarah
authors.initials: S
authors.lastname: Rowland-Jones
authors.forename: Francis
authors.initials: F
authors.lastname: Plummer
authors.forename: Joshua
authors.initials: J
authors.lastname: Kimani
authors.forename: Binshan
authors.initials: B
authors.lastname: Shi
authors.forename: Rupert
authors.initials: R
authors.lastname: Kaul
authors.forename: Job
authors.initials: J
authors.lastname: Bwayo
authors.forename: Omu
authors.initials: O
authors.lastname: Anzala
authors.forename: Harold
authors.initials: H
authors.lastname: Burger
mesh_terms: D000328:Adult; D015331:Cohort Studies; D004279:DNA, Viral / Q000235:genetics; D005260:Female; D016679:Genome, Viral; D015658:HIV Infections / Q000453:epidemiology / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007630:Kenya / Q000453:epidemiology; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA; D011477:Sex Work; D015163:Superinfection / Q000453:epidemiology / Q000235:genetics*
chemical_list: D004279:DNA, Viral; D012367:RNA, Viral