title: Inter- and intra-genic intersubtype HIV-1 recombination in rural and semi-urban Uganda.
abstract: OBJECTIVE
  To investigate the number and variety of viruses with discrepant subtypes between env and gag and within gag in two cohorts in Uganda.
  
  
  METHODS
  Sequences were generated from PCR products amplified directly (without cloning) from patient blood and compared in the v3/v4 region of env and the p17 and p24 regions of gag to reference subtype strains by phylogenetic analysis. Gag sequences with a discrepant subtype between p17 and p24 were analysed further to indicate approximate sites of recombination.
  
  
  RESULTS
  Envelope subtypes D and A were predominant, but subtypes B, C and G were also found. From analysis of three short regions of the HIV genome we found 15 different combinations of subtype assortment, including 11 different recombinant permutations. Approximately 30% of viruses (29/104) in this part of Uganda appear to be recombinants between the env and gag genes and 10% (11/104) are recombinant within the gag gene. There was no clear pattern of crossover points within the gag gene. There seems to be no evidence of new circulating recombinant forms.
  
  
  CONCLUSIONS
  Both inter-genic and intra-genic inter-subtype recombination appear to be a relatively common occurrence in this geographical region where two subtypes of virus co-circulate. These results have implications for cross-clade vaccine design.
authors.affiliation: Centre for HIV Research, ICAPB, University of Edinburgh, Edinburgh, UK.
authors.forename: David L
authors.initials: DL
authors.lastname: Yirrell
authors.forename: Pontiano
authors.initials: P
authors.lastname: Kaleebu
authors.forename: Dilys
authors.initials: D
authors.lastname: Morgan
authors.forename: Christine
authors.initials: C
authors.lastname: Watera
authors.forename: Brian
authors.initials: B
authors.lastname: Magambo
authors.forename: Frederick
authors.initials: F
authors.lastname: Lyagoba
authors.forename: James
authors.initials: J
authors.lastname: Whitworth
mesh_terms: D000328:Adult; D001483:Base Sequence; D015331:Cohort Studies; D004279:DNA, Viral; D015683:Gene Products, gag / Q000235:genetics; D015488:HIV Antigens / Q000235:genetics; D016655:HIV Core Protein p24 / Q000235:genetics; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D015658:HIV Infections / Q000097:blood / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000235:genetics; D010802:Phylogeny; D011995:Recombination, Genetic; D012424:Rural Population; D014454:Uganda; D014505:Urban Population; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus
chemical_list: D004279:DNA, Viral; D015683:Gene Products, gag; D015488:HIV Antigens; D016655:HIV Core Protein p24; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus; C054858:p17 protein, Human Immunodeficiency Virus Type 1