title: Characterization of subtype A HIV-1 from Africa by full genome sequencing.
abstract: OBJECTIVE
  To improve our understanding of the genetic complexity of HIV-1 subtype A by increasing the number of subtype A isolates that have been sequenced in their entirety.
  
  
  METHODS
  Nine HIV-1-seropositive patients from Africa living in Sweden contributed peripheral blood mononuclear cells (PBMC) for this study. Sequencing of the C2-V3 region of env had shown them to be subtype A. DNA from virus cultures was used for the amplification of virtually full-length proviral sequences, and the resulting fragment was sequenced.
  
  
  RESULTS
  Six of the nine viral isolates were subtype A throughout the genome, or non-recombinant, and all of these were from east Africa. One virus from the Ivory Coast had the AG(IbNG) genetic form, a recombinant form common in west Africa. Two of the isolates were novel recombinants: one was an A/C recombinant and the other was A/D. Analysis of gag reveals three subclusters within the A subtype: one containing the AG(IbNG) subtype viruses, one containing the AE(CM240) viruses and one containing the non-recombinant A viruses. These genetic clusters have different geographical distributions in Africa.
  
  
  CONCLUSIONS
  The prevailing view of HIV-1 subtype A forming a uniform band across the center of sub-Saharan Africa needs revision. In all probability, the most common subtype in west Africa and west central Africa is the AG recombinant, AG(IbNG), whereas in east central Africa it is the non-recombinant subtype A.
authors.affiliation: Henry M. Jackson Foundation, Rockville, MD, USA. jcarr@hiv.hjf.org
authors.forename: J K
authors.initials: JK
authors.lastname: Carr
authors.forename: T
authors.initials: T
authors.lastname: Laukkanen
authors.forename: M O
authors.initials: MO
authors.lastname: Salminen
authors.forename: J
authors.initials: J
authors.lastname: Albert
authors.forename: A
authors.initials: A
authors.lastname: Alaeus
authors.forename: B
authors.initials: B
authors.lastname: Kim
authors.forename: E
authors.initials: E
authors.lastname: Sanders-Buell
authors.forename: D L
authors.initials: DL
authors.lastname: Birx
authors.forename: F E
authors.initials: FE
authors.lastname: McCutchan
mesh_terms: D000349:Africa; D004279:DNA, Viral; D005260:Female; D016679:Genome, Viral; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D006679:HIV Seropositivity / Q000097:blood / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D008297:Male; D010446:Peptide Fragments / Q000235:genetics; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments