title: HIV-1 subtype H near-full length genome reference strains and analysis of subtype-H-containing inter-subtype recombinants.
abstract: OBJECTIVE
  To characterize near-full-length genomes of two HIV-1 subtype H strains. To extend sequence data to include full env and gag, and analyse and redefine, previously documented subtype H strains.
  
  
  METHODS
  Near-full-length genomes of HIV-1 env subtype H strains VI991 and VI997 were amplified, cloned, sequenced, phylogenetically analysed and compared with a panel of 23 HIV-1 group M reference isolates. The mosaic nature of previously published subtype H strains VI557 and CA13 was reanalysed.
  
  
  METHODS
  Peripheral blood mononuclear cells (PBMC) from individuals harbouring strains VI991 and VI997 were co-cultivated with PHA stimulated donor PBMC. Near-full-length genomes of VI991 and VI997, and gag and env genes of CA13 and VI557, were amplified by polymerase chain reaction, cloned and sequenced. Intersubtype recombination analyses were performed by similarity plot, bootscanning and phylogenetic analysis.
  
  
  RESULTS
  Near-full-length clones of HIV-1 VI991 and VI997 are representative of subtype H. They form a phylogenetic cluster with the only previously described subtype H representative HIV-1 90CF056.1, regardless of the genome region analysed. VI557 is redefined as a gag and env subtype H mosaic virus containing unclassified fragments. CA13 is a complex intersubtype recombinant between subtypes A, H and unclassified strains
  
  
  CONCLUSIONS
  Near-full-length genome analysis identified HIV-1 VI991 and VI997 as two new subtype H representatives. These reagents will allow defining and classifying non-recombinant as well as recombinant HIV-1, eventually helping to solve the puzzle of HIV-1 subtypes.
authors.affiliation: Department of Microbiology, Institute of Tropical Medicine, Antwerp, Belgium. wjanssens@itg.be
authors.forename: W
authors.initials: W
authors.lastname: Janssens
authors.forename: T
authors.initials: T
authors.lastname: Laukkanen
authors.forename: M O
authors.initials: MO
authors.lastname: Salminen
authors.forename: J K
authors.initials: JK
authors.lastname: Carr
authors.forename: G
authors.initials: G
authors.lastname: Van der Auwera
authors.forename: L
authors.initials: L
authors.lastname: Heyndrickx
authors.forename: G
authors.initials: G
authors.lastname: van der Groen
authors.forename: F E
authors.initials: FE
authors.lastname: McCutchan
mesh_terms: D001483:Base Sequence; D004279:DNA, Viral; D015752:Genes, env; D015750:Genes, gag; D016679:Genome, Viral; D015658:HIV Infections / Q000097:blood / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D012015:Reference Standards
chemical_list: D004279:DNA, Viral