title: Virtually full-length subtype F and F/D recombinant HIV-1 from Africa and South America.
abstract: For reliable classification of HIV-1 strains appropriate reference sequences are needed. The HIV-1 genetic subtype F has a wide geographic spread, causing significant epidemics in South America, Africa, and some regions of Europe. Previously only two full-length sequences of each of the HIV-1 subtype F subclusters F1 and F2 have been described. To extend the knowledge of subtype F variation on a complete genome level, three new virtually full-length F1 sequences were cloned and sequenced, two from Africa and one from South America. Comparison of the new and previously described sequences showed that monophyletic clustering of the subcluster F1 of subtype F is consistent and highly supported in all genome regions. Two additional full-length strains were shown to be mosaics of subtypes F and D. These epidemiologically unrelated F/D sequences showed similar chimeric structure, suggesting that they may represent a previously undescribed circulating recombinant form (CRF). This was supported by partial sequences from three additional unlinked F/D recombinants. Genetic distances in the phylogenetic trees suggest that the recombination event leading to the putative CRF occurred relatively long ago, close to the divergence of the F1 and F2 subclusters. Furthermore, all five F/D recombinants are linked to the Democratic Republic of Congo, suggesting that the original recombination event took place in central Africa.
authors.affiliation: HIV Laboratory, Department of Infectious Disease Epidemiology, National Public Health Institute, Mannerheimintie 166, Helsinki, FIN-00300, Finland.
authors.forename: T
authors.initials: T
authors.lastname: Laukkanen
authors.forename: J K
authors.initials: JK
authors.lastname: Carr
authors.forename: W
authors.initials: W
authors.lastname: Janssens
authors.forename: K
authors.initials: K
authors.lastname: Liitsola
authors.forename: D
authors.initials: D
authors.lastname: Gotte
authors.forename: F E
authors.initials: FE
authors.lastname: McCutchan
authors.forename: E
authors.initials: E
authors.lastname: Op de Coul
authors.forename: M
authors.initials: M
authors.lastname: Cornelissen
authors.forename: L
authors.initials: L
authors.lastname: Heyndrickx
authors.forename: G
authors.initials: G
authors.lastname: van der Groen
authors.forename: M O
authors.initials: MO
authors.lastname: Salminen
mesh_terms: D000349:Africa; D003001:Cloning, Molecular; D019143:Evolution, Molecular; D005260:Female; D015686:Gene Products, env / Q000235:genetics; D015683:Gene Products, gag / Q000235:genetics; D015684:Gene Products, pol / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D011993:Recombinant Fusion Proteins / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D013020:South America
chemical_list: D015686:Gene Products, env; D015683:Gene Products, gag; D015684:Gene Products, pol; D011993:Recombinant Fusion Proteins