title: Novel evolutionary analyses of full-length HIV type 1 subtype C molecular clones from Cape Town, South Africa.
abstract: Understanding the origin, distribution, and evolving dominance of HIV-1 subtype C strains is an important component in the design and evaluation of a globally effective AIDS vaccine. To better understand subtype C viruses, we constructed complete molecular clones of primary, CCR-5-using isolates from South Africa and analyzed the molecular phylogenies of these clones using best fitting evolutionary substitution models. Analyses were performed on three full-length sequences, and on the individual genes. All clones were nonrecombinant, and although two of three had open reading frames and intact splice sites, they were not infectious. At the genomic level, the models demonstrated the increasing variability of subtype C in South Africa. At the subgenomic level, they revealed marked differences in the evolutionary patterns of individual genes, a finding that suggests that the genes are under different selective pressures and constraints. These data underscore the dynamic nature of the subtype C epidemic and emphasize the need for continuous monitoring of local strains.
authors.affiliation: Vaccines Research, Chiron Corporation, Emeryville, California 94608, USA. Jan_zur_Megede@Chiron.com
authors.forename: Jan
authors.initials: J
authors.lastname: zur Megede
authors.forename: Susan
authors.initials: S
authors.lastname: Engelbrecht
authors.forename: Tulio
authors.initials: T
authors.lastname: de Oliveira
authors.forename: Sharon
authors.initials: S
authors.lastname: Cassol
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Scriba
authors.forename: Estrelita Janse
authors.initials: EJ
authors.lastname: van Rensburg
authors.forename: Susan W
authors.initials: SW
authors.lastname: Barnett
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000821:virology; D000818:Animals; D001483:Base Sequence; D019556:COS Cells; D019143:Evolution, Molecular; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D013019:South Africa