title: Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning.
abstract: Subtype C is the most prevalent clade in the HIV-1 pandemic. Previous studies suggested that African HIV-1 subtype C lacks a well-defined phylogenetic structure. Here we show that, by sequential pruning of ambiguously positioned taxa, a well-defined intrasubtype C phylogenetic structure becomes apparent, with 52% African HIV-1 subtype C isolates analyzed in envelope sequences branching within 11 clusters, also supported in a tree of full-length genomes, and all with geographical associations. Among 46 viruses recently transmitted in South Africa, 70% branched within 7 clusters (41% in the largest one) and 15% additional isolates were intercluster recombinants. Choice of the outgroup sequence and inclusion of intrasubtype recombinant viruses in the analyses could greatly affect support of clusters. The identification of clusters comprising a large proportion of African HIV-1 subtype C viruses may have implications for the design of vaccines intended for use in areas where subtype C is prevalent.
authors.affiliation: Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo Km. 2, Majadahonda, Madrid, Spain. mthomson@isciii.es
authors.forename: Michael M
authors.initials: MM
authors.lastname: Thomson
authors.forename: Aurora
authors.initials: A
authors.lastname: Fernández-García
mesh_terms: D016915:AIDS Vaccines; D000349:Africa; D001483:Base Sequence; D015658:HIV Infections / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D010802:Phylogeny; D011995:Recombination, Genetic; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D016915:AIDS Vaccines; D054299:env Gene Products, Human Immunodeficiency Virus