HIV type 1 subtype C gag and nef diversity in Southern Africa

Helba Bredell, Darren P. Martin, Joanne Van Harmelen, Arvind Varsanii, Haynes W. Sheppard, Richard Donovan, Clive M. Gray, Carolyn Williamson

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


Several HIV-1 subtype C-specific gag- and/or nef-based vaccines are currently intended for clinical trial in southern Africa. Here we provide sequences of 64 gag and 45 nef genes sampled in Malawi, Zambia, Zimbabwe, and South Africa and assess the degree of southern African HIV-I diversity that will confront these vaccines. Whereas reasonable phylogenetic evidence exists for geographical clustering of subtype C gag and nef sequences from various other parts of the world, there is little evidence of similar population founder effects in the southern African epidemic. The entire breadth of subtype C diversity is represented in the southern African genes suggesting there may be no advantage in producing region- or country-specific subtype C vaccines. We do not, however, find much evidence of intersubtype recombination in the Southern African genes, implying that the likelihood of vaccine failure due to the emergence of intersubtype recombinants is probably low.

Original languageEnglish (US)
Pages (from-to)477-481
Number of pages5
JournalAIDS Research and Human Retroviruses
Issue number3
StatePublished - Mar 2007
Externally publishedYes

ASJC Scopus subject areas

  • Immunology
  • Virology
  • Infectious Diseases


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