Characterization of subtype A HIV-1 from Africa by full genome sequencing

Objective: To improve our understanding of the genetic complexity of HIV-1 subtype A by increasing the number of subtype A isolates that have been seq uenced in their entirety. Methods: Nine HIV-1-seropositive patients from Africa living in Sweden cont ributed peripheral blood mononuclear cells (PBMC) for this study. Sequencin g of the C2-V3 region of env had shown them to be subtype A. DNA from virus cultures was used for the amplification of virtually full-length proviral sequences, and the resulting fragment was sequenced. Results: Six of the nine viral isolates were subtype A throughout the genom e, or non-recombinant and all of these were from east Africa. One virus fro m the ivory Coast had the AG(IbNG) genetic form, a recombinant form common in west Africa. Two of the isolates were novel recombinants: one was an A/C recombinant and the other was A/D. Analysis of gag reveals three subcluste rs within the A subtype: one containing the AG(IbNC) subtype viruses, one c ontaining the AE(CM240) viruses and one containing the non-recombinant A vi ruses. These genetic clusters have different geographical distributions in Africa. Conclusion: The prevailing view of HIV-1 subtype A forming a uniform band a cross the center of sub-Saharan Africa needs revision. In all probability, the most common subtype in west Africa and west central Africa is the AG re combinant, AG(IbNC), whereas in east central Africa it is the non-recombina nt subtype A. (C) 1999 Lippincott Williams & Wilkins.