Characterization of the South African HIV type 1 subtype C complete 5′ long terminal repeat, nef, and regulatory genes
Human immunodeficiency virus type 1 (HIV-1) subtype C has become the major etiological agent in the global and especially African epidemic. To gain better understanding of the genetic diversity and rapid transmission of HIV-1 subtype C, we have characterized the complete 5′ long terminal repeat (LTR) region along with the regulatory genestat andrev as well as the accessory genenef of 14 South African HIV-1 subtype C isolates. Phylogenetic analysis revealed a subtype C 5′ LTR cluster, as well as subclustering of ournef sequences with various subtype C strains separate from the India and China subclusters. At least 3 NF-κB sites were present in the 5′ LTR of most isolates and 13 isolates had the subtype C-specific Rev truncation. Some length variation in exon 2 and the absence of a critical cysteine were found in Tat. Residue variation in the myris-toylation signal and motifs involved in CD4 and MHC-I downregulation was recorded in our nef gene sequences.