Genetic and functional diversity of human immunodeficiency virus type 1 subtype B Nef primary isolates

We have characterized the functional integrity of seven primary Nef isolate s: five from a long term nonprogressing human immunodeficiency virus (HIV)- infected individual and one each from two patients with AIDS. One of the se ven Nefs was defective for CD4 downregulation, two others were defective fo r PAK-2 activation, and one Nef was defective for PAK-2 activation and majo r histocompatibility complex (MHC) class I down regulation. Five of the Nef s were tested and found to be functional for the enhancement of virus parti cle infectivity. The structural basis for each of the functional defects ha s been analyzed by constructing a consensus nef, followed by mutational ana lysis of the variant amino acid residues. Mutations A29V and F193I were del eterious to CD4 downregulation and PAK-2 activation, respectively, while S1 89R rendered Nef defective for both MHC class I downregulation and PAK-2 ac tivation. A search of the literature identified HIVs from five patients wit h Nefs predominantly mutated at F193 and from one patient with Nefs predomi nantly mutated at A29. A29 is highly conserved in all HIV subtypes except f or subtype E. F193 is conserved in subtype B (and possibly in the closely r elated subtype D), but none of the other HIV group M subtypes. Our results suggest that functional distinctions may exist between HIV subtypes.