In vivo genetic variability of the HIV-1 vif gene

The human immunodeficiency virus type 1 (HIV-1) vif gene encodes a 23-kDa protein (viral infectivity factor) whose exact mechanism of action is not entirely clear. Vif is believed to be highly conserved among different HIV-1 strains. We have analyzed the proviral vif sequences of 61 peripheral blood mononuclear cell samples from HIV-1 positive patients by direct solid phase sequencing and temperature gradient gel electrophoresis of polymerase chain reaction products. Inter- and intraindividual sequence variations, conserved motifs, and prevalent vif subtypes were investigated. The consensus proviral vif DNA sequence of the 61 samples as well as the consensus sequence of the 61 deduced vif amino acid sequences were found to be less conserved than previously thought. The vif proviral sequences were 58% conserved, with the 5' end of the vif gene being the most conserved region (84%). Of the vif amino acids only 45% were absolutely conserved in the 61 samples, i.e., the absolutely conserved and as such possibly functionally important domains of the vif protein comprised less than half of the vif amino acids. In two-thirds of the variable positions residues belonging to different amino acid groups were found. In individual patients the prevalent vif sequence changed with the course of disease, but the differences found in two serial samples of a patient were < or = 10%. Phylogenetic analysis revealed that one African vif subtype had been introduced in the investigated population.