HIGH-RESOLUTION STRUCTURE OF AN HIV-1 QUASI-SPECIES - IDENTIFICATION OF NOVEL CODING SEQUENCES

Objective: To characterize an HIV-1 quasispecies in vivo at high resolution (1%) in order to determine its genetic structure. Methods: The first coding exon of tat was amplified by polymerase chain reaction from uncultured peripheral blood mononuclear cells of an HIV-1-infected patient. The products were cloned into M13mp18 RF, and 106 clones were sequenced. Results: Thirty-one different Tat protein variants were found. Amongst these, five major forms with frequencies of 44, 11, 8 and 5% were identified. All of the remaining 26 sequences were unique, 15 of which were defective. Within the variant spectrum a small number of genomes encoded novel open reading frames, for example, a tat-vpu fusion product. Conclusion: Some of the myriad proviruses present in an individual harbour novel coding sequences. While these are probably of little importance for AIDS pathogenesis they emphasize the ability of HIV to explore a huge range of genetic configurations.