Analysis of transition from long-term nonprogressive to progressive infection identifies sequences that may attenuate HIV type 1

Long-term nonprogressive human immunodeficiency virus type 1 (HIV-1) infect ion and its transition to progressive infection presents an opportunity to identify the molecular determinants of HIV-1 attenuation and pathogenesis. We studied an individual who underwent a transition from long-term nonprogr essive to rapidly progressive infection. Because HIV-1 RNA genomes in plasm a represent replicating virus, we developed a technique to clone full-lengt h HIV-1 RNA genomes from plasma and used this technique to obtain clones fr om this individual before and during the transition. Most clones assayed we re infectious, demonstrating that the RNA genomes encoded viable virus. Ana lysis of 20 complete HIV-1 RNA genomic sequences revealed one major differe nce between sequences found during the two phases of infection. During the nonprogressive phase, the predominant sequences had a large deletion in an Sp1-binding site and adjacent promoter in the U3 part of the long terminal repeat (LTR); when the infection became progressive, all viruses had intact Sp1 and promoter sequences and were derived from a minor species present e arlier. Analysis of 184 clones of the LTR region obtained at five time poin ts spanning a 7-year period confirmed this switch. In an in vitro assay, th e deletion downregulated LTR-driven transcription of a reporter gene. In ad dition, analysis of cytotoxic T lymphocyte (CTL) epitopes predicted from th e complete viral RNA genomes revealed multiple potential escape mutants tha t accumulated by the time of progression. These studies suggest that during the nonprogressive phase, the Sp1 enhancer-promoter deletion is likely to have played a role in decreasing replication, thereby attenuating HIV-1. Th e accumulation of CTL escape mutants suggests that a breakdown in immunolog ic surveillance may have allowed proliferation of intact virus, thus leadin g to rapid disease progression. These data reveal the viral and immune inte ractions characterizing a transition from long-term nonprogressive to rapid ly progressive infection.