PREDOMINANCE OF DEFECTIVE PROVIRAL SEQUENCES IN AN HIV PLUS LONG-TERMNONPROGRESSOR

We examined the accessory genes and envelope V3 region of provirus obt ained over a 5 year period from an HIV+ long-term non-progressor with very low viral load and no in vitro recoverable virus during that same time span. LTR sequences supported normal Tat-mediated promoter activ ity. Multiple clones of nef sequences were highly conserved with < 10% containing frame shift or stop codon mutations. Functional analysis o f the predominant nef sequence indicated wild type downregulation of s urface CD4 and good function in a complementation infectivity assay. B y contrast, inactivating mutations were found in 64% of amplicons cont aining vif, vpi, vpu, tat1, and rev1, and in 41% of amplicons containi ng env V3. Identical inactive sequences were obtained at an interval o f 2 years, suggesting persistence of quiescent defective provirus in a long-lived clonal cell population. Furthermore, generic distance vers us time analysis revealed an absence of progressive evolution or arbor ization of quasispecies over time. This contrasts with data generated from other asymptomatic HIV+ individuals. The non-progressive pattern of ena sequence diversity and low R(2) for genetic divergence over tim e suggests that the defective provirus circulating in the periphery of this patient represents a randomly sampled 'fossil record' of earlier replication competent HIV-1 genomes.