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Viral population in a long term non progressor carrying CRF02-AG HIV-1 virus variants with a truncated RT gene and attenuated virus replication was analyzed. The proportion of mutant and wild-type RT sequences was determined by clonal analysis of HIV-1 DNA and RNA from blood samples and peripheral blood mononuclear cell (PBMC) culture supernatants. Recombinant HIV-1 strains were generated by reverse genetics to evaluate the replicative capacity of RT variants in PBMC cultures. HIV-1 RNA and DNA sequences in PBMC cultures showed a mixture of stop codons (RT(STOP)), recombinant forms, (RT(RF)), and full length (RT(FL)) strains. In plasma, proportion of HIV-1 RNA sequences with a truncated RT gene fluctuated over time (0% in 2005, 100% in 2007 and 8.3% in 2010), while in proviral DNA was constant (96.5% to 100%). Reconstituted RT(STOP) strains were unable to replicate in PBMC. However, RT(FL) strains could trans-complement the loss of function of RT(STOP) variants. In vivo selection of stop codons in the RT gene resulted in the accumulation of replication-defective virus strains. Nevertheless, the observed release of defective viral particles in plasma was probably the result of viral protein complementation between replication-competent and replication-incompetent HIV-1 variants. The divergence in the proportion of RT(STOP) and RT(FL) variants as well as in the mutation's pattern to antiretroviral drug resistance between HIV-1 plasma RNA and PBMC proviral DNA, suggested that circulating lymphocytes expressing full-length RT might be negatively selected for by a specific T-cell response, possibly contributing to the slow progression to AIDS observed in this patient.

During replication, HIV-1 reverse transcriptase lacks proof reading activity and is error prone. In addition APOBEC-driven hypermutation of HIV-1 Gag and Pol genes may generate replication-deficient viral variants with in-frame stop codons. Virus variants with several stop codons in the RT gene were identified in a subject with residual HIV-1 replication during antiretroviral treatment. A role for the T-cell response in the selection of replication-deficient variants was hypothesized. Clonal analysis of HIV-1 DNA and RNA sequences from three sequential blood samples was performed. Moreover, the HIV-1-specific memory CD8(+) T-cell response was investigated using a peptide-based cultured ELISPOT assay. The accumulation of HIV-1 variants with stop codons in the Pol gene (from 0% to 100%) was observed in sequential plasma samples. The cultured ELISPOT showed a sustained response to a Pol region downstream from the last stop codon. A more detailed analysis of the Pol region encompassing the detected stop codons showed a strong response to a peptide at the end of the RT region containing stop codons (positions 206 to 220) and including the last stop codon (212). These results suggest a role for a peptide-specific immunologic response in the positive selection of cells expressing the truncated HIV-1 RT and the accumulation of replication-deficient viral variants in plasma. The antigen-specific CD8(+) T-cell response could be exploited to redirect the response to HIV-1 infection toward in vivo selection of viral variants with reduced or abolished pathogenicity.