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Background HIV-1 DNA is found both integrated in the host chromosome and unintegrated in various forms: linear (DNAL) or circular (1-LTRc, 2-LTRc or products of auto-integration). Here, based on pre-established strategies, we extended and characterized in terms of sensitivity two methodologies for quantifying 1-LTRc and DNAL, respectively, the latter being able to discriminate between unprocessed or 3′-processed DNA. Results Quantifying different types of viral DNA genome individually provides new information about the dynamics of all viral DNA forms and their interplay. For DNAL, we found that the 3′-processing reaction was efficient during the early stage of the replication cycle. Moreover, strand-transfer inhibitors (Dolutegravir, Elvitegravir, Raltegravir) affected 3′-processing differently. The comparisons of 2-LTRc accumulation mediated by either strand-transfer inhibitors or catalytic mutation of integrase indicate that 3′-processing efficiency did not influence the total 2-LTRc accumulation although the nature of the LTR-LTR junction was qualitatively affected. Finally, a significant proportion of 1-LTRc was generated concomitantly with reverse transcription, although most of the 1-LTRc were produced in the nucleus. Conclusions We describe the fate of viral DNA forms during HIV-1 infection. Our study reveals the interplay between various forms of the viral DNA genome, the distribution of which can be affected by mutations and by inhibitors of HIV-1 viral proteins. In the latter case, the quantification of 3′-processed DNA in infected cells can be informative about the mechanisms of future integrase inhibitors directly in the cell context.

Raltegravir (MK-0518) is clinically used against viruses resistant to other antiretroviral compounds. However, it has been reported that Raltegravir induces integrase (IN) resistance very soon after the administration of the drug. Some residues in the protein seem to be preferentially targeted: E92Q, N155H, and the double mutant G140S/Q148H. It was demonstrated that most of these mutations altered both 3'-processing and strand transfer activities of IN. In this report, we addressed for the first time by real time PCR the kinetics of the integrase mutants as well their resistance towards Raltegravir. Furthermore, we characterised the activities of the recombinant proteins. Our data highly suggest that the resistance towards Raltegravir is due to the mutation Q148H. This mutation results in a slower replication kinetic which is compensate by the G140S mutation. These data explain why only the double mutant G140S/Q148H is observed in clinical trials as one of the most prevalent profile of raltegravir resistance. Two patients receiving raltegravir as part as their regimen were followed. After a viral load decrease, these patients harbored virological failure and selection of raltegravir resistance mutations in the integrase gene (N155H for patient 1 and G140S + Q148H for patient 2). At failure, patients harbouring viruses with these raltegravir mutations showed HIV viral load rebound corresponding to baseline values.

Retroviral integration is central to viral persistence and pathogenesis, cancer as well as host genome evolution. However, it is unclear why integration appears essential for retrovirus production, especially given the abundance and transcriptional potential of non-integrated viral genomes. The involvement of retroviral endonuclease, also called integrase (IN), in replication steps apart from integration has been proposed, but is usually considered to be accessory. We observe here that integration of a retrovirus from the spumavirus family depends mainly on the quantity of viral DNA produced. Moreover, we found that IN directly participates to linear DNA production from 2-LTR circles by specifically cleaving the conserved palindromic sequence found at LTR-LTR junctions. These results challenge the prevailing view that integrase essential function is to catalyze retroviral DNA integration. Integrase activity upstream of this step, by controlling linear DNA production, is sufficient to explain the absolute requirement for this enzyme. The novel role of IN over 2-LTR circle junctions accounts for the pleiotropic effects observed in cells infected with IN mutants. It may explain why 1) 2-LTR circles accumulate in vivo in mutants carrying a defective IN while their linear and integrated DNA pools decrease; 2) why both LTRs are processed in a concerted manner. It also resolves the original puzzle concerning the integration of spumaretroviruses. More generally, it suggests to reassess 2-LTR circles as functional intermediates in the retrovirus cycle and to reconsider the idea that formation of the integrated provirus is an essential step of retrovirus production.