Persistence of frequently transmitted drug-resistant HIV-1 variants can be explained by high viral replication capacity

Abstract

Background: In approximately 10% of newly diagnosed individuals in Europe, HIV-1 variants harboring transmitted drug resistance mutations (TDRM) are detected. For some TDRM it has been shown that they revert to wild type while other mutations persist in the absence of therapy. To understand the mechanisms explaining persistence we investigated the in vivo evolution of frequently transmitted HIV-1 variants and their impact on in vitro replicative capacity.

Results: We selected 31 individuals infected with HIV-1 harboring frequently observed TDRM such as M41L or K103N in reverse transcriptase (RT) or M46L in protease. In all these samples, polymorphisms at non-TDRM positions were present at baseline (median protease: 5, RT: 6). Extensive analysis of viral evolution of protease and RT demonstrated that the majority of TDRM (51/55) persisted for at least a year and even up to eight years in the plasma. During follow-up only limited selection of additional polymorphisms was observed (median: 1).To investigate the impact of frequently observed TDRM on the replication capacity, mutant viruses were constructed with the most frequently encountered TDRM as site-directed mutants in the genetic background of the lab strain HXB2. In addition, viruses containing patient-derived protease or RT harboring similar TDRM were made. The replicative capacity of all viral variants was determined by infecting peripheral blood mononuclear cells and subsequently monitoring virus replication. The majority of site-directed mutations (M46I/M46L in protease and M41L, M41L + T215Y and K103N in RT) decreased viral replicative capacity; only protease mutation L90M did not hamper viral replication. Interestingly, most patient-derived viruses had a higher in vitro replicative capacity than the corresponding site-directed mutant viruses.

Conclusions: We demonstrate limited in vivo evolution of protease and RT harbouring frequently observed TDRM in the plasma. This is in line with the high in vitro replication capacity of patient-derived viruses harbouring TDRM compared to site-directed mutant viruses harbouring TDRM. As site-directed mutant viruses have a lower replication capacity than the patient-derived viruses with similar mutational patterns, we propose that (baseline) polymorphisms function as compensatory mutations improving viral replication capacity.

Figure 1

Impact of frequently observed transmitted drug-resistance mutations on viral replicative capacity. The replicative capacity of site-directed mutant (SDM) viruses and patient-derived viruses was determined by infecting donor peripheral blood mononuclear cells with equal amounts of viral p24. In all experiments, control viruses HIV-M184V, −M184I and –M184T and wild type (WT) HIV were used as reference viruses. Representative experiments are shown in A-C and D-F. Error bars indicate standard deviation (SD) of mean within one experiment. Four biological replicates were performed for all viruses. (A-C) Replicative capacity of SDM-viruses (B, C) compared to control viruses (A). (D-F) Replicative capacity of patient-derived viruses (E, F) compared to control viruses (D). RC of WT and control viruses (A, D) is indicated in the corresponding graphs by a square, and the range in RC of WT and M184T by the grey area. (G) The median p24 production of both experiments as a percentage of WT in the corresponding experiment for all protease or reverse transcriptase mutant viruses. Error bars indicate range (n = 4).