Lack of evidence for protease evolution in HIV-1-infected patients after 2 years of successful highly active antiretroviral therapy.

The mechanisms involved in maintaining a latent replication-competent integrated human immunodeficiency virus type 1 (HIV-1) reservoir after successful highly active antiretroviral therapy (HAART) have not been fully described. The objective of this study was to assess whether low-level, persistent HIV-1 replication can be detected in the protease gene, in 10 HIV-1-infected patients who have undergone 2 years of successful HAART. Peripheral blood mononuclear cells (PBMCs) were collected from 10 HIV-1-infected patients receiving a triple-drug combination therapy (2 nucleoside analogues and 1 protease inhibitor). HIV-1 RNA levels and CD4+ and CD8+ T cell counts were longitudinally determined during a follow-up period of 108 weeks. Similarly, proviral fragments of the protease-coding region, obtained at baseline and at week 108 of HAART, were amplified by polymerase chain reaction from PBMCs, and 10-25 individual clones were sequenced for each time point. Only 1 of 271 individual protease clones showed a major resistance substitution (M46I [patient D]). Phylogenetic analysis revealed that, in all patients, the genetic distances from the deduced most recent common ancestor, in samples obtained at week 108 of HAART, were not longer than those in samples obtained at baseline. Moreover, the pattern of amino acid divergence during therapy showed an absence of positive selection in the protease-coding region. Taken together, these results show a lack of clinically relevant evolution in the protease-coding region after 2 years of successful HAART.