The role of the HIV-1 protease substrate in therapy resistance

In Switzerland and Germany up to a half of the first-line regimens include protease inhibitors (PIs) [1, 2]. Although in the Swiss HIV Cohort Study (SHCS) most patients under antiretroviral therapy (ART) have suppressed viral loads [3], every third patient is or has been affected by drug resistances [4] which are one of major causes for therapy failure.
HIV resistance against PIs is typically characterized by the accumulation of structural alterations in the viral protease (PR). However, a number of cases of clinical therapy failure under PI-containing regimes have been reported, where genotypic resistance testing did not reveal sufficient explanation from information on the PR and regimen compliance [5, 6]. And certain alterations in the natural substrate of the PR, Gag polyprotein, have been associated with the development of PI resistance [7-13]. Nevertheless, until today most algorithms evaluating PI resistances take solely the protease gene itself into account.
In the SHCS protease inhibitor use and successful treatment are monitored regularly for all patients and every newly enrolled patient receives a genotypic resistance test. We used in vivo cross-sectional sequence data from SHCS patients to scrutinize PI resistance mutational pathways across Gag and PR. Roles of certain mutations as well as of their interactions were investigated.
Here we demonstrate that roughly every fifth of the SHCS patients carries resistance mutations in Gag. And since Gag is not considered by the current genotyping systems the overall level of PI resistance for these patients is underestimated. We report novel Gag mutations of potential clinical relevance and provide additional details on known resistance mutational patterns. Additionally our data support a new potential role of p6 alterations in PI resistance mediated by its phosphorylation. Taken together, our results suggest the relevance of Gag sequence information for the routine genotyping of PI-treated patients of the SHCS.