Primary and secondary mutations in the RT and protease gene in HIV-1 infected patients predict failing to specific antiretroviral combination therapy

To identify agents with reduced effectiveness, due to primary and secondary mutations in the reverse transcriptase (RT) and protease (PR) genes, detected by sequencing, to specific antiretroviral compounds of the current antiretroviral therapy (ART). Plasma samples from 117 patients with viral rebound were included. Genotyping by sequencing (VGI TruGene HIV-1 Assay) was performed successfully on all patient samples. Twenty-one distinct primary mutations (14 in RT, seven in PR) and 27 secondary mutations (15 and 12 respectively) were analyzed. VL, CD4 cells, medical/treatment history at the time of viral rebound were also assessed. The majority of patients included in the analysis was heavily pretreated (> 2 failing regimens) at the date of presentation. Patients were either on triple ART (n = 80), quadruple ART (n = 21) or double ART (n = 16) at the time of virological failure. The mean VL at that time was 4.43 log sub(10) and the mean CD4 count 295/ mu l. For 3TC (M184V), nevirapine (K103N, Y181C) efavirenz (K103N), indinavir (M46I/L, V82#), ritonavir (M46I/L, V82#) and nelfinavir (N88#, D30N, L90M) a statistical significant correlation (P < 0.05) between the presence of primary mutations and failing of current treatment was found. However, there was a weak correlation for primary mutations specific for AZT (T215Y, K70R), abacavir (L74V, M184) and saquinavir (G48V, L90M). For ddC, d4T and ddI no specific primary mutation pattern was associated with failure. Different factors (i.e. resistance, suboptimal drug-levels) may contribute to virological ART failure. We demonstrated that genotyping helps identifying failing drugs of a current ART but the significance of the testing differs highly with regard to the agents. For a number of drugs we found a significant correlation between failure and presence of mutations. AZT and saquinavir specific primary mutations were detected even though the compounds were not part of the regimen, suggesting that these mutations exist for longer periods without a specific selective pressure.