Analysis of Low-Frequency Mutations Associated with Drug Resistance to Raltegravir before Antiretroviral Treatment

Abstract

Raltegravir is highly efficacious in the treatment of HIV-1 infection. The prevalence and impact on virologic outcome of low-frequency resistant mutations among HIV-1-infected patients not previously treated with raltegravir have not been fully established. Samples from HIV treatment-experienced patients entering a clinical trial of raltegravir treatment were analyzed using a parallel allele-specific sequencing (PASS) assay that assessed six primary and six secondary integrase mutations. Patients who achieved and sustained virologic suppression (success patients, n ‫؍‬ 36) and those who experienced virologic rebound (failure patients, n ‫؍‬ 35) were compared. Patients who experienced treatment failure had twice as many raltegravir-associated resistance mutations prior to initiating treatment as those who achieved sustained virologic success, but the difference was not statistically significant. The frequency of nearly all detected resistance mutations was less than 1% of viral population, and the frequencies of mutations between the success and failure groups were similar. Expansion of pre-existing mutations (one primary and five secondary) was observed in 16 treatment failure patients in whom minority resistant mutations were detected at baseline, suggesting that they might play a role in the development of drug resistance. Two or more mutations were found in 13 patients (18.3%), but multiple mutations were not present in any single viral genome by linkage analysis. Our study demonstrates that low-frequency primary RAL-resistant mutations were uncommon, while minority secondary RALresistant mutations were more frequently detected in patients naïve to raltegravir. Additional studies in larger populations are warranted to fully understand the clinical implications of these mutations.

Efficacy and safety of antiretroviral regimens including raltegravir to treat HIV-infected patients with hemophilia

“…Primary resistance mutations could be detected through use of a more sensitive method. Secondary and additional mutations are detected more frequently in baseline samples from therapy-naive and treatmentexperienced patients (12)(13)(14). The frequency of all detected mutations was < 1% of the viral population, but the frequency of variation was similar in patients that responded to raltegravir and patients that did not respond to raltegravir, suggesting that these lowfrequency resistance mutations do not significantly result in treatment failure.…”

Primary Infection by a Human Immunodeficiency Virus with Atypical Coreceptor Tropism

“…All env genes sequenced at three early time points after infection contained this motif, as did all but 2 of 1,390 genomes analyzed by PASS. lt is important to note that this frequency (0.15%) is well above the level of background in this assay (39); therefore, a variant capable of using CCR5 efficiently in vitro was present in the acutely infected patient but was overshadowed in vivo by a variant with poorer in vitro CCR5 use. Importantly, all V3 sequences obtained from three different PCR primer sets (whole env gene, partial env gene, and half viral genome) were identical, except two GPGK variants identified by PASS.…”

Evolution of Drug-Resistant Viral Populations during Interruption of Antiretroviral Therapy

“…By comparing each spot's normalized values at the two channels, the position was classified as WT or mutant. Finally, the linkage pattern of all mutations on each viral genome was determined by compiling mutation information at all analyzed sites with the Linksys program (22).…”