Low-level resistance and minority populations: cross resistance between nevirapine and efavirenz occurs even in the absence of genotypic mutations found using population sequencing

Commercially available resistance assays are unable to detect minority virus that is present at less than 10-20% of an individual’s viral population and this is recognised as one of their limitations. It may also explain why randomised trails for these tests are difficult to design to show the additional benefit that they undoubtedly offer.

Mellors and colleagues looked at the role of minor NNTRI mutations from the ACTG 398 study. This study randomised 212 NNRTI-naïve and 269 NNRTI-experienced patients to efavirenz, abacavir, adefovir and amprenavir plus either a second PI or placebo. Not surprisingly, failure to achieve viral suppression (<200 copies/ml) was associated with previous NNRTI experience and NNRTI mutations at baseline. However, genotyping did not detect NNRTI mutations in 50/216 baseline samples in the NNRTI experienced patients (23%), but this group performed no better than those that had shown NNRTI resistance, and much worse that the NNRTI-naïve group who similarly showed no mutations.

Minor resistant variants were sought using single genome PCR and sequencing in a subgroup of patients who were failing treatment without evidence of resistance, and variants encoding NNRTI resistance were identified by single genome sequencing in 6/10 NNRTI-experienced and in 1/8 NNRTI-naive patients. A second assay used to measure the frequency of efavirenz resistance (yeast-based chimeric Ty1/HIV-RT assay) detected efavirenz resistance in 8/10 (range of frequencies 10.9% – 0.8%) and 2/8 (0.6% and 0.3%).

The study concluded that prior NNRTI experience had selected for mutations but at a level that was too low to be detected by standard genotyping, and that this lead to failure of the efavirenz-based regimens.

Lecossier and colleagues from the Hopital Bichat-Claude Bernard in Paris looked more closely at the resistance samples from 16 patients failing a nevirapine-based combination that showed Y181C indicating nevirapine resistance but not K103N (which determines efavirenz cross-resistance).

Sequence selective real-time PCR was used and each sample was screened for either of the codon change for 103N, which were detected >1% viral population in 5/16 patients (range 1%-76%).

References are to the XII International HIV Drug Resistance Workshop, Los Cabos, Mexico, 10-14 June 2003; published as part of Antiviral Therapy Volume 8 Issue 3.