Virologic failures on initial boosted-PI regimen infrequently possess low-level variants with major PI resistance mutations by ultra-deep sequencing

Abstract

Background: It is unknown whether HIV-positive patients experiencing virologic failure (VF) on boosted-PI (PI/r) regimens without drug resistant mutations (DRM) by standard genotyping harbor low-level PI resistant variants. CASTLE compared the efficacy of atazanavir/ritonavir (ATV/r) with lopinavir/ritonavir (LPV/r), each in combination with TVD in ARV-naïve subjects.

Objective: To determine if VF on an initial PI/r-based regimen possess low-level resistant variants that may affect a subsequent PI-containing regimen.

Methods/results: Patients experiencing VF on a Tenofovir/Emtricitabine+PI/r regimen were evaluated by ultra deep sequencing (UDS) for mutations classified/weighted by Stanford HIVdb. Samples were evaluated for variants to 0.4% levels. 36 VF subjects were evaluated by UDS; 24 had UDS for PI and RT DRMs. Of these 24, 19 (79.2%) had any DRM by UDS. The most common UDS-detected DRM were NRTI in 18 subjects: M184V/I (11), TAMs(7) & K65R(4); PI DRMs were detected in 9 subjects: M46I/V(5), F53L(2), I50V(1), D30N(1), and N88S(1). The remaining 12 subjects, all with VLs<10,000, had protease gene UDS, and 4 had low-level PI DRMs: F53L(2), L76V(1), I54S(1), G73S(1). Overall, 3/36(8.3%) subjects had DRMs identified with Stanford-HIVdb weights >12 for ATV or LPV: N88S (at 0.43% level-mutational load 1,828) in 1 subject on ATV; I50V (0.44%-mutational load 110) and L76V (0.52%-mutational load 20) in 1 subject each, both on LPV. All VF samples remained phenotypically susceptible to the treatment PI/r.

Conclusion: Among persons experiencing VF without PI DRMs with standard genotyping on an initial PI/r regimen, low-level variants possessing major PI DRMs were present in a minority of cases, occurred in isolation, and did not result in phenotypic resistance. NRTI DRMs were detected in a high proportion of subjects. These data suggest that PIs may remain effective in subjects experiencing VF on a PI/r-based regimen when PI DRMs are not detected by standard or UDS genotyping.

Figure 1. Description and UDS results for virologic failure samples.

a: Virologic failure samples for UDS. UDS: Ultra Deep Sequencing; VF: Virologic Failure. 78 subjects had virologic failure at week 48 and/or 96. *21 samples were either exhausted or could not be located. 57 patients with virologic failure without PI resistance had samples for UDS. 21 patients failed with HIV RNA<1,000 copies and UDS could not be performed. 36 unique patients had UDS data. b: UDS results for 36 Virologic Failures. VF: Virologic Failure; PR: Protease; RT: Reverse Transcriptase. UDS: Ultra Deep Sequencing; DRMs: Drug Resistance Mutations. 36 patients without PI resistance mutations at VF by standard genotype were evaluated by UDS. 36 patients with VF had PR evaluated by UDS. 24/36 samples had HIV VL>10,000 c/ml. 9/24 had PI DRMs at low levels. 12/36 samples had HIV VL<10,000 c/ml. 4/12 had PI DRMs at low levels. Only 3/36 patients with VF had PI mutations with HIVdb weight >12 for ATV or LPV. 24/36 patients with HIV VL>10,000 c/ml had RT evaluated by UDS. 18/24 samples had NRTI DRMs.