Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study

Abstract

Background: CASTLE compared the efficacy of atazanavir/ritonavir with lopinavir/ritonavir, each in combination with tenofovir-emtricitabine in ARV-naïve subjects from 5 continents.

Objectives: Determine the baseline rate and clinical significance of TDR mutations using ultra-deep sequencing (UDS) in ARV-naïve subjects in CASTLE.

Methods: A case control study was performed on baseline samples for all 53 subjects with virologic failures (VF) at Week 48 and 95 subjects with virologic successes (VS) randomly selected and matched by CD4 count and viral load. UDS was performed using 454 Life Sciences/Roche technology.

Results: Of 148 samples, 141 had successful UDS (86 subtype B, 55 non-B subtypes). Overall, 30.5% of subjects had a TDR mutation at baseline; 15.6% only had TDR(s) at <20% of the viral population. There was no difference in the rate of TDRs by B (30.2%) or non-B subtypes (30.9%). VF (51) and VS (90) had similar rates of any TDRs (25.5% vs. 33.3%), NNRTI TDRs (11.1% vs.11.8%) and NRTI TDRs (24.4% vs. 25.5%). Of 9 (6.4%) subjects with M184V/I (7 at <20% levels), 6 experienced VF. 16 (11.3%) subjects had multiple TAMs, and 7 experienced VF. 3 (2.1%) subjects had both multiple TAMs+M184V, and all experienced VF. Of 14 (9.9%) subjects with PI TDRs (11 at <20% levels): only 1 experienced virologic failure. The majority of PI TDRs were found in isolation (e.g. 46I) at <20% levels, and had low resistance algorithm scores.

Conclusion: Among a representative sample of ARV-naïve subjects in CASTLE, TDR mutations were common (30.5%); B and non-B subtypes had similar rates of TDRs. Subjects with multiple PI TDRs were infrequent. Overall, TDRs did not affect virologic response for subjects on a boosted PI by week 48; however, a small subset of subjects with extensive NRTI backbone TDR patterns experienced virologic failure.

Figure 1. Results of Ultra Deep Sequencing Analysis.

148 samples recovered and sent for UDS: Subtype B (n = 90), Non-B (n = 58); 53 were VF and 95 were VS. 141 samples had UDS data: Subtype B (n = 86), Non-B (n = 55) 51 VF and 90 VS. Of the 7 samples without UDS data, 2 had partial UDS data and were not included; 3 samples were exhausted; and 2 had low viral loads and unable to amplify. VF: Virologic Failure, VS: Virologic Success.

Figure 2. Transmitted Drug Resistance by ARV Class and Virologic Outcome.

Transmitted Drug Resistance by ARV Class and Virologic Outcome: Note: TDRs are not mutually exclusive (i.e. a subject could have a TDR from more than one ARV class). VS: Virologic Success, VF: Virologic Failure N(t)RTI(s)- nucleoside(tide) reverse transcriptase inhibitor; NNRTI – non-nucleoside reverse transcriptase inhibitor, PI – protease inhibitor. Any: Any transmitted drug resistance mutations. Any TDR: p-value = 0.35, NRTI: p-value = 1, NNRTI: p-value = 1, PI: p-value = 0.02.