Drug resistance and integrase inhibitors: potential impact of HIV subtype
Simon Collins, HIV i-Base
Although dolutegravir and cabotegravir have been notable for the lack of integrase resistance that in integrase-naive patients, several case studies were presented at the workshop about resistance in this class.
Cabotegravir and rilpivirine in the LATTE study
The two drug oral combination of cabotegravir and rilpivirine in a Phase 2b Latte study, designed as a prestudy for later use of long acting injectable formulations of each drug, reported a case of dual integrase and NNRTI resistance. 
At week 48 in this dose finding study, 4/243 people had virologic failure (one in each of the 10 mg and 30 mg cabotegravir arms and two in the efavirenz control arm). Treatment-emergent resistance (INI Q148R and NNRTI E138Q) was detected in a single patient in the 10 mg cabotegravir group who had had persistently low drug levels of both drugs (<50% mean C tough). Viral load had been undetectable from week 2 to 40 but rebounded to 18,000 copies/mL at week 48.
The Q148R integrase mutation resulted in a 3.08 fold-change in sensitivity to cabotegravir and 30.0 fold change to raltegravir with impact on replicative capacity of 8.1%. The E138Q mutation resulted in a 1.83 fold change in sensitivity to rilpivirine and changed replicative capacity by 44%.
Raltegravir resistance very common with virological failure in the NEAT001 study
The NEAT001 study was an open label, Phase 3, treatment-naive (n=805) study of darunavir/ritonavir with either raltegravir in a nuke-sparing combination or with tenofovir/FTC as standard ART.  In the primary virological endpoint at 96 weeks presented at CROI 2014, the raltegravir arm was non-inferior but this dual combination was less effective in people with high baseline viral load. 
An analysis of the resistance test results presented at the workshop reported high levels of genotypic resistance in the raltegravir arm, with 1 in 4 samples at failure showing integrase mutations. In contrast, no mutations were reported from the tenofovir/FTC arm.
Resistance test results were available for 110/127 patients with virologic failure (defined as confirmed viral load >50 copies/mL or any single viral laod >500 copies/mL at or after week 32). This was for 61/69 patients in the raltegravir arm and 49/58 patients in the tenofovir/FTC arm although not all tests were successful.
Of the 14/55 amplified raltegravir group samples with integrase resistance, 12 had N155H alone, 1 had N155H + Q148R and 1 had Y143C. Although these were naive patients without exposure to NRTIs or PIs, 3/53 had NRTI mutations (M184I, K65R, M41L), and 1/57 had a primary protease mutation (L76V).
The frequency of integrase mutations was associated with higher baseline viral load: 7.1% when <100, 000 copies/mL, 21.4% when 100,000-500,000 copies/mL, and 53.8% when >500,000 copies/mL, p=0.006 for the trend). However, viral load at failure was not significantly different in those patients who failed with vs without INI mutations: median 615 copies/mL (IQR: 192 – 14864) vs. 361 copies/ mL (IQR: 137 – 990) respectively, p=0.27. Of note, integrase mutations were detected in four patients with viral load between 50 and 200 copies/mL.
All sequenced viruses at virologic failure remained susceptible to dolutegravir.
Impact of E157Q on dolutegravir
A case study reported a new raltegravir associated mutation that conferred cross resistance to dolutegravir. 
This was in a patient who after five months on initial raltegravir/abacavir/3TC treatment still had viral load at 3.9 log copies/mL. This combination was chosen to minimise drug interactions to immunosuppressant drugs related to a recent kidney transplant.
Raltegravir was switched to dolutegravir 50 mg twice-daily which had no impact on viral load. Retrospective resistance testing showed that the E157Q mutation present at the time of the switch was preexisting at baseline. Phenotypic testing confirmed high level resistance to dolutegravir (with an inhibitory quotient of 37.9). The patient achieved viral suppression with a second switch of dolutegravir to darunavir/ritonavir.
Subtype B may have higher vulnerability to integrase resistance
Raltegravir and elvitegravir both have a lower genetic barrier to HIV drug resistance and mutations rapidly accumulate in the context of suboptimal viral suppresion. This significantly reduces sensitivity to both dolutegravir and cabotegravir. Limited information is available on the role of HIV subtype and susceptibility to integrase resistance as clinical studies were predominantly in patients with subtype B.
A UK study suggested that vulnerability to resistance might be higher in patients with subtype B compared to non-B subtypes, and this finding might be clinically important in resource-limited settings. The group analysed sequences from 255 people who were raltegravir-experienced, 209/255 of which (82%) were subtype B. Non-B subtypes were predominantly subtype C and CRF02 but included nine other variants including A, D, F, G, CRF01, CRF06, and CRF09. 
Overall 113/255 (44%) patients had one or more major integrase mutation: N155H (n=57, 22%), G140S (n=33, 13%), Q148H (n=28, 11%), and Q148R (n=15, 6%). A total of 36/44 (82%) patients with Q148H/R/K also had the G140A/C/S compensatory mutation that restores the fitness of mutations at position 148.
Mutations at both codons 148 and 140 were both significantly more prevalent in subtype B compared to non-B sequences, which resulted in higher predicted cross resistance to dolutegravir, see Table 1. These differences were not explained by slightly higher viral load in subtype B (approximately 3,500 copies/ml (IQR: 1,470-25,700) vs. 1,800 (IQR: 550-11,660), respectively (p=0.33).
Table 1: Prevalence of major integrase mutations in raltegravir-experienced patients
|Q148H/R/K||42/209 (20%)||2/46 (4%, subtypes C and G)||0.009|
|G140A/C/S||36/209 (17%)||1/46 (2%, subtype G)||0.005|
|predicted cross-Rx to dolutegravir||42 (20%)||2 (4%) in B vs. non-B||0.009|
A second analysis of 533 sequences from samples from raltegravir-naive patients (subtype B 399/533, 75%) found no major integrase mutations. Analysis of sequences showed that emergence of G140S required a single nucleotide substitution in subtype B but all non-B sequences analysed required two substitutions.
The significantly lower rates on resistance in non-B subtypes further emphasises the potential role for use in resource-limited settings were other subtypes are more dominant.
Unless stated otherwise, references are to the Programme and Abstracts of the XXIV International HIV Drug Resistance Workshop, 21-22 February 2015, Seattle, Washington.
- Duda K et al. Characterization of NNRTI and INI resistance mutations observed in a study subject on oral two-drug maintenance therapy with 10 mg cabotegravir + 25 mg rilpivirine. Poster abstract 13.
- Lambert-Niclot S et al. Analyses of emergent drug resistance from the NEAT 001/ ANRS 143 trial: raltegravir + darunavir/ritonavir vs. tenofovir/ emtricitabine + darunavir/ ritonavir. Abstract 21.
- Raffi F et al. First-line raltegravir (RAL) + darunavir/ritonavir (DRV/r) is non-inferior to tenofovir/emtricitabine (TDF/FTC) + DRV/r: the NEAT 001/ANRS 143 randomised trial. 21st CROI, 3–6 March 2014, Boston. Late breaker oral abstract 84 LB.
- Danion F et al. Non virological response to a dolutegravir-containing regimen in a patient harboring a E157Q- mutated virus in the integrase iegion. Abstract 43.
- Geretti AM et al. HIV-1 Subtype influences the pathways of genotypic resistance to integrase inhibitors. Abstract 75.