Baseline characteristics prior to integrase inhibitor therapy
A total of 79 subjects enrolled in the SCOPE cohort initiated an integrase inhibitor based regimen (73 raltegravir and 6 elvitegravir). Integrase genotypic and phenotypic resistance testing was performed prior to integrase inhibitor therapy in 45/79 subjects; the median fold-change in IC50
to raltegravir was 0.89. The median replicative capacity was 114%. Four of 45 subjects had a secondary integrase inhibitor associated mutation at baseline (1 subject with E138K, 3 subjects with V151I) 10
; there were no primary integrase mutations.
Integrase inhibitor resistance at first virologic failure
Among the 79 subjects who initiated an integrase inhibitor based regimen, 50 had evidence of durable viral suppression. The remaining 29 subjects (23 raltegravir, 6 elvitegravir) failed to achieve and maintain an undetectable viral load and were included in the failure analyses. Prior to initiating an integrase inhibitor based regimen, the median baseline CD4+ T cell count and plasma HIV RNA level was 62 cells/mm3 and 4.65 log10 copies/mL, respectively (). The cohort was highly treatment-experienced and was followed for a median 15.8 months. The median CD4+ T cell count and plasma HIV RNA level at the time of first virologic failure was 118 cells/mm3 and 4.44 log10 copies RNA/mL, respectively. Subjects had been on an integrase inhibitor for a median 4.9 months at the time of first virologic failure.
Baseline Characteristics, Integrase Inhibitor Failure Cohort (n=29)
Nineteen of the 23 subjects who exhibited incomplete viral suppression on a raltegravir-based regimen had at least one genotypic/phenotypic resistance tested performed after a median 4.1 months of therapy. At the first failure time-point, the most common integrase genotype was wild-type (no known primary mutations, n=13), followed in order of frequency by Q148H/K/R (n=3), N155H (n=3), and Y143R/H/C (n=1) (notably, one subject had a mixture of resistant virus subpopulations that contained mutations at either codon 148 or 155). The G140S was present in four subjects, typically in association with Q148H/K/R. The E92Q mutation was observed in one raltegravir failure, which also contained mixtures of resistant virus at codons 148, 155, and 140. The median viral load in subjects failing with wild-type versus resistant integrase was 3.86 and 4.28 log10 copies/mL, respectively (p=0.177).
We also identified six subjects who were participants in a phase II study of elvitegravir. The most common integrase resistance mutation at the first failure time-point was E92Q (3/5 subjects with available genotypes, while the remaining 2 subjects had wild-type virus). The E92Q mutation was associated with low-level phenotypic resistance to raltegravir.
Absence of integrase inhibitor resistance in “blippers”
Six of 50 subjects who had viral suppression on a raltegravir-based regimen had episodes of detectable viremia < 1000 copies/mL during otherwise effective therapy (median 177 copies/mL, IQR 71–300). Virus was successfully amplified from at least one time-point for 5/6 of these subjects and found to have no genotypic or phenotypic evidence of resistance to raltegravir.
Evolution of integrase inhibitor resistance over time
The genotypic and phenotypic level of integrase resistance increased gradually over time among subjects who remained on an integrase inhibitor-based regimen despite persistent viremia. The proportion of viruses lacking primary or secondary integrase resistance mutations declined at each subsequent time-point, while the proportion of viruses with more than one integrase mutation increased (). Similar changes were observed in the evolution of phenotypic resistance (). Moreover, the level of phenotypic resistance to raltegravir in subjects failing with either the Q148H/K/R or Y143R/H/C mutations was consistently high (> 100 fold-change in IC50), whereas the level of phenotypic resistance to raltegravir was much lower in those failing with the N155H mutation (< 50 fold-change in IC50).
Figure 1 Incomplete viral suppression on an integrase inhibitor based regimen is associated with continued viral evolution, as defined by the number of primary and secondary integrase mutations present at each consecutive visit (Panel A) and by the level of phenotypic (more ...)
Role of adherence in predicting resistance during failure
We next assessed the relationship between adherence and the risk of virologic failure and integrase inhibitor resistance. The cohort was divided into three groups: subjects who had durable virologic success (including those with episodes of detectable viremia < 1000 copies/mL during otherwise effective therapy), subjects who exhibited virologic failure with at least one primary integrase inhibitor associated mutation, and subjects who failed without any integrase inhibitor mutations. The average self-reported level of adherence in the previous 30 days to all antiretroviral drug doses was 97.8% in subjects who had durable virologic success, 98.7% in subjects who failed with integrase inhibitor resistance, and 90.7% in subjects who failed with wild-type virus (Wilcoxon rank-sum test: p=0.004 for wild-type failure vs. success, p=0.007 for wild-type failure vs. resistance failure). The findings were similar when the analyses were limited to adherence to integrase inhibitor doses (data not shown).
There were no obvious differences in the replicative capacity of viruses containing the Y143R/H/C, Q148H/K/R, or N155H mutations (data not shown), although the number of subjects in each group was limited. Among the subjects who developed clear evidence of integrase inhibitor resistance (n=11, ), there appeared to be a decline in integrase replicative capacity over time (). In contrast, there was no consistent change in replicative capacity among those who failed without evidence of integrase inhibitor resistance (data not shown). Moreover, for the 10 subjects who developed phenotypic/genotypic evidence of integrase inhibitor resistance and had pre-/post-failure samples available, the median decrease in replicative capacity between the pre-integrase inhibitor baseline and the last failure time-point was 45% (p= 0.0002; ).
Figure 2 Evolution of integrase replicative capacity. Among subjects failing with integrase inhibitor resistance, there was a decrease in replicative capacity between pre-therapy baseline and the last failure time-point on drug (n=10, Panel A). Long-term virologic (more ...)
Raltegravir treatment interruption and possible continued partial benefit
One individual harboring a virus with the N155H + V151I + D232N mutations (41-fold change in IC50) discontinued raltegravir while remaining on a stable background regimen. In contrast to most of the other subjects in the cohort, this individual never had evidence of advanced HIV disease (pre-integrase inhibitor CD4+ T cell count and plasma viral load of 331 cells/mm3 and 4.07 log10 copies/mL, respectively). After an initial virologic response to raltegravir, the subject’s viral load rebounded to a steady-state level of approximately 4 log10 copies/mL. Because of concerns of ongoing viral evolution and relatively preserved CD4+ T cell counts, raltegravir was interrupted in an attempt to preserve this class for future antiretroviral regimens. Interestingly, plasma HIV RNA levels remained relatively stable for one week in the absence of raltegravir, suggesting limited residual antiviral activity (). However, viral load subsequently increased by 10-fold as genotypic/phenotypic evidence for raltegravir resistance waned over the next month. In addition, replicative capacity increased as the raltegravir inhibitor mutations waned ().
Figure 3 Interruption of raltegravir. One individual harboring a virus with the N155H + V151I + D232N mutations (41-fold change in IC50) discontinued raltegravir while remaining on a stable background regimen. Shaded area indicates the period when raltegravir (more ...)