Comparison of the population sequence- and model-predicted time-to-20% for HCV subtypes 1a (A) and 1b (B).

<p>The X-axis represents the inferred time-to-loss of detectable resistance by population sequencing and reflects the first visit wherein the patient did not have detectable resistant variants. The Y-axis relies on the algorithms defined here, wherein the rate of loss is modeled continuously for each patient. The majority of the data points fall to the right of the unity line, indicating that the model predicts more rapid times-to-20% than those estimated from population sequence data.</p

Population sequence-based and model-predicted median reversion times.

1<p>The 95% CI assumes a single value for each patient and does not incorporate uncertainity of individual predictions (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003772#pcbi.1003772.s005" target="_blank">Text S1</a>).</p

Model fit for patients with genotype 1b HCV.

<p>(A): Histogram of the log₁₀ objective function values (φ; see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003772#pcbi.1003772.e021" target="_blank">Equation 5</a>) for all patients with genotype 1b. Dashed lines and numbers show quantile information for the fits. Also shown are representative fits for patients whose objective function values fall in the (B) 70%, (C) 90%, (D) 95%, and (E) 100% quantiles. Solid lines represent the model predictions, solid points represent the clonal sequence data, and error bars show the range for population sequence results.</p

Kaplan-Meier curves for time-to-20% determined by population sequencing, model-predicted time-to-20%, and model-predicted time-to-1%.

<p>Results for patients with HCV subtypes 1a and 1b are shown in plots (A) and (B), respectively. Hash marks (∧) denote the censored observations indicating the time of the last visit for patients with virus that did not revert to <20% resistant. For clarity, these patients are explicitly denoted on the population sequence (“Pop. Seq.”) and model-predicted time-to-20% resistance curves only.</p

Hypothetical viral dynamics for a patient with viral breakthrough during telaprevir-based treatment.

<p>(A) Dynamics for the total viral load (Total, green), wild-type virus (WT, blue), and a telaprevir-resistant variant (Resistant, red) during and after treatment with telaprevir-based treatment. LOD is the limit of detection for the ‘total’ viral load quantification, and Seq. LOD is the limit of detection above which sequencing can be reliably performed (1000 IU/ml). The treatment phase is shown by the gray bar. (B) Corresponding percent resistance dynamics on a linear scale. Viral sequencing can be performed when the total viral load exceeds the sequencing assay LOD (solid red curve). The dashed lines at 20% and 5% show the limits of detection for population and clonal sequence data, respectively.</p

Treatment Outcome in Patients from Phase 3 Telaprevir Studies.

<p>Data from ADVANCE includes only the T12PR arm and data from REALIZE includes pooled TVR arms. ‘Other’ includes patients with missing SVR assessment and patients with HCV RNA>25 IU/mL at last study dose but who did not have viral breakthrough. ‘Relapse’ here is calculated using a denominator of total number of patients, and so differs from a relapse rate calculated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034372#pone-0034372-g008" target="_blank">Figure 8</a> which uses patients with undetectable HCV RNA at the end of treatment. ‘SVR’ rates here are calculated as in the INCIVEK USPI, which utilized the last recorded HCV RNA assessment; in case of missing data, the last HCV RNA assessment from week 12 of follow-up onward was used. For the determination of SVR and relapse rates, the lower limit of quantification (<25 IU/ml) of the HCV RNA assay was used. These rates differ from SVR rates calculated according to the study protocol, which used the HCV RNA assessment at week 24 without carrying forward the prior HCV RNA data point in case of missing data, and the limit of detection (10–15 IU/ml) of the HCV RNA assay for SVR and relapse rate determination. SVR rates using the protocol analysis were: 75% for T12PR, 69% for T8PR and 44% for PR (ADVANCE, Jacobson 2011); 72%, 92% and 88% were recorded for the overall study (all patients), T12PR24 and T12PR48 randomized arms, respectively (ILLUMINATE, Sherman 2011); and 64%, 66% and 17% for T12PR48, lead-in T12PR48 and PR, respectively (REALIZE, Zeuzem 2011).</p

Proportion of Patients with Loss of Resistant Variants after Treatment Failure during Follow-up.

<p>Of patients with available HCV population sequence data after failing to achieve SVR, a similar fraction of treatment-naive (T12/PR arm, ADVANCE) and treatment-experienced patients (Pooled TVR Arms, REALIZE) had resistance initially after failure. ‘After Failure’ indicates resistance profile at the visit representative of treatment failure. ‘End of Follow-up’ indicates the end of the follow-up observation period (end of study), with a median time of 12 months (range: 0 to 17 months) in ADVANCE and 9 months in REALIZE (range: 0 to 17 months).</p

Variants of Interest from a Pooled Analysis of Subjects Who Did Not Achieve an SVR in Phase 2 and 3 Studies.

a<p>Replicon IC₅₀ values are the mean from at least three independent experiments with fold-change relative to wild-type (WT) replicon cells. The mean (SD) IC₅₀ value of telaprevir in G1b WT (mADE) replicon cells is 0.482 (0.122) µM (n = 15). In G1a WT replicon the mean (SD) IC₅₀ value of telaprevir is 0.961 (0.132) µM (n = 8).</p>b<p>Numerator is number of subjects that possess the given variant; denominator is total count of subjects that have sequence data available at that position.</p>c<p>Treatment-Failure Occurrence indicates the number of subjects in TPR or T/P containing groups from Phase 2 and 3 studies who did not achieve an SVR that had the given variant at the treatment-failure timepoint. The denominator is the total number of subjects from Phase 2 and 3 studies who did not achieve an SVR with treatment-failure timepoint sequencing data available.</p>d<p>The value tests for enrichment of the variant in the treatment-failure population (Alpha[Bonferroni corrected]: 1a, 0.0000919; 1b, 0.000102).</p>e<p>Was determined in replicon 1b.</p>f<p>The replicon IC₅₀ is greater than 30 µM, the maximum concentration of telaprevir used in the assay.</p

Frequency of Phenotypic Resistance Profiles in Patients with On-Treatment Virologic Failure during the TVR Treatment Phase by Prior Response and Subtype in Phase 3 Studies (includes the T12/PR arm of ADVANCE and pooled TVR arms of REALIZE).

<p>Higher-level resistance (red) is defined as >25-fold increase in IC₅₀ and lower-level resistance (yellow) is defined as 3- to 25-fold increase in IC₅₀ from wild-type.</p

Phenotypic Resistance Profiles in Patients Who Did Not Achieve SVR with a TVR-based Regimen.

<p>Data from ADVANCE include only the T12PR arm and data from REALIZE include pooled TVR arms. Higher-level resistance (red) is defined as >25-fold increase in IC₅₀ and lower-level resistance (yellow) is defined as 3- to 25-fold increase in IC₅₀ from wild-type. Grey (n/a) indicates patients with no sequence data available due to HCV RNA levels below the LOD of the sequencing assay or lost-to-follow-up.</p