Clinical Applications of Resistance Stuart C. Ray, MD

Clinical Applications of Resistance Stuart C. Ray, MD Professor of Medicine and Oncology Director, Infectious Diseases Fellowship Training Program Johns Hopkins University School of Medicine

Disclosures Dr. Ray is a paid member of Data Safety Monitoring Boards for Boehringer-Ingelheim The terms of this arrangement are being managed by the Johns Hopkins University in accordance with its conflict of interest policies

Learning Objectives º Understand principles of the virologic basis of resistance º Identify options to prevent HCV resistance º Distinguish clinical tests for detecting HCV resistance

Virology and Dynamics

Worldwide Diversity of HBV, HIV, and HCV G hominoids E D C A B HBV 3181 sites F 0.1 7 2 1a 1c 1 1b 5 F D B G AE A K J C H 4 HIV 8316 sites 0.1 6 Ray SC, Thomas DL. Mandell s PPID 7th ed., 2009, chap. 154 HCV 9198 sites 0.1 3

HCV Life Cycle Ray SC, Bailey JR, Thomas DL. Fields Virology 6 th ed., 2013, chap. 27

Life Cycles of HIV, HBV, and HCV HIV HBV HCV (+) (-) (+) RT Human RNApol RT RT NS5B NS5B HIV HBV HCV Stable genome Provirus cccdna (none) Virion NA polymerase Host RNApol HBV RT HCV NS5B Error-prone replications per cell One Multiple Multiple Plasticity of genome High Constrained Very high Recombination Common Common Rare

Resistance: It s just evolution (diversification + selection)

HCV: Resistant Variants Are Present Before Treatment º HCV exists as a mixture of populations of genetically distinct, but closely related, virions in every patient. [1] º Most resistant variants are relatively unfit and are undetectable prior to therapy with current technology. [2,3] º Note: DAAs do not increase viral mutation rate they select for resistance. 1. Pawlotsky JM. Clin Liver Dis. 2003;7:45-66 2. Kuntzen T, et al. Hepatology. 2008;48:1769 3. Bartels DJ, et al. J Infect Dis. 2008;198:800

Baseline Presence Versus Generation of Resistant Variants Time Prior to first dose Nucleotide Differences Probability Virions Generated per Day 0 0.91 9.1 x 10 11 Number of Possible Mutants Fraction of All Possible Mutants Generated per Day 1 0.087 8.7 x 10 10 2.9 x 10 4 1 2 0.0042 4.2 x 10 9 4.1 x 10 8 1 3 0.00013 1.3 x 10 8 4.0 x 10 12 3.4 x 10-5 End of first day of therapy 0 0.91 9.1 x 10 6 1 0.087 8.7 x 10 5 2.9 x 10 4 1 2 0.0042 4.2 x 10 4 4.1 x 10 8 1.0 x 10-4 3 0.00013 1.3 x 10 3 4.0 x 10 12 3.4 x 10-10 Rong L, et al. Sci Transl Med. 2010;2:30ra32

Critical to Discontinue Failing Regimen º Continued replication in the presence of drug will likely lead to further evolution of the viral population. º Further evolution, in theory, can result in a more fit, drug-resistant viral population that may remain enriched in the patient, even in the absence of drug pressure. º This should be prevented by discontinuing the DAA if HCV RNA levels fail to decrease to undetectable levels during therapy. Important to know and implement "stopping rules" for each drug.

Virologic Barriers to Resistance º Genetic barrier Number and complexity of nucleotide changes required for a virus to acquire clinical resistance to an antiviral regimen. º Fitness Resistance mutations frequently compromise viral function and thus reduce viral fitness. º Example: HIV PIs are generally more potent than NRTIs and have a higher genetic barrier to resistance. NRTI-resistance mutants may or may not be associated with reduction in viral fitness.

Phase 2a (7 centers in US) Prior nonresponders to P+R Def: < 2 log 10 drop during 12+ wks Genotype 1, no cirrhosis Daclatasvir = BMS-790052 daily NS5A inhibitor Asunaprevir = BMS-650032 BID NS3/4A PI Group A (24 weeks): Daclatasvir + asunaprevir P+R added for breakthrough Group B (24 weeks): P+R + daclatasvir + asunaprevir

Dual DAA (Group A) NS3 R 155 K at baseline + NS5A Q 30 E at relapse Resistance detected in all breakthroughs: NS5A - Q 30 R - L 31 MV - Y 93 CN NS3 - R 155 K - D 168 AETVY LLOQ LLOD Lok A, et al. NEJM. 2012; 366(3):216

Dual DAA Rescue (Group A + PR) Lok A, et al. NEJM. 2012; 366(3):216

ABT450/ RTV Daily ABT333 BID RBV Daily Beyond the barrier : host factors contribute to resistance 250 mg/ 100 mg 400 mg 1.0-1.2g Treatment-naïve 150 mg/ 100 mg 400 mg 1.0-1.2g Treatment-naïve 150 mg/ 100 mg 400 mg 1.0-1.2g Prior null-/partialresponders to pegifn+rbv Poordad NEJM 2013; 368(1): 45

Reversion of telaprevir resistance by subgenotype Sullivan J, et al. CID 2013 May 7; online

Reversion of telaprevir resistance by variant Sullivan J, et al. CID 2013 May 7; online

RAVs after TVR monotherapy (14d) deep sequencing 4±1.2 years later Thomas XV, et al. PLoS One 2012;7(7):e41191

Preventing resistance º Adherence º Regimen potency º Stop a failing regimen! HCV RNA level ( Viral load ) may be most important resistance test

Detecting Resistance

RAVs Detection at Baseline: Current DAAs º Pretreatment detection of high-level RAVs (V36M, T54A/S, V55A, and/or R155K) is Uncommon (4-5%) Associated with similar rate of SVR (in response to P+R+DAA) to those who do not have RAVs at baseline º Baseline testing for PI resistance is not recommended by any major society/guideline RAVs = Resistance-Associated Variants FDA briefing document UCM252343 (boceprevir), section 9.3 Telaprevir package insert, May 2011

Resistance-associated variants Baseline and at Time of Failure Failure* Subgenotype NS3-base NS3-fail NS5Bbase NS5B-fail BT 1a - R155K > D168[A>V] - G554S BT 1a - D168A - M414T BT 1a - D168V - C316Y > D559G BT 1a - D168[E>Y] - G554S > S556G > M414V + G554S BT 1a - D168V - S556G BT 1b D168[E>T] D168K - C316Y Rel 1a - D168[Y>V>A] - S556G > M414T Rel 1a - - - - Rel 1a - D168V - S556G *BT = breakthrough Rel = relapse Poordad NEJM 2013; 368(1): 45

QUEST-1: Simeprevir (SMV) + P/R P/R: º SVR12 (subgenotype 1a & 1b) was 50% SMV+P/R: º SVR12 (1a) was 71% º SVR12 (1b) was 90% º Subtype 1a: 60/146 (41%) had baseline Q80K SVR12 similar to placebo + P/R º Subtype 1a (Q80) SVR12 90%, same as subtype 1b Jacobson I, et al. EASL 2013

Resistant Testing for HCV: Limited Options Currently º LabCorp offers Monogram HCVGenoSure NS3/4A Reports resistance-associated variants in NS3 and NS4A Reports assessment of anticipated impact on sensitivity http://www.monogrambio.com/pdf/hcv_genosure_sample_report.pdf

HCV Resistance: Reasons for Optimism º Significant resistance to some agents (like sofosbuvir) has not been observed Efficacy against genotype 3 is limited S282T rarely observed º Near-uniform successful therapy with combinations that hit multiple targets º Baseline RAVs don t consistently predict failure

Resistant Testing for HCV: Lingering Questions º Is the baseline result predictive? Perhaps, but: Only for some regimens May not be more informative than a combination of subgenotype + on-treatment kinetics What is number needed to test to avoid one failure? If <5% have baseline genotypic resistance, and most of those have SVR anyway... Utility may depend on alternatives (will it affect therapy?) º Is the post-failure result predictive? If so, then: Is it more strongly predictive than subgenotype + on-treatment kinetics? Is the predictive effect durable? º Will broader use generate higher-fitness mutants that are sofosbuvir-resistant?

HCV Resistance, Held in the Mirror of HIV º Recognize risk factors for DAA resistance: Risk factors for nonresponse (prior nonresponse, cirrhosis, HIV coinfection, nonadherence, inadequate dosing, perhaps IL28B?) Genotype 1a (for current agents) Continuation (by the provider) of a failing regimen º Resistance is cured by SVR. º It is hoped that reversion may restore activity. º During therapy, the best test for resistance may be the plasma viral RNA level ( viral load ). º Real-world use will generate more resistance than clinical trials have.