Introduction to the Impact of Resistance in Hepatitis C Sponsored by AbbVie 2/1/2017 Presented by Sammy Saab, MD, MPH, FACG, AGAF, FAASLD February 1 st, 2017 1
AbbVie disclosures This is an Abbvie sponsored educational webinar which is being presented by Sammy Saab, MD, on behalf of AbbVie The purpose of this medical educational webinar is to foster increased awareness of the latest science in the management of HCV HCV, hepatitis C virus. Speaker disclosures Speakers Bureau and Consultant: AbbVie, BMS, Gilead, Merck, Intercept 2
Contents How does HCV resistance arise? How long do treatment emergent RASs persist? How often should physicians expect to see RASs in clinical practice? How does a physician test for virologic resistance? Summary RAS, resistance associated substitution. How does HCV resistance arise? 3
HCV has high genetic heterogeneity HCV has an inherently high mutation rate that results in considerable heterogeneity throughout the genome 1,2 High mutability is caused by: HCV lifecycle A high viral replication rate, with the production and clearance of 10 10 to 10 12 virions per day 1 4 NS5B RNA polymerase has poor fidelity and lacks proofreading activity, resulting in a high rate (10 3 to 10 5 ) of misincorporations per nucleotide per replication 1 RNA, ribonucleic acid. 1. Sarrazin C, et al. Gastroenterology. 2010;138:447 462. 2. Bartenschlager R, et al. J Gen Virol. 2000;81:1631 1648. 3. Herrmann E, et al. Antivir Ther. 2000;5:85 90. 4. Neumann AU, et al. Science. 1998;282:103 107. Image reproduced from Lindenbach BD, et al. Nature. 2005;436:933 938. DAAs target 1 of 3 viral proteins: NS3/4A, NS5A, and NS5B 1,2 NS5A protein Component of the HCV replication complex NS3/4A protease Viral protein production NS5B polymerase HCV replication DAA, direct acting antiviral. 1. Bartenschlager R, et al. J Gen Virol. 2000;81:1631 1648. 2. Pawlotsky JM. Gastroenterology. 2016;151:70 86. Image reproduced from Lindenbach BD, et al. Nature. 2005;436:933 938. 4
Terminology and definitions Variant: a viral particle, which may or may not be resistant to a particular drug Polymorphism: a naturally occurring change in the viral genome, which may or may not result in an amino acid change in the resulting protein RAP (resistance associated polymorphism): an amino acid change that results in resistance to a drug; occurs naturally, ie, without drug exposure RAS (resistance associated substitution): an amino acid change that results in resistance to a drug; occurs under selection pressure of DAA treatment Resistant variant: a variant carrying one or more RASs The term RAV (resistance associated variant) is used interchangeably in the literature to refer to both RASs and the resistant variants which carry them. This term is inaccurate and should no longer be used Pawlotsky JM. Gastroenterology. 2016;151:70 86. RASs develop as a result of changes in the nucleotide sequence of codons HCV genome 1 p C E1 E2 7 NS2 NS3 NS NS4B NS5A NS5B 5 UTR 4A 3 UTR NS5A domain 1 (213 amino acids for GT1) Example: Codon 93 of HCV NS5A 2,3 mrna Amino acid Codon 93 Codon 93 UAC Tyr (Y) Y93 Wild type Nucleotide substitution A codon is a sequence of 3 nucleotides in a DNA or RNA molecule (eg, UAC) that code for a single amino acid (eg, tyrosine) in a protein (eg, NS5A) 3,4 DNA, deoxyribonucleic acid; GT, genotype; UTR, untranslated region. 1. Ahmed A, Felmlee DJ. Viruses. 2015;7:6716 6729. 2. Lontok E, et al. Hepatology. 2015;62:1623 1632. 3. OpenStax College. Chapter 3: Biological Macromolecules. OpenStax College, Biology. Dec 19, 2016:65 102. Available at: https://d3bxy9euw4e147.cloudfront.net/oscms prodcms/media/documents/biology OP.pdf. Accessed January 2017. 4. OpenStax College. Chapter 15: Genes and Proteins. OpenStax College, Biology. Dec 19, 2016:389 414. Available at: https://d3bxy9euw4e147.cloudfront.net/oscms prodcms/media/documents/biology OP.pdf. Accessed January 2017. CAC His (H) Y93H NS5A RAS A change in a codon can result in a different amino acid being incorporated into the protein 3,4 5
These codon changes can result in a change in the interaction between the viral protein and the DAA Wild type protein Variant protein DAA DAA Impaired binding Factors that determine the barrier to resistance to a particular DAA: 2 Binding affinity of the DAA for its target site Potency and pharmacokinetics of the DAA HCV genotype and subtype Patient adherence to the DAA regimen Impaired binding of the DAA to the protein may result in reduced efficacy 1 1. Romano KP, et al. PLoS Pathog. 2012;8:e1002832. 2. Sarrazin C, et al. Gastroenterology. 2010;138:447 462. Drug susceptibility of resistant variants depends on the genetic barrier to resistance The genetic barrier to resistance to a particular antiviral agent is the number and type of nucleotide changes required for a variant to acquire clinical resistance to the antiviral agent 1,2 HCV is more prone to developing resistance than 2 Example: R155 in the NS3/4A protease PAGHAVGIFRAAVCTRGVAKAVDFIP S V AGA AAA (R155K) AGA ACA (R155T) CGA AAA (R155K) CGA ACA (R155T) Selection of R155K/T requires 1 mutation in Selection of R155K/T requires 2 mutations in 1. Pawlotsky JM. Gastroenterology. 2016;151:70 86. 2. Perales C, et al. Viruses. 2015;7:5746 5766. 6
Outgrowth of resistant variants depends on fitness The fitness of a variant is its ability to replicate, and is independent of the drug resistance conferred by the RASs it carries Fitness associated substitutions can be naturally present or emerge during DAA therapy Fitness associated substitutions may increase the fitness of resistant variants, leading to their rapid outgrowth during treatment (breakthrough) or after treatment (relapse) During treatment, outgrowth of resistant variants depends more on their fitness than on the level of resistance conferred by the RASs they carry. After treatment, competition for growth between the variants also depends on their relative fitness Pawlotsky JM. Gastroenterology. 2016;151:70 86. Inadequate drug pressure can select for resistant variants and may contribute to treatment failure 1,2 Treatment Post treatment Viral load Selection of resistant variants Drug susceptible variants Drug resistant variants Patients begin treatment with viral variants Time Virologic failure 1. Ahmed A, et al. Viruses. 2015;7:6716 6729. 2. Forum for Collaborative HIV Research and HCV Drug Development Advisory Group (HCV DrAG ResisSS 2013 v.1). #2 HCV Resistance: Barriers, Selection and Monitoring of Resistance. Aug 12, 2013. Available at: http://www.hivforum.org/storage/documents/2013/hcvressis2013/2_hcv%20resistance_barriers,%20selection%2 0and%20monitoring%20of%20resistance_8_8.pdf. Accessed January 2017. 7
Inadequate drug pressure can select for resistant variants and may contribute to treatment failure 1,2 Treatment Post treatment Viral load Selection of resistant variants Drug susceptible variants Drug resistant variants Following treatment failure, drug susceptible variants may begin to re emerge Time Patients begin treatment Virologic failure with viral variants The timeline for re emergence depends on the viral fitness of resistant variants 1. Ahmed A, et al. Viruses. 2015;7:6716 6729. 2. Forum for Collaborative HIV Research and HCV Drug Development Advisory Group (HCV DrAG ResisSS 2013 v.1). #2 HCV Resistance: Barriers, Selection and Monitoring of Resistance. Aug 12, 2013. Available at: http://www.hivforum.org/storage/documents/2013/hcvressis2013/2_hcv%20resistance_barriers,%20selection%2 0and%20monitoring%20of%20resistance_8_8.pdf. Accessed January 2017. How long do treatmentemergent RASs persist? 8
Persistence of RASs post treatment NS5A RASs tend to persist far longer than those of NS3 and NS5B RASs (%) 100 90 80 70 60 50 40 30 20 10 Estimated clearance time for RASs NS5A inhibitors <50% of NS3 RASs persist 24 weeks PT >95% of NS5A RASs persist 48 weeks PT <60% of NS5B RASs persist 48 weeks PT <10% of NS3 RASs persist 48 weeks PT Days 24 48 Weeks post treatment PT, post treatment. Pawlotsky JM. Gastroenterology. 2016;151:70 86. How treatments can overcome resistance Drug susceptible virus Drug resistant virus Increase treatment duration and/or add additional agents Viral load If reliable tests are available, conduct resistance testing to determine the most appropriate retreatment regimen Use DAA combination therapy with multiple MOAs* Time MOA, mechanism of action. *Note that DAA monotherapy is not recommended in any clinical scenario. AASLD ISDA. Recommendations for Testing, Managing, and Treating Hepatitis C. Oct 2016. Available at: http://hcvguidelines.org/sites/default/files/hcv Guidance_October_2016_a.pdf. Accessed January 2017. EASL Recommendations on Treatment of Hepatitis C 2016. J Hepatol. 2017;66:153 194. 9
How often should physicians expect to see RASs in clinical practice? Prevalence of frequently observed protease inhibitor (NS3/4A) RASs by population sequencing Overall prevalence of baseline NS3 RASs 1 * 60 57 50 Prevalence of key baseline NS3 RASs 2 48 Prevalence (%) 40 20 19 0 Many NS3 RASs do not confer high resistance to NS3 inhibitors 3 *Data from a Phase 3 trial of an NS3 containing DAA combination regimen in treatment naïve HCV GT1 infected individuals. Baseline NS3 resistance data was available for 151 and 129 patients. 1 RASs with a >2 fold change in comparison to wild type in a phenotypic assay. 1. Zeuzem S, et al. Ann Intern Med. 2015;163:1 13. 2. Sarrazin C. J Hepatol. 2016;64:486 504. 3. Lontok E, et al. Hepatology 2015; 62:1623 1632. 10
Prevalence (%) Prevalence of frequently observed NS5A RASs by NGS sequencing (15% cutoff) Overall prevalence of baseline NS5A RASs* 60 12 40 20 0 14 22 Prevalence of key baseline NS5A RASs (North America only)* 11 n.a., not applicable. *Pooled data from 5 Phase 3 trials of an NS5A containing DAA combination regimen in HCV GT1 infected individuals. Baseline NS5A resistance data were available for 420 and 143 patients. Sarrazin C, et al. J Hepatol. 2016;64(Suppl):S214 (EASL 2016; poster #LBP503. Available at: http://www.natap.org/2016/easl/easl_22.htm. Accessed January 2017). 10 8 6 4 2 0 0.4 Q30E/R 1.1 L31M 8.7 M28T/V 3.6 3.6 Y93 (any) n.a Q30E/R L31M/V M28T/V n.a Y93 (any) Prevalence (%) Prevalence of frequently observed NS5B RASs by NGS sequencing (15% cutoff) Overall prevalence of baseline NS5B RASs 1 * 60 40 20 0 2 29 Most NS5B RASs confer minimal impact on resistance 2,3 Prevalence of key baseline NS5B RASs In HCV infected patients 1 * 60 53 *Pooled data from 5 Phase 3 trials of an NS5B containing DAA combination regimen in HCV GT1 infected individuals. Baseline NS5B resistance data were available for 145 patients. 1. Sarrazin C, et al. J Hepatol. 2016;64(Suppl):S214 (EASL 2016; poster #LBP503. Available at: http://www.natap.org/2016/easl/easl_22.htm. Accessed January 2017). 2. Sarrazin C. J Hepatol. 2016;64:486 504. 3. Lontok E, et al. Hepatology 2015; 62:1623 1632. 40 20 0 1.9 29 9.1 20 20 N.Am. Eur. ROW N.Am. Eur. ROW C316N S556G 11
How does a physician test for virologic resistance? Testing for HCV Resistance Resistance testing requires PCR amplification of large fragments of the genes encoding the NS3 protease, NS5A protein, and NS5B protein In contrast to HIV resistance tests, no standardized assays* for HCV resistance are available as purchasable kits and in house techniques based on population or deep sequencing may be used Alternatively, there are a number of reference laboratories that have made such tests available in the USA and Europe (i.e. Monogram, Quest) HIV, human immunodeficiency virus; PCR, polymerase chain reaction. *Different assays use different primers, reaction conditions, and sequencing cutoffs. Pawlotsky JM. Gastroenterology. 2016;151:70 86. 12
RASs can be identified by population based or deep sequencing techniques Population based sequencing 1,2 Next generation sequencing (NGS) 1,2 Sanger method Sensitivity of 10 25% Meaningful, but may not detect all clinically relevant variants Tends to be used in: clinical practice Deep sequencing Sensitivity of ~1% Variants with a prevalence of 15% tend to have poor fitness and may not be clinically relevant Tends to be used in: clinical trials It is likely that a 15% cutoff better predicts treatment failure due to the selection of resistant viruses than a 1% cutoff. A cutoff of 15% is now generally adopted in clinical trials and real world studies, and in clinical practice 2 1. Fourati S, Pawlotsky JM. Viruses. 2015;7:6346 6359. 2. Pawlotsky JM. Gastroenterology. 2016;151:70 86. Quest Diagnostics sample report The assays listed on this slide are trademarks of their respective owners and are not trademarks of AbbVie Inc. The makers of these assays are not affiliated with and do not endorse AbbVie Inc. or its products, nor does their inclusion here constitute an endorsement by AbbVie. Quest Diagnostics. http://www.questdiagnostics.com. Accessed January 2017. 13
Monogram Biosciences sample report The assays listed on this slide are trademarks of their respective owners and are not trademarks of AbbVie Inc. The makers of these assays are not affiliated with and do not endorse AbbVie Inc. or its products, nor does their inclusion here constitute an endorsement by AbbVie. Monogram Biosciences. http://www.monogrambio.com. Accessed January 2017. Interpretation of HCV resistance will require continued education Tests vary between laboratories 1 The sensitivity of population sequencing varies Cutoffs for deep sequencing are not standardized Not all RASs are clinically meaningful 1 Selection of resistant variants is largely dependent on their fitness with respect to other variants in the population, independent of the RASs they carry 1 The impact of a RAS may differ in treatment naïve and experienced patients, and in those with different disease states (eg, non cirrhotic vs cirrhotic) 2 Overall, the number of possible resistance patterns at baseline is almost infinite, and their potential impact on SVR is unknown 1 SVR, sustained virologic response. 1. Pawlotsky JM. Gastroenterology. 2016;151:70 86. 2. Monogram Biosciences. http://www.monogrambio.com. Accessed January 2017. 14
Considerations for baseline HCV resistance testing 1. It would be beneficial to have a standardized assay with a sensitivity of 15% as a purchasable kit 1 2. Interpretation and reporting of HCV resistance data should be homogenized and standardized through recommendations by an international organization 1 3. Clinically relevant RASs should be clearly identified as these are most relevant for treatment decisions 1 4. International societies should provide guidelines based on data from clinical trials and real life studies that reported strong predictive values of the different RAS profiles 1 Although routine baseline HCV resistance testing is not currently recommended by AASLD IDSA HCV guidelines, 2 treatment can be optimized for groups of patients known to have specific RASs that reduce response to therapy AASLD, American Association for the Study of Liver Diseases; IDSA, Infectious Diseases Society of America. 1. Pawlotsky JM. Gastroenterology. 2016;151:70 86. 2. AASLD ISDA. Recommendations for Testing, Managing, and Treating Hepatitis C. Oct 2016. Available at: http://hcvguidelines.org/sites/default/files/hcv Guidance_October_2016_a.pdf. Accessed January 2017. Summary Resistance can arise from the naturally high mutation rate of HCV RNA polymerase or selective pressure from DAAs Baseline NS5A RASs have been observed in approximately 10 20% of DAA naïve patients The vast majority of NS5A RASs may persist for extended periods of time while NS3 and NS5B RASs typically return to wild type within a year or two The interpretation of HCV resistance tests is challenging due to non standardization of assays and the fact that the impact of RASs on treatment response can depend on multiple factors 15
Questions? Please email: webinars@amcp.org 2/1/2017 16