pawlotzky du hepatites-resistance

Hépatite C: Résistance

aux Traitements

Prof. Jean-Michel Pawlotsky

CNR des Hépatites B, C et delta

Laboratoire de Virologie & INSERM U635

Hôpital Henri Mondor

Université Paris XII

Créteil

Mechanisms of HCV

Resistance

HCV RNA-Dependent

RNA Polymerase

• Errors during replication:• frequent

• spontaneous

• at random positions

• Lack of “proofreading” activity

=> Accumulation of genomic mutations

=> Selection

Properties of HCV RdRp

Mutant Selection

• At the level of populations of infected

individuals:

• Genotypes and subtypes

• At the level of an infected individual:

• Viral quasispecies

Quasispecies Distribution

of Viruses

sensitive

resistant

Mechanisms of Resistance

sensitive

resistant

sensitive

resistant

sensitive

resistant

Drug Stop drug

resistant

sensitive

resistant

sensitive

resistant

Drug Stop drug

resistant

sensitive

resistant

sensitive

resistant + fit

Drug Stop drug

resistant

sensitive

resistant

Drug Stop drug

resistant

sensitive

resistant + very fit

sensitive

DAA Monotherapy

HCV Lifecycle

Inhibition of polyprotein

processing

(Pawlotsky JM, Antivir Ther 2012;17:1109-17)

1st-wave, 1st-generation

Telaprevir (Janssen)

Boceprevir (Merck)

2nd-wave, 1st-generation

Simeprevir (Janssen)

Paritaprevir/r (Abbvie)

Asunaprevir (BMS, Japan)

Sovaprevir (Achillion)

Vedroprevir (Gilead)

Vaniprevir (Merck, Japan)

2nd-generation

Grazoprevir (Merck)

ACH-2684 (Achillion)

Narrow genotypic activity

Low barrier to resistance

All genotypes except 3

Pangenotypic (~)

Higher barrier to

resistance

NS3/4A Protease Inhibitors

(Raney et al., J Biol Chem 2010:285:22725-31)

Protease Inhibitor Resistance

(HCV DRAG, Forum for Collaborative HIV Research, April 2014)

MK-5172 Resistance Profile

MK-5172

BMS-032

simeprevir

GS-9551

boceprevirtelaprevir

1000.0

10000.0

MK-5172 BMS-032 simeprevir GS-9551 boceprevir telaprevir

(Lahser et al., AASLD 2012)

HCV Lifecycle

Inhibition of HCV

replication

Nucleotide analogues

Sofosbuvir (Gilead)

MK-3682 (Merck)

AL-335 (Janssen)

Pangenotypic

High barrier to resistance

Nucleoside/Nucleotide Analogue

Inhibitors of HCV RdRp

Catalytic

Nucleoside/Nucleotide Analogue

Inhibitors of HCV RdRp

(Kindly provided by Dr F. Penin)

Sofosbuvir Acts as a

Chain Terminator

RNA chain

cannot be

elongated

5’ AG C

C GA CGGG

Template strand

Primer strand

2’C-Me-ATP in the catalytic site

(Migliaccio et al., J Biol Chem 2003;278:49164-70)

HCV Resistance to 2’-C-Methyl

Nucleoside Inhibitors

Sofosbuvir ResistanceFDA analysis of NGS data

• Post-hoc analysis of NGS data from FISSION, FUSION, POSITRON,

NEUTRINO, and pretransplant study:

• 982 subjects treated by SOF/RBV or SOF/RBV/PEG

• 224 failed treatment

Selection of 3 substitutions of interest

• L159F (n=12)

• V321A (n=5)

• S282R (n=1)

One baseline polymorphism that potentially reduced SOF

efficacy in genotype 1b (exceptional in 1a*)

• N316 (n=6, including 4 also with L159F)

(Donaldson et al., Hepatology 2014; epub ahead of print) *C316: 99.9% in 1a, 81.8% in 1b

(Donaldson et al., Hepatology 2014; epub ahead of print)

Interaction with the catalytic triad

C316 N316

Thumb-1 inhibitors

Beclabuvir (BMS)

Thumb-2 inhibitors

GS-9669 (Gilead)

Palm-1 inhibitors

Dasabuvir (Abbvie)

Genotype 1 ~only

Non-Nucleoside Inhibitors (NNI)

Genotype 1 ~only

Non-Nucleoside Inhibitors (NNI)

Thumb IBMS-791325

Thumb IIGS-9669

Palm IDasabuvir

Palm II

(Adapted from Dr F. Penin)

HCV NNI Resistance Mutations

(courtesy of Isabel Najera, Roche)

411448

142 96

411448

142 96

411448

142 96

FingersThumb

HCV Lifecycle

Inhibition of HCV

assembly and release

Inhibition of HCV

replication

1st-generation

Daclatasvir (BMS)

Ledipasvir (Gilead)

Ombitasvir (Abbvie)

2nd-generation

Elbasvir (Merck)

GS-5816 (Gilead)

Genotypes 1 and 4, other

genotypes variable

Pangenotypic

Slightly higher barrier

to resistance

NS5A Inhibitors

NS5A Protein

Domain III

Domain II

Domain I

Required for HCV RNA

replication

Required for HCV viral

particle assembly

May be involved in the

release of HCV particles

NS5A Dimer

ER membrane

Cytosol

ER lumen

NS5A Inhibitor Resistance

(HCV DRAG, Forum for Collaborative HIV Research, April 2014)

MK-8742 Resistance Profile

(Merck, unpublished data)

MK-8742

Daclatasver

GS-5885

MK-8742 Daclatasver GS-5885

GS-5816, a 2nd-Generation

NS5A Inhibitor

(Gilead, data on file)

Barrier to Resistance

Low-barrier drug High-barrier drug

Protease inhibitors

NS5A inhibitors

Non-nucleoside RdRp inhibitors

Nucleoside/nucleotide analogue

RdRp inhibitors

Triple Combination of PegIFNa,

Ribavirin and a DAA

Triple Combination Treatment Failures

Depend on the Patient’s IFN Responsiveness

BOC/RGT

IFN nonresponsive

(<1 log HCV RNA

decrease during lead-in)

IFN-responsive

(≥1 log HCV RNA

decrease during lead-in)

(Poordad et al., N Engl J Med 2011;364:1195-206)

Pre-existing Resistant Variants May Influence the

Outcome of Triple Combination Treatment

(Simeprevir + PegIFNa + Ribavirin)

(Jacobson et al., AASLD 2013; Choe et al., AASLD 2013; FDA AVDAC, Oct 24, 2013)

*Q80K prevalence in the US: GT 1a, 32.5%; GT 1b, 0.1%

N=84 N=165

1a Q80K 1a no Q80K 1b

Triple Combination Failures are Associated

with the Selection of DAA-Resistant Variants

• Protease inhibitor-containing treatment failures

in Phase III trials:

• Boceprevir: 53% have dominant resistant virus

• Telaprevir: 77% have dominant resistant virus

• Simeprevir: >90% have dominant resistant virus

(Sullivan et al., Clin Infect Dis 2013;57:221-9; Barnard et al., Virology 2013;444:329-36; Jacobson et al., Lancet

2014;384:403-13; Manns et al., Lancet 2014;384:414-26)

Median time to wild-type by population

sequencing =7 months (95% CI: 5-8)

0 2 4 6 8 10 12 14 16 18

Time after treatment failure (months)

median

(Sullivan et al., Clin Infect Dis 2013;57:221-9)

DAA-Resistant Viruses are Progressively

Replaced by Wild-type Sensitive Viruses

after Treatment Failures (Telaprevir)

(Lenz et al., EASL 2014)

DAA-Resistant Viruses are Progressively

Replaced by Wild-type Sensitive Viruses

after Treatment Failures (Simeprevir)

Summary

• Triple combination treatment failures are the result of

poor IFN responsiveness, which is patient-dependent

• Pre-existing resistant variants may influence the

outcome of triple combination treatment (Q80K with

simeprevir).

• Triple combination failures (telaprevir, boceprevir,

simeprevir,…) are associated with the selection of

DAA-resistant viruses

• Protease inhibitor-resistant viruses are progressively

replaced by wild-type viruses after treatment failure

• In contrast with viruses resistant to protease inhibitors,

NS5A inhibitor-resistant viruses appear to persist for

years, maybe forever, after treatment failure (no data in

combination with PegIFNa and ribavirin)

• No resistant viruses are selected by the triple

combination of PegIFNa, ribavirin and sofosbuvir due

to the high barrier to resistance of sofosbuvir

Summary

IFN-Free DAA Regimens

Questions

• Does the presence of pre-existing resistance

substitutions at treatment initiation impact SVR with

IFN-free regimens?

• Is resistance going to be observed in patients receiving

IFN-free regimens who fail on treatment (breakthrough)

or after treatment (relapse)?

• How long will resistant viruses persist after treatment,

and will this impair retreatment?

Questions

IFN-free regimens?

SVR According to the Presence of

NS5A RAVs at Baseline (ION-1, -2, -3)

(Dvory-Sobol et al., International Workshop on Antiviral Drug Resistance, June 2014)

Cutoff for NS5A RAVs detection: 1%

Sofosbuvir + Simeprevir ± RBVCOSMOS Cohort 2- Gen 1, Naive and NR, F3-F4

(Lawitz et al., Lancet 2014; epub ahead of print)

SOF+SIM+RBVAll patients SOF+SIM+RBVSOF+SIM

N=80 N=27 N=14 N=24

12 weeks 24 weeks

93%93%

SOF+SIM

100%94%

Sofosbuvir + Simeprevir ± RBVCOSMOS Pooled cohorts 1 & 2- Subtype 1a, Q80K

(Lawitz et al., Lancet 2014; epub ahead of print)

SOF+SIM+RBVAll patients SOF+SIM+RBVSOF+SIM

N=80 N=27 N=14 N=24

12 weeks 24 weeks

83%89%

SOF+SIM

Summary

• The detection of pre-existing resistance-associated

variants at baseline may be associated with a very

modest (if any) reduction in SVR rates with some

IFN-free regimens

• The SVR rates remain very high in patients

harboring such variants, the presence of which

does not contra-indicate therapy with the given

regimen

Questions

IFN-free regimens?

The Henri Mondor Experience

161 patients treated

in IFN-free regimens

in clinical trials

Protease inhibitors

received

Paritaprevir/r

Simeprevir

Faldaprevir

Asunaprevir

Danoprevir/r

NS5A inhibitors

received

Daclatasvir

Ombitasvir

Ledipasvir

Nucleotide analogue

received

Sofosbuvir

161 patients treated

in IFN-free regimens

in clinical trials

13 did not achieve

an SVR

8 relapses 3 breakthroughs 2 intolerant

Region Observed substitutions

NS3 protease

V36M, D103N, R155K

Q80K, R155K

A147V, D168V

A4M, V36M, R155K

P146S, Q80L

NS5AY93C

L31V, Y93H

NS5B RNA polymerase

Q65R, S189N/S

• Of the 23 patients who had a relapse, 15

had NS5A RAVs at the time of relapse

• Of the 15 with NS5A RAVs, 9 had the

variants detectable at baseline, whereas 6

did not.

• No patient selected the S282T substitution

Sofosbuvir/Ledipasvir FDC ± RBVION-3-Phase III, Gen 1, Rx-naïve

(Kowdley et al., N Engl J Med 2014;370:1879-88)

Treatment Failures in

SAPPHIRE-I

Patient GTType of

Virologic FailureNS3 NS5A NS5B

1 1aOn-treatment failure at

Week 12

R155K,

D168VQ30R S556G, 559N

2 1a Relapse at PT Week 2 D168V M28T S556G

3 1a Relapse at PT Week 2 V36A, D168V M28T none

4 1a Relapse at PT Week 8 none M28V*, H58P* none

5 1a Relapse at PT Week 8 D168V Q30R Y561H

6 1a Relapse at PT Week 8 D168V Q30R none

7 1a Relapse at PT Week 12 D168V Y93N* S556G

8 1b Relapse at PT Week 2 Y56H, D168V L31M*, Y93H* S556G*

(Feld et al., N Engl J Med 2014;370:1594-603)

Summary

• The majority of patients receiving an IFN-free

regimen will achieve an SVR

• However, 5 to 10% of patients in clinical trials,

possibly more in real-life, fail to achieve an SVR

• At the time of breakthrough or relapse, these

patients harbor viruses that are resistant to one or

more of the DAA administered (protease inhibitor,

NS5A inhibitor, non-nucleoside inhibitor of RdRp)

Questions

IFN-free regimens?

(Lenz et al., EASL 2014)

Replacement of PI-Resistant

Viruses by Wild-Type Viruses

0 2 4 6 8 10 12 14 16 18

Time after treatment failure (months)

(McPhee et al., Hepatology 2013;58:902-911; Wang et al. Antimicrob Agents Chemother 2013;57:2054-65)

Persistence of NS5A Inhibitor-

Resistant Viruses

Summary

• NS3 protease inhibitor-resistant viruses disappear

by population sequencing within 18 months on

average in patients who failed to achieve an SVR

• The time needed to clear variants that are

resistant to NS5A inhibitors or non-nucleoside

inhibitors of the HCV polymerase is unknown

• Whether persistence of such variants as dominant

species after treatment impacts retreatment

strategies is unknown

Clinical Utility of HCV

Resistance Testing

Resistance Testing Methods

• No commercially available assays yet

• In-house population sequencing of NS3

protease, NS5A and polymerase regions

• Potential interest of ultra-deep

pyrosequecing

HCV Resistance Testing-1

• Given the very high SVR rates with IFN-

free regimens, systematic pretreatment

resistance testing in treatment-naïve

patients or in patients who failed

PegIFNa-ribavirin therapy should not be

performed

• Resistance testing at treatment failure is

not recommended, because most of these

patients harbor viruses that are resistant

to one or more of the administered DAAs

• Resistance testing could be considered

at retreatment of patients who failed

DAA-containing regimens, provided that

data is generated to inform treatment

decisions based on the results of

resistance testing

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@JMPawlotsky

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