Pawlotzky hcv resistances.pptx du16

1. HCV Resistance and
DAA Treatment Failures
Prof. Jean-Michel Pawlotsky, MD, PhD
National Reference Center for Viral
Hepatitis B, C and delta
Department of Virology & INSERM U955
Henri Mondor Hospital
University of Paris-Est
Créteil, France

2. I
HCV Genetic Variability and
Mechanisms of Resistance

3. HCV RNA-Dependent
RNA Polymerase

4. • Errors during replication:
• frequent
• spontaneous
• at random positions
• Lack of “proofreading” activity
=> Accumulation of genomic mutations
=> Selection
Properties of HCV RdRp

5. Mutant Selection
• At the level of populations of infected
individuals:
• Genotypes and subtypes
• At the level of an infected individual:
• Viral quasispecies

6. Quasispecies Distribution
of Viruses

7. sensitive
resistant
Mechanisms of Resistance

8. sensitive
resistant
Drug
Mechanisms of Resistance

9. sensitive
resistant
Drug
resistant
Mechanisms of Resistance
sensitive

10. sensitive
resistant
Drug Stop drug
resistant
Mechanisms of Resistance
sensitive

11. sensitive
resistant
sensitive
resistant
Drug Stop drug
resistant
Mechanisms of Resistance
sensitive

12. sensitive
resistant
Drug Stop drug
resistant
Mechanisms of Resistance
sensitive
resistant + very fit
sensitive

13. II
HCV DAAs and Resistance

14. HCV Lifecycle
(Pawlotsky JM, Antivir Ther 2012;17:1109-17)

15. Available HCV DAA Classes
(Pawlotsky JM, Antivir Ther 2012;17:1109-17)
NS3/4A protease
inhibitors

16. Available HCV DAA Classes
(Pawlotsky JM, Antivir Ther 2012;17:1109-17)
NS3/4A protease
inhibitors
Nucleotide
analogues

17. Available HCV DAA Classes
(Pawlotsky JM, Antivir Ther 2012;17:1109-17)
NS3/4A protease
inhibitors
Nucleotide
analogues
Non-nucleoside
inhibitors

18. Available HCV DAA Classes
(Pawlotsky JM, Antivir Ther 2012;17:1109-17)
NS3/4A protease
inhibitors
Nucleotide
analogues
Non-nucleoside
inhibitors
NS5A
inhibitors
NS5A
inhibitors

19. Summary
Low-barrier drug High-barrier drug
NS3 protease inhibitors
NS5A inhibitors
Non-nucleoside RdRp inhibitors
Nucleotide analogues

20. Nucleotide analogue
inhibitors of HCV RdRp

21. Catalytic
Site
Nucleotide Analogue
Inhibitors of HCV RdRp

22. Nucleotide analogues
Sofosbuvir (Gilead)
MK-3682 (Merck)
AL-335 (Janssen)
Pangenotypic
High barrier to resistance
Nucleotide Analogue
Inhibitors of HCV RdRp

23. Nucleotide Analogue Resistance
(Lontok et al., Hepatology 2015;62:1623-32)

24. NS5A inhibitors

25. 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

26. 1st-wave
Daclatasvir (BMS)
Ledipasvir (Gilead)
Ombitasvir (Abbvie)
2nd-wave
Elbasvir (Merck)
Velpatasvir (Gilead)
Odalasvir (Janssen)
Ravidasvir (Presidio)
Pangenotypic
(except ledipasvir)
Low barrier to resistance
Pangenotypic
Slightly higher barrier
to resistance?
NS5A Inhibitors
2nd-generation?
ABT-530 (Abbvie)
MK-8408 (Merck)
Pangenotypic
Higher barrier
to resistance?
1st-generation

27. NS5A Inhibitor Resistance
(Adapted from Tellinghuisen et al., Nature 2005;435:374-9)
H1
Conserved
surface
H1
58
Chain B
Amino Acids at RAV positions
24
30
28
58
9231
32 38
92
93 30
31
24
28
38
32
93
Chain A
NB: Residues 32 and 38 behind molecule

28. NS5A Inhibitor Resistance
(Lontok et al., Hepatology 2015;62:1623-32)

29. NS3/4A protease inhibitors

30. NS3 Protease Inhibitors
(Raney et al., J Biol Chem 2010:285:22725-31)

31. 1st-wave
Telaprevir (Janssen)
Boceprevir (Merck)
2nd-wave
Simeprevir (Janssen)
Paritaprevir/r (Abbvie)
Asunaprevir (BMS, Asia)
Vaniprevir (Merck, Asia)
2nd-generation
Grazoprevir (Merck)
ABT-493 (Abbvie)
GS-9857 (Gilead)
Only genotype 1
Low barrier to resistance
All genotypes except 3
Low barrier to resistance
Pangenotypic (~)
Higher barrier to
resistance
NS3/4A Protease Inhibitors
*Not approved yet in US and EU
1st-generation

32. Protease Inhibitor Resistance
(Lontok et al., Hepatology 2015;62:1623-32)

33. Non-nucleoside
inhibitors of HCV RdRp

34. Non-Nucleoside Inhibitors (NNI)
Thumb I
Thumb II
Palm I
Palm II
A
B
C
D

35. Palm-1 inhibitors
Dasabuvir (Abbvie)
Non-Nucleoside Inhibitors (NNI)
Genotype 1 only
Low barrier to resistance

36. NNI Resistance
(Lontok et al., Hepatology 2015;62:1623-32)

37. III
HCV Resistance in
IFN-Free Regimens

38. BaselinePrevalence of RAVs

39. S282T RAV in RdRp (NS5B)
• No S282T (0/8598) was detected in any pretreatment patient
samples (deep sequencing, cutoff = 1%)
Europe
n=1,767
Asia
n=954
Oceania
n=1,094
Africa
n=17
North America
n=4,766
(Gane et al., AASLD 2015)

40. Prevalence of NS5A RAVs (G1a)
Deep sequencing, 1% cutoff
(Zeuzem et al., AASLD 2015)
Europe
25% (130/517)
Asia Pacific
15% (4/27)
Oceania
27% (89/328)
North America
26% (686/2638)
USA
Canada
Puerto Rico
Belgium
Switzerland
Czech Republic
Germany
Spain
France
United Kingdom
Italy
Netherlands
Poland
China
India
Japan
Korea
Russia
Taiwan
Australia
New Zealand

41. Prevalence of NS5A RAVs (G1a)
Akin to population sequencing, 15% cutoff
(Zeuzem et al., AASLD 2015)
Europe
14%
Asia Pacific
7%
Oceania
16%
North America
13%
USA
Canada
Puerto Rico
Belgium
Switzerland
Czech Republic
Germany
Spain
France
United Kingdom
Italy
Netherlands
Poland
China
India
Japan
Korea
Russia
Taiwan
Australia
New Zealand

42. Prevalence of NS5A RAVs
by Region (G1a)
Prevalence(%)
4.9%
3.7%
2.1%
4.8%
4.1%
4.4%
1.2%
4.4%
7.6%
5.8%
2.4%
7.6%
0
5
10
15
20
Q30H/R L31M Y93H Multiple RAVs
North America Europe Oceania
N=2638 N=2638 N=2638 N=2638N=517 N=517 N=517 N=517N=328 N=328 N=328 N=328
Asia Pacific not included due to
low number of patients with GT1a
(n=27)
NB: Q30H/R, L31M and Y93H RAVs confer >100 fold shift to LDV.
(Zeuzem et al., AASLD 2015)

43. Prevalence of NS5A RAVs (G1b)
Deep sequencing, 1% cutoff
(Zeuzem et al., AASLD 2015)
Europe
25% (105/416)
Asia Pacific
26% (150/570)
Oceania
26% (26/99)
North America
23% (184/802)
USA
Canada
Puerto Rico
Belgium
Switzerland
Czech Republic
Germany
Spain
France
United Kingdom
Italy
Netherlands
Poland
China
India
Japan
Korea
Russia
Taiwan
Australia
New Zealand

44. Prevalence of NS5A RAVs (G1b)
Akin to population sequencing, 15% cutoff
(Zeuzem et al., AASLD 2015)
Europe
17%
Asia Pacific
20%
Oceania
19%
North America
16%
USA
Canada
Puerto Rico
Belgium
Switzerland
Czech Republic
Germany
Spain
France
United Kingdom
Italy
Netherlands
Poland
China
India
Japan
Korea
Russia
Taiwan
Australia
New Zealand

45. Prevalence of NS5A RAVs
by Region (G1b)
(Zeuzem et al., AASLD 2015)
8.5%
14.6%
1.1%
9.4%
16.1%
1.2%
13.1%
14.1%
1.0%
3.9%
18.2%
2.1%
0
2
4
6
8
10
12
14
16
18
20
L31M/I/V Y93H Multiple RAVs
North America Europe Oceania Asia Pacific
NB: L31M/I/V confer 3-43 fold shift to LDV; Y93H confers >100 fold shift to LDV
N=802 N=416 N=99 N=570 N=802 N=416 N=99 N=570 N=802 N=416 N=/99 N=570
Prevalence(%)

46. Influence of Baseline RAVs on
IFN-Free Treatment Outcomes

47. Sofosbuvir + Simeprevir ± RBV
COSMOS Cohort 2- Gen 1, Naive and NR, F3-F4
(Lawitz et al., Lancet 2014;384:1756-65)
93%
SVR12rate(%)
0
10
20
30
40
50
60
70
80
90
100
SOF+SIM+RBVAll patients SOF+SIM+RBVSOF+SIM
N=80 N=27 N=14 N=24
12 weeks 24 weeks
93%93%
SOF+SIM
N=15
100%
94%

48. Sofosbuvir + Simeprevir ± RBV
COSMOS Pooled cohorts 1 & 2- Subtype 1a, Q80K
88%
SVR12rate(%)
0
10
20
30
40
50
60
70
80
90
100
SOF+SIM+RBVAll patients SOF+SIM+RBVSOF+SIM
N=80 N=27 N=14 N=24
12 weeks 24 weeks
83%
89%
SOF+SIM
N=15
100%
88%
(Lawitz et al., Lancet 2014;384:1756-65)

49. 92%
Any
RAV
N=318
97%
No
RAVs
N=1629
SVR According to Baseline NS5A RAVs
ION-1, -2, -3: Sofosbuvir + Ledipasvir ± RBV
SVR12rate(%)
0
10
20
30
40
50
60
70
80
90
100
(Sarrazin et al., manuscript submitted)

50. 92%
Any
RAV
N=318
97%
No
RAVs
N=1629
SVR According to Baseline NS5A RAVs
ION-1, -2, -3: Sofosbuvir + Ledipasvir ± RBV
97%
SVR12rate(%)
0
10
20
30
40
50
60
70
80
90
100
K24R
86%
M28T
94%
Q30H
82%
Q30R
91%
L31M
92%
Y93H
N=68 N=28 N=80 N=89N=29 N=48
(Sarrazin et al., manuscript submitted)

51. SVR to Sofosbuvir/Ledipasvir According
to NS5A RAVs (513 cirrhotic patients)
(Sarrazin et al., EASL 2015)

52. SVR According to Baseline NS5A RAVs
(Zeuzem et al., AASLD 2015)
SVR12(%)
Without cirrhosis With cirrhosis
Rx-Naive Rx-Exp’dRx-Naive Rx-Exp’d
*HCV RNA < 6 million IU/mL.
8 Wks* 12 Wks 12 Wks 12 Wks 12 Wks +
RBV
12 Wks +
RBV
24 Wks24 Wks
No RAVsWith RAVs
100
80
60
40
20
0
98 99 99 99
90
99 96 96
100 100
88
100
89
96
87
100
N=32 N=108 N=189 N=509 N=88 N=300 N=27 N=68 N=10 N=27 N=9 N=19 N=66 N=214 N=15 N=84

53. Grazoprevir + Elbasvir
C-EDGE TN– Phase III, Rx-naïve, Gt 1, w/o cirrhosis, 12 weeks
89%
SVR12rate(%)
0
10
20
30
40
50
60
70
80
90
100
Bs
NS3
RAVs
97%
N=86 N=65 N=25 N=104
100%
96%
N=19 N=135
99%
58%
N=18 N=112
100%
94%
No Bs
NS3
RAVs
Bs
NS3
RAVs
No Bs
NS3
RAVs
Bs
NS5A
RAVs
No Bs
NS5A
RAVs
Bs
NS5A
RAVs
No Bs
NS5A
RAVs
GT 1a GT 1b GT 1a GT 1b
(Zeuzem et al., Ann Intern Med 2015;163:1-13)

54. Grazoprevir + Elbasvir + RBV
Integrated analysis of patients with G1a from Phase II and III trials,
TN or TE, w/o cirrhosis, 12 or 16-18 weeks
(Thompson et al., AASLD 2015)
No NS5A RAVs (73%)
N=38
100%
NS5A RAVs (27%)
N=14
100%
SVR12rate(%)
0
10
20
30
40
50
60
70
80
90
100
No NS5A RAVs (66%)
N=289
98%
NS5A RAVs (34%)
N=150
91%
Rx-naïve and PR relapsers
12 weeks, no RBV
PR nonresponders
16-18 weeks, + RBV

55. Influence of Baseline NS5A RAVs
Grazoprevir-Elbasvir, 12 (no RBV) or 16-18 weeks (+RBV), prior NR
(Jacobson et al., AASLD 2015)
Pts with RAVs by population sequencingPts without RAVs
GT1a, Previous nonresponse GT1b, Previous nonresponse
100% 100%
N=51
EBR/GZR 12 wks EBR/GZR + RBV
16/18 wks
EBR/GZR 12 wks EBR/GZR + RBV
16/18 wks
SVR12(%)
100
80
60
40
20
0
EBR
RAVs
NS5A class
RAVs
EBR
RAVs
NS5A class
RAVs
EBR
RAVs
NS5A class
RAVs
EBR
RAVs
NS5A class
RAVs
97%
29%
N=61 N=7
96%
64%
N=54 N=14
100% 100%
N=44 N=8
100%
67%
N=28 N=6
100%
83%
N=22 N=12
100% 100%
N=26 N=12
100% 100%
N=22 N=16N=1

56. Summary
• The detection, by means of population
sequencing, of HCV RAVs at baseline has an
impact on the rate of SVR with IFN-free
regimens
• Parameters that matter include:
• The genotype/subtype
• The treatment regimen received (drugs, duration, RBV)
• The proportion of RAVs in the viral quasispecies at baseline
• The level of resistance conferred by the substitutions

57. Selection of RAVs in Patients
who Fail to Achieve an SVR

58. 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
(Data on file; unpublished)

59. The Henri Mondor Experience
161 patients treated
in IFN-free regimens
in clinical trials
13 did not achieve
an SVR
8 relapses 3 breakthroughs 2 intolerant
(Data on file; unpublished)

60. The Henri Mondor Experience
Region Observed substitutions
NS3 protease
V36M, D103N, R155K
I71V
R155K
Q80K, R155K
A147V, D168V
A4M, V36M, R155K
P146S, Q80L
NS5A
Y93C
L31V, Y93H
NS5B RNA polymerase
L433F
Q65R, S189N/S
S47E
(Data on file; unpublished)

61. Selection of RAVs in Patients
who Failed after LDV (no SOF)
16%
(12/76)
84%
(64/76)
Before
LDV Treatment
99%
(72/73)
1%
At Virologic Failure With LDV
Treatment
Patients without NS5A RAVs
Patients with NS5A RAVs
Patients who failed after a
ledipasvir-containing treatment
(without sofosbuvir)
(Dvory-Sobol et al., EASL 2015)

62. Treatment Failures in SAPPHIRE-2
Genotype 1, Rx-experienced, 3D ± Ribavirin
Virologic failure in 7/297 patients (2.4%)
(Zeuzem et al., N Engl J Med 2014;370:1604-1614)

63. Summary
• In most (if not all) patients who fail to achieve
an SVR on an IFN-free regimen, viruses that
are resistant to one or more of the DAAs
administered are present as the dominant
species at the time of relapse

64. Post-treatment RAV Persistence
in Patients who Fail to Achieve an SVR

65. Replacement of PI-Resistant
Viruses by Wild-Type Viruses
(Lenz et al., J Hepatol 2015;62:1008-14)

66. Persistence of RAVs in Patients
who Failed after LDV (no SOF)
98% 100% 98% 100%
95%
82%
0
20
40
60
80
100
VF
Parent
Study
Baseline FU-12 FU-24 FU-48 FU-96
PatientsWithNS5ARAVs(%)
Registry Study
N=63 N=58 N=43 N=45 N=55 N=58
(Dvory-Sobol et al., EASL 2015)

67. Persistence of RAVs in Patients
who Relapsed after 3D
67/2510 patients with genotype 1a
and virologic failure after 3D
(Krishnan et al., EASL 2015)
NS5A RAVs
(ombitasvir)
NS5B RAVs
(dasabuvir)
NS3 RAVs
(paritaprevir)
24 wks post-treatment
48 wks post-treatment
PrevalenceofRAVs(%)
0
10
20
30
40
50
60
70
80
90
100
N=70 N=44 N=35N=51N=67 N=57
46%
9%
97% 96%
75%
57%

68. Summary
• After IFN-free treatment failure, HCV variants
resistant to protease inhibitors progressively
disappear by population sequencing,
replaced by wild-type virus
• In contrast, viruses resistant to NS5A
inhibitors and to NNIs persist for years,
maybe for ever, as dominant species

69. IV
Retreatment Options

70. Retreatment of Patients who
Failed an IFN-Free Regimen
• Recommendations are based on indirect evidence and
subject to change when more data become available
• The retreatment regimen should contain
• Sofosbuvir because of the high barrier to resistance
• 1 or 2 other DAA(s), if possible with no cross-resistance
with the DAA(s) already administered
• Ribavirin
• Treatment duration should be 12 or 24 weeks (24
weeks recommended in F3-F4)
(European Association for the Study of the Liver. J Hepatol 2015;63:199-236)

71. SVR12rate(%)
0
10
20
30
40
50
60
70
80
90
100
87%
Total
80%
Genotype 1a
100%
Genotype 1b
Retreatment of NS5A Inhibitor Failures
with Sofosbuvir + Simeprevir 12 wks
100%
Genotype 4
(Hézode et al., AASLD 2015)
N=15 N=10 N=3 N=2

72. SVR12rate(%)
0
10
20
30
40
50
60
70
80
90
100
92%
1a, no cirrhosis
12 wks + RBV
100%
1a, cirrhosis
24 wks + RBV
100%
1b
12 wks, no RBV
Retreatment of DAA Failures with
Sofosbuvir + 3D 12 wk (QUARTZ-I)
(Poordad et al., AASLD 2015)
N=15 N=6 N=2

73. 100%
Overall
N=23
Retreatment with Sofosbuvir + Grazoprevir/Elbasvir + RBV
C-SWIFT Retreatment- G1, short (4-6-8 wk) SOF-GZR-EBR treatment failures
(Lawitz et al., AASLD 2015)
100%
SVR12rate(%)
0
10
20
30
40
50
60
70
80
90
100
No
100%
Yes
100%
4 wk
100%
6-8 wk
100%
No
100%
Yes
N=18 N=8 N=5 N=18N=5 N=15
Cirrhosis Prior Rx
duration
Baseline
NS5A RAVs

74. V
Utility of HCV
Resistance Testing

75. Utility of HCV Resistance Testing
• Lack of standardization of the assays
• Best timing for testing
• Prior to therapy
• At the time of relapse
• At the time of retreatment
• Guidelines for interpretation and
retreatment decisions

76. VI
Avoiding Treatment Failures

77. European Association for the Study of the Liver. J Hepatol 2015;63:199-236

78. Characteristics that Inform
Treatment Option Selection
Treatment
selection
Prior
treatment
experience
HCV
genotype/
subtype
Severity of
liver
disease
Patient co-
morbidities
PK profile
of
treatment
Drug-drug
interactions
(European Association for the Study of the Liver. J Hepatol 2015;63:199-236)

79. SVR12rate(%)
0
10
20
30
40
50
60
70
80
90
100
90%
12 wk
No RBV
96%
12 wk
+RBV
98%
24 wk
No RBV
Sofosbuvir/Ledipasvir ± RBV
Rx-experienced patients with compensated cirrhosis
100%
24 wk
+RBV
(Reddy et al., Hepatology 2015;62:79-86)

80. SVR to Sofosbuvir/Ledipasvir According
to NS5A RAVs (513 cirrhotic patients)
88% 94% 85% 100%95% 97% 100% 100%
0
20
40
60
80
100
LDV/SOF LDV/SOF+RBV LDV/SOF LDV/SOF+RBV
SVR12(%)
N=26 N=91 N=34 N=169 N=20 N=113 N=14 N=44
12 Weeks 12 Weeks 24 Weeks 24 Weeks
Pre-existing NS5A RAVs No pre-existing NS5A RAVs
(Sarrazin et al., EASL 2015)

81. Ombitasvir/Paritaprevir/r + Dasabuvir ± RBV
TURQUOISE II-Phase III, Genotype 1, Rx-naïve and -experienced,
Compensated cirrhosis (CPA), 12-24 weeks
(Poordad et al., N Engl J Med 2014;370:1973-82)
92%
93% 100%
80%
93% 100% 100% 93%
0
20
40
60
80
100
Naive Prior
relapse
Prior partial
response
Prior null
response
N=64 N=15N=56 N=13 N=11 N=50N=10 N=42
SVR12(%)
12 weeks
24 weeks
Genotype 1a

82. Conclusions
• Optimizing first-line treatment is required
to avoid DAA-based treatment failures
associated with HCV resistance
• Retreatment options exist, based on the
combination of sofosbuvir plus 2 or 3
other DAAs, eventually with ribavirin

83. Follow me on Twitter
@JMPawlotsky