1. 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
2. HCV Resistance
• IFN--ribavirintreatmentfailure
• HCV resistance to DAAs
• TreatmentFailurewith the Triple
Combination of Peg-IFN, Ribavirin and
Telaprevir or Boceprevir
• HCV Resistance in All-oral,
IFN-freeregimens
13. Summary
• HCV resistance to IFN- antiviral effect
exists
• Its molecular mechanisms are unknown
and probably complex
• It accounts for only a small part of IFN-
-based treatment failures
14. Genome-Wide Association
Studies (GWAS)
A population with > 3 billion nucleotides GWAS chip Bioinformatics to SNP association
distinct clinical > 10 million SNPs > 500,000 ‘tag’ SNPs process data and
phenotypes > 90% coverage of associate
common genetic genotype with
variation phenotype
15. SNP and SVR in the IDEAL Trial
IL28B
(Ge et al, Nature, 2009;461:399-401)
16. SVR in the IDEAL Trial According
to SNP rs12979860 (genotype 1)
100%
Sustained virological response (%)
80%
60%
40%
20%
0%
TT CT CC
N=186 N=559 N=392
(Ge et al., Nature 2009;461:399-401)
21. VK on High-Dose Peg-IFN
According to IL28BGenotype
Weeks of therapy
0 4 8 12 16 20 24
0
HCV RNA reduction (Log10 IU/mL)
-1 NS
P=0.045
-2
P=0.021
TT
-3
-4 CT
P=0.004
-5
-6 P=0.0005
(Chevaliez S, et al., Gastroenterology 2011;141:119-127)
22. SVR Predictors
Odds Ratio 95% CI p-value
rs12979860 CC vs non-CC 5.2 4.1 6.7 <0.0001
HCV RNA ≤ 600,000 IU/mL 3.1 2.3 4.1 <0.0001
Caucasian vs African American 2.8 2.0 4.0 <0.0001
Hispanic vs African American 2.1 1.3 3.6 0.004
METAVIR score ≤F2 2.7 1.8 4.0 <0.0001
Fasting blood sugar < 5.6 mmol/L 1.7 1.3 2.2 <0.0001
(Thompson et al., Gastroenterology 2010;139:1181-9)
23. IL28B vs RVR to Predict SVR
Sensitivity (%) Specificity (%) PPV (%) NPV (%)
CC vs non CC 56 (52-60) 79 (76-82) 69 (65-74) 68 (65-71)
Caucasian
RVR vs non
RVR 25 (21-29) 96 (94-97) 84 (77-89) 59 (56-62)
(Thompson et al., Gastroenterology 2010;139:1181-9)
24. Improvement in SVR Prediction
by Combining IL28B and IP-10
N=272
89%
79%
100%
64%
50% 48% 24%
CC
20%
0% CT
< 600 pg/ml > 600 pg/ml TT
serum IP-10
(Darling et al.,Hepatology 2010;53:14-22)
25. Summary
• In patients infected with HCV genotype 1,
the rs12979860 genotype:
• Is strongly associated with the SVR
• Explains 60% of the ethnic influence on SVR
• Influences HCV kinetics on therapy
• Is probably a marker of patient cell “resistance“
to the effect of IFN- through mechanisms that
remain to be elucidated
49. Nucleoside/Nucleotide Analogue
Inhibitors of HCV RdRp
Median/mean log
Drug Phase Dose Duration HCV RNA
levelreduction
Sofosbuvir (Gilead) III 400 mg qd 3 days -3.7
Mericitabine (Roche) II 1500 mg bid 14 days -2.7
IDX184 (Idenix) II 100 mg qd 3 days -0.7
VX-135 (ALS-2200, Vertex) II 200 mg qd 7 days -4.5
50. HCV Resistance to 2’-C-Methyl
Nucleoside Inhibitors
2’C-Me-ATP in the catalytic site
(Migliaccio et al., J Biol Chem 2003;278:49164-70)
51. Non-NucleosideInhibitors of
HCV RdRp (NNIs)
Median/mean log
Drug Phase Dose Duration
HCV RNA reduction
Tegobuvir (Gilead) II 40 mg bid 8 days -1.4
Setrobuvir (Roche) II 800 mg bid 3 days -2.9
BI207127 (BI) II 800 mg q8h 3 days -3.1
ABT-333 (Abbott) II 600 mg bid 2 days -1.5
ABT-072 (Abbott) II 600 mg qd 3 days -1.6
VX-222 (Vertex) II 750 mg bid 3 days -3.7
BMS-791325 (BMS) II ? ? ?
56. Antiviral Efficacy of
Cyclophylin Inhibitors
Median/meanl
Drug Phase Dose Duration og HCV RNA
reduction
Alisporivir (DEBIO-025) III 1200 mg bid 14 days -3.6
SCY-465 II 900 mg qd 15 days -2.2
57. Alisporivir Resistance in vitro
HCV EMCV
neo NS4
5’UTR NS3 NS5A NS5B 3’UTR
IRES IRES A
A B
36 213 250 342 356 447
Domain I Domain II Domain III
A241P R262Q R318W D320E
A241P + A241P +
A241P + A241P + R262Q + R318W + R262Q + R262Q +
R262Q R318W R318W D320E R318W R318W +
D320E
Fold-
change 1.02 1.58 1.37 3.67 1.72 3.89
vs wt
(Coelmont et al., EASL 2009)
60. MathematicalModeling
• “…all possible single and double mutants are
predicted to begenerated multiple times eachday“
• “…all viable single and double mutants that confer
drugresistancepreexist and maycompetewith the
wild-type virus duringtherapy“
• “[triple mutants] canbeselected by sequential
mutations when single or double mutants
replicate“
(Rong et al., Sci Transl Med 2010;2:30ra32)
62. Summary
• Viruseswithaminoacid substitutions
known to confer resistance to HCV
proteaseinhibitorspre-exist, generally
(but not always) as minor viral
populations, in 100% of HCV-infected
patients
65. DAA Resistance
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
-1
-2
-3
-4
-5
Study Time
(Pawlotsky JM. Hepatology 2011;53:1742-51)
66. DAA Resistance
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
-2
-3
-4
-5
Study Time
(Pawlotsky JM. Hepatology 2011;53:1742-51)
67. DAA Resistance
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
-2
Resistant HCV
-3
-4
-5
Study Time
(Pawlotsky JM. Hepatology 2011;53:1742-51)
68. Summary
• The administration of a proteaseinhibitoralone
selects pre-existingresistant viral variant
populations,
whichgrowexponentiallyuntiltheybecome
dominant if treatmentiscontinued
70. TreatmentFailures on Triple
Combinationwith a DAA
• Due to an inadequateresponseto Peg-
IFN and ribavirin
• Results in
uncontrolledoutgrowthofresistantHCV
variantsselected by the
proteaseinhibitor
(Pawlotsky JM. Hepatology 2011;53:1742-51)
71. SVR According to Lead-in
(SPRINT-2, non-black)
100
90 82% 82%
% of patients with SVR
80
70
60 <1 log HCV RNA
50 decrease
39%
40 ≥1 log HCV RNA
29% decrease
30
20
10
0
BOC/RGT BOC/PR48
(Poordad et al., N Engl J Med 2011;364:1185-206)
72. SVR According to Lead-in
(RESPOND-2, non-black)
100
90
79%
% of patients with SVR
80 73%
70
60 <1 log HCV RNA
50 decrease
40 33% 34% ≥1 log HCV RNA
30 decrease
20
10
0
BOC/RGT BOC/PR48
(Bacon et al., N Engl J Med 2011;364:1207-17)
74. DAA Resistance
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
-2
Resistant HCV
-3
-4
-5
Study Time
(Pawlotsky JM. Hepatology 2011;53:1742-51)
75. Median HCV RNA Change
from Baseline (Log10 IU/mL)
-5
-4
-3
-2
-1
0
1
Study Time
Triple Combo Failure
76. Triple Combo Failure
Potent IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
-1
-2
-3
-4
-5
Study Time
77. Triple Combo Failure
Potent IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
-2
-3
-4
-5
Study Time
78. Triple Combo Failure
Potent IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
-2
Resistant HCV
-3
-4
-5
Study Time
79. Triple Combo Failure
Potent IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
-2
-3
-4
CURED Resistant HCV
-5
Study Time
80. Triple Combo Failure
Moderate IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
-1
-2
-3
-4
-5
Study Time
81. Triple Combo Failure
Moderate IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
-2
-3
-4
-5
Study Time
82. Triple Combo Failure
Moderate IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
-2
Resistant HCV
-3
-4
-5
Study Time
83. Triple Combo Failure
Moderate IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
CURED -1
-2
or Resistant HCV
-3
RELAPSE with RESISTANT VIRUS -4
-5
Study Time
84. Triple Combo Failure
Modest or null IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
-1
-2
-3
-4
-5
Study Time
85. Triple Combo Failure
Modest or null IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
-2
-3
-4
-5
Study Time
86. Triple Combo Failure
Modest or null IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
-2
Resistant HCV
-3
-4
-5
Study Time
87. Triple Combo Failure
Modest or null IFN-ribavirin effect
1
from Baseline (Log10 IU/mL)
Median HCV RNA Change
0
Wild-type, sensitive HCV
-1
RELAPSE or BREAKTHROUGH
Resistant HCV -2
with RESISTANT VIRUS -3
-4
-5
Study Time
88. Summary
• Treatment failure (i.e. the failure to eradicate
HCV infection) with the triple combination of
Peg-IFN, ribavirin and a protease inhibitor is
due to an inadequate response to IFN and
ribavirin
• The outgrowth of viral populations resistant
to the protease inhibitor is the consequence
of treatment failure, not its cause
90. Boceprevir Resistance in
Patients withTreatmentFailure
300
250
32
Dominant virus at 200
Patients, n
the time of failure
150 117
No sequence available
100
Dominant resistant virus 15
Dominant wild-type virus 38
50 97
43
0
1a 1b
Total n=342*
(Zeuzem S., et al., EASL 2011)
91. Boceprevir Resistance in
Patients withTreatmentFailure
Frequency and distribution of resistance
substitutionsaccording to the subtype
(% substitutions detected by subtype)
100
90 Subtype 1a
80 Subtype 1b
70 68
61
Variants, %
60
50
42
40 37
32
30 24 26
19
20
10 6 8 5 5 75 5
33 3 3 3 43 3
03 03 10 0 0 0 10 10 0 0
0
(Zeuzem S., et al., EASL 2011)
92. Treatment Failure-PROVE2
H28Q+R155K
100%
H28Q+R155K+S54T+Y52C
% of variants in the quasispecies
80% H28Q+R155K+S54T+Y52C+V36M+H5
7L+P96H
60%
8
40%
HCV RNA(Log10 IU/mL)
6
20%
0% 4
0
2
29
0
57
Days of therapy
85
Viral populations
*PyroLink®
(Chevaliez S., et al., EASL 2011)
93. Summary
• In Phase III trials, approximatelyhalf of the
patients whofailed to eradicate HCV
wereinfected by dominant viral populations
thatwereresistant to telaprevir or
boceprevirat the time of viral
escape, depending on the ability of therapy
to clearwild-type, sensitive virusesat the
time of failure
95. Probability of Telaprevir-
Resistant Variant Detection
1.0
0.9 Median time to wild-type by population
0.8 sequencing =7 months (95% CI: 5-8)
0.7
Probability
0.6
median
0.5
0.4
0.3
0.2
0.1
0.0
0 2 4 6 8 10 12 14 16 18
Time after treatment failure (months)
(Sullivan et al., EASL 2011)
96. Probability of Telaprevir-
Resistant Variant Detection
1.0
0.9
0.8 1a
0.7
Probability
0.6
median
0.5
0.4
1b
0.3
0.2
0.1
0.0
0 2 4 6 8 10 12 14 16 18
Time after failure (months)
(Sullivan et al., EASL 2011)
97. Treatment Failure-PROVE2
100% H28Q+R155K
% of variants in the quasispecies
H28Q+R155K+S54T+Y52C
% of mutations in the whole quasispecies
80% H28Q+R155K+S54T+Y52C+V36M+H57
L+P96H
V36M+R155K+H57L
60% R155K
40% 8
HCV RNA (Log10 IU/mL)
HCV RNA (Log10 IU/mL)
20%
6
0%
0
4
29
57
85
2
182
595
0
Days of treatment
Days of therapy
686
*PyroLink® 903 Viral populations
(Chevaliez S., et al., EASL 2011)
98. Post-FailureFollow-up
(Boceprevir)
Genotype 1a Genotype 1b
100% 100%
% resistant viral variants detected
90% 90% All
% Variant viral résistantdétecté
80% 80% T54S
T54A
70% 70%
60% 60%
50% 50%
40% 40%
All
30% 30%
T54S
20% R155K 20%
10% V36M 10%
0% 0%
0 0.5 1 1.5 2 0 0.5 1 1.5 2
Time after treatment failure (years) Time after treatment failure (years)
(Barnard et al., CROI 2011)
99. Summary
• The decrease of telaprevir- or boceprevir-resistant
viral populations starts immediately after
administration of the protease inhibitor is stopped
• This decrease is slow and leads, after a few months
to years, to their replacement by a wild-type (i.e.
protease inhibitor-sensitive) dominant
population, which coexists with minor populations
made of resistant viruses, i.e. a situation similar to
the pretherapeutic one
102. Practical Recommendations
• Prior to therapy:
• All patients shouldbeconsidered as harboringminor viral
populations that are resistant to telaprevir and boceprevir
• There is no indication for resistancetestingatbaseline
103. Practical Recommendations
• In case of treatmentfailure:
• Proteaseinhibitor-resistant viral populations have been
enriched in every patient treatedwithtelaprevir or
boceprevirwhodid not clear infection
• There is no indication for resistancetestingduring and
aftertherapy, as the resultwill have no impact on
treatmentdecisions
• Resistance testingisrequired in clinical trials and global
surveillance studies (research setting)
