1. HCV Alert: New Data on Resistance to DAAs and Implications for Therapy
Jointly provided by the Annenberg Center for Health Sciences at Eisenhower and Clinical Care Options, LLC
HCV Alert: New Data on Resistance to DAAs and Implications for Therapy
Nezam H. Afdhal, MD, FRCPI
Professor of Medicine
Harvard Medical School Beth Israel Deaconess Medical Center Boston, Massachusetts
This activity is supported by an independent educational grant from Janssen Therapeutics.
Image: pockygallery/Copyright©2014 Shutterstock Images LLC. All Rights Reserved Image: djem/Copyright©2014 Shutterstock Images LLC. All Rights Reserved

2. Virologic Barriers to Resistance
Genetic barrier
Number and type of nucleotide changes required for a virus to acquire resistance to an antiviral regimen[1]
Viral fitness
Relative capacity of a viral variant to replicate in a given environment
Fitness of Polymerase Inhibitor Mutants[2,3] 1
.75
% Fitness .5
.25
Wild Type
L419M
M423T
I482L
L419M/M423T
S282T
1. Rong L, et al. Sci Transl Med. 2010;2:30ra Le Pogam S et al. J Virol ;80: Le Pogam S, et al. J Infect Dis. 2010;202:

3. Resistant Variants Are Present Before and Can Be Selected During Treatment
HCV is a mixture of related but distinct populations of virions in each pt[1]
Most resistant variants are unfit and may be undetectable prior to therapy[2,3]
Antiviral therapy eliminates sensitive variants
Resistant variants expand
Sensitive virus
Resistant virus
Antiviral therapy
HCV, hepatitis C virus.
1. Pawlotsky JM. Clin Liver Dis. 2003;7: Kuntzen T, et al. Hepatology. 2008;48: Bartels DJ, et al. J Infect Dis. 2008;198: Image reproduced and adapted with permission from Forum for Collaborative HIV Research.

4. HCV NS3/4A Protease Resistance
Q80
R155
D168
F43
A156
Lenz O, et al. Antimicrob Agents Chemother. 2010;54: Reproduced with permission from American Society for Microbiology. doi: /AAC Copyright © 2010, American Society for Microbiology. All Rights Reserved.

5. No Cirrhosis (OPTIMIST-1[1]) Cirrhosis (OPTIMIST-2[2])
Impact of Treatment Exp, Q80K Depends on Cirrhosis (12 Wks’ SMV + SOF in GT1)
No Cirrhosis (OPTIMIST-1[1])
Cirrhosis (OPTIMIST-2[2])
100 97 97 95 96 97
100 92 88 83 79 80 80 74 60 60
SVR12 (%) 40 40 20 20
GT, genotype; HCV, hepatitis C virus; SMV, simeprevir; SOF, sofosbuvir; SVR, sustained virologic response.
150/ 155
112/ 115
38/ 40
44/ 46
68/ 70
86/ 103
44/ 50
42/ 53
25/ 34
35/ 38
n/N =
n/N =
All pts
Naive
Exp’d
1a + Q80K
1a no Q80K
All pts
Naive
Exp’d
1a + Q80K
1a no Q80K
Treatment History
HCV GT
Treatment History
HCV GT
1. Kwo P, et al. EASL Abstract LP Lawitz E, et al. EASL Abstract LP04.

6. OPTIMIST-2: Resistance Analysis in GT1 Cirrhotics in Whom SMV + SOF Failed
Treatment-emergent NS3 mutations detected in 79% (11/14) of evaluable pts who did not achieve SVR12
Observed at position 168, R155K, or combinations
NS5B polymorphism S282T not detected at baseline or at time of treatment failure
No NS3 baseline polymorphisms observed aside from Q80K
GT, genotype; SVR, sustained virologic response.
Lawitz E, et al. EASL Abstract LP04.

7. AASLD/IDSA Guidance for Resistance Testing When Considering SMV + SOF
In pts with both genotype 1a HCV infection and compensated cirrhosis, if considering SMV + SOF, test for Q80K polymorphism
If Q80K variant is present, consider a regimen other than SMV + SOF
Applies to treatment-naive and treatment-experienced pts
Q80K testing not required for:
Pts with genotype 1b HCV infection
Pts without cirrhosis
Pts in whom you are considering other DAAs
AASLD, American Association for the Study of Liver Diseases; HCV, hepatitis C virus; IDSA, Infectious Diseases Society of America; SMV, simeprevir; SOF, sofosbuvir; Tx, treatment.
AASLD/IDSA/IAS-USA. HCV Guidance.

8. ION-2: DAAs Effective Against NS3 RAVs After Boceprevir or Telaprevir96 97
100 98 98
100
100 93 94
Treatment History 80
Failure of pegIFN/RBV 60
Failure of PI
SVR12 (%) 40 20
40/ 43
62/ 66
45/ 47
62/ 64
58/ 58
49/ 50
58/ 59
51/ 51
DAA, direct-acting antiviral; LDV, ledipasvir; pegIFN, peginterferon; PI, protease inhibitor; RAV, resistance associated variants; RBV, ribavirin; SOF, sofosbuvir; SVR, sustained virologic response.
LDV/SOF
LDV/SOF + RBV
LDV/SOF
LDV/SOF + RBV
12 Wks
24 Wks
Virologic failure: 1 breakthrough in 24-wk LDV/SOF + RBV due to nonadherence; 11 relapses (7 in 12-wk LDV/SOF, 4 in 12-wk LDV/SOF + RBV)
14% of pts had NS5A RAVs at baseline; 89% of these achieved SVR12; 71% of pts had NS3 RAVs at baseline; 98% of these achieved SVR12
Afdhal N, et al. N Engl J Med. 2014;370:

9. ION-2: NS3 RAVs After Boceprevir or Telaprevir Respond to DAAs
100 98 98
100
100 96 97 93 94
Treatment History 80
Failure of pegIFN/RBV 60
Failure of PI
SVR12 (%) 40 20
40/ 43
62/ 66
45/ 47
62/ 64
58/ 58
49/ 50
58/ 59
51/ 51
DAA, direct-acting antiviral; LDV, ledipasvir; pegIFN, peginterferon; PI, protease inhibitor; RAV, resistance associated variants; RBV, ribavirin; SOF, sofosbuvir; SVR, sustained virologic response.
Virologic failure: 1 breakthrough in 24-wk LDV/SOF + RBV due to nonadherence; 11 relapses (7 in 12-wk LDV/SOF, 4 in 12-wk LDV/SOF + RBV)
14% of pts had NS5A RAVs at baseline; 89% of these achieved SVR12; 71% of pts had NS3 RAVs at baseline; 98% of these achieved SVR12
LDV/SOF
LDV/SOF + RBV
LDV/SOF
LDV/SOF + RBV
12 Wks
24 Wks
Afdhal N, et al. N Engl J Med. 2014;370:

10. Resistance Analysis of Select NS5A Inhibitors in Genotype 1 HCV
Fold-Change in EC50
Genotype 1a
Genotype 1b
Position
M28T
Q30R
L31M/V
Y93H/N
L31V
FDA approved
Daclatasvir[1,3]
> 100 x
> 1000 x
< 10 x
< 100 x
Ledipasvir[1]
20 x
> 1000 x/?
Ombitasvir[2]
< 3 x
> 10,000 x
> 100 x
3 to 100 x
< 3 x
HCV, hepatitis C virus, EC50, half maximal effective concentration.
1. Cheng G, et al. EASL Abstract Krishnan P, et al. Antimicrob Agents Chemother. 2015;59: Yang G, et al. EASL Abstract Ng T, et al. CROI Abstract 639.

11. Treatment Experienced
Impact of Duration of LDV/SOF on SVR12 in Pts With Baseline NS5A Resistance
NS5A RAVS with < 100 x resistance
NS5A RAVS with > 100 x resistance
No NS5A RAVs
Treatment Naive
100 95
100 96 97
100 92
100 83 96 80 60
SVR12 (%) 40
12/ 12
24/ 29
184/ 193
27/ 27
44/ 46
362/ 373
8/ 8
24/ 25
174/ 183 20
n/N =
8 Wks
12 Wks
24 Wks
Treatment Experienced
100 95
100
100 99
LDV, ledipasvir; RAV, resistance associated variants; SOF, sofosbuvir; SVR, sustained virologic response.
100 65 80 60
SVR12 (%) 40
5/ 5
11/ 17
110/ 116
7/ 7
6/ 6
95/ 96 20
n/N =
12 Wks
24 Wks
Sarrazin C. AASLD Abstract 1926.

12. Durability of Treatment-Emergent NS5A RAVs After Virologic Failure
Study of pts not achieving SVR after receiving LDV without SOF
NS5A RAVs persisted in majority of pts for 96 wks
100
100 98 98
100 95 86 80 60
Pts With NS5A RAVs (%) 40
FU, follow-up; LDV, ledipasvir; RAV, resistance associated variant; SOF, sofosbuvir; SVR, sustained virologic response; VF, virologic failure. 20
62/ 63
58/ 58
42/ 43
45/ 45
52/ 55
50/ 58
n/N = VF
Baseline
FU-12
FU-24
FU-48
FU-96
Registry Study
Dvory-Sobol H, et al. EASL Abstract O059.

13. Pooled Analysis: RAV Persistence After Failure of PTV/RTV-, OMV-, DSV-Based Tx
Follow-up Wk Follow-up Wk 48
PTV-Containing Regimens
OMV-Containing Regimens
DSV-Containing Regimens
100
100
100 97 97 96
100 93 89 90 80 77 80 80 77 75 60 60 60 57
RAVs (%)
RAVs (%)
RAVs (%) 46 40 38 40 40 29
DSV, dasabuvir; OMV, ombitasvir; PTV, paritaprevir; RAV, resistance associated variant; RTV, ritonavir; Tx, treatment. 20 20 20 9
n/N =
31/ 67
21/ 55 4
10/ 13
n/N =
68/ 70
49/ 51
32/ 33
21/ 21
38/ 41
25/ 28
n/N =
33/ 44
20/ 35
27/ 30
17/ 22
5/57
2/53
2/7
Any
D168
R155K
Any
M28V/T
Q30E/K/R
Any
S556G
NS3/4A Position
NS5A Position
NS5B Position
Krishnan P. EASL Abstract O057.

14. AVIATOR: No Impact of Baseline RAVs in GT1a Pts Treated With OMV/PTV/RTV + DSV
Treatment naive pts or null responders to previous pegIFN/RBV
All differences in SVR24 with vs without baseline RAVs were nonsignificant
With RAV
Without RAV
100
100
100
100
100
100 94 92 92 92 93 88 92 91 91 86 80 80 80 80 60 60 60 50
SVR24 (%)
SVR24 (%)
SVR24 (%) 40 40 40
DSV, dasabuvir; OMV, ombitasvir; pegIFN, peginterferon; PTV, paritaprevir; RAV, resistance associated variant; RBV, ribavirin; RTV, ritonavir. 20 20 20
n/N =
78/ 89
122/ 130
200/ 218
n/N =
12/ 14
192/ 209
3/ 3
201/ 220
1/ 1
203/ 222
4/ 5
200/ 218
n/N =
7/ 7
220/ 239
1/ 2
226/ 244
0/1
Q80K
D168
M28V/T
Q30R
L31V
Y93C/N/H
S556G
C316Y
NS3 RAVs
NS5A RAVs
NS5B RAVs
Krishnan P, et al. Antimicrob Agents Chemother. 2015;59:

15. GT1 HCV with previous SOF failure (29% cirrhotic)*
LDV/SOF + RBV in GT 1 HCV Pts With Previous Failure on Sofosbuvir Regimens
Phase II trial
12 Wks
SVR12, %
98†
GT1 HCV with previous SOF failure (29% cirrhotic)*
(N = 51)
LDV/SOF + RBV
*25 pts (49%) were previously treated with SOF + pegIFN/RBV, 21 (41%) with SOF ± RBV, 5 (10%) with SOF placebo plus pegIFN/RBV or GS-0938 monotherapy, 1 (2%) with SOF monotherapy.
†1 pt who relapsed found to have GT3a HCV infection and enrolled in error.
GT, genotype; HCV, hepatitis C virus; LDV, ledipasvir; pegIFN, peginterferon; RBV, ribavirin; SOF, sofosbuvir; SVR, sustained virologic response.
Wyles DL, et al. Hepatology. 2015;61:

16. 24 Wks of LDV/SOF Retreatment After Failure of 8-12 Wks of LDV/SOF-Based Tx
GT1 HCV–infected pts with and without cirrhosis previously treated with 8 or 12 wks of LDV/SOF ± RBV or LDV/SOF + GS-966
100
100 80 80 74 71 68 60 60 46
SVR12 (%) 40
BL, baseline; LDV, ledipasvir; RAV, resistance associated variant; SOF; sofosbuvir; SVR, sustained virologic response; Tx, treatment. 20
29/ 41
15/ 22
14/ 19
24/ 30
5/ 11
11/ 11
18/ 30
n/N =
All No
Yes
8 Wks
12 Wks No
Yes
Cirrhosis
Previous Tx
Duration
BL NS5A RAVs
Lawitz E, et al. EASL Abstract O005.

17. 24 Wks of LDV/SOF After Failure of LDV/ SOF-Based Tx: Effect of Baseline RAVs
NS5B variants emerged during retreatment in 33% of pts (4/12) with virologic failure
S282T: n = 2; L159F: n = 1; S282T + L159F: n = 1
SVR12 by Baseline NS5A RAVs, n/N (%)
LDV/SOF for 24 Wks
Number of RAVs
11/11 (100) 1
11/16 (69)
≥ 2
7/14 (50)
Single NS5A RAV
Q30R or M28T
5/5 (100)
L31M
4/5 (80)
Y93H/N
2/6 (33)
LDV, ledipasvir; RAV, resistance associated variant; SOF; sofosbuvir; SVR, sustained virologic response; Tx, treatment.
Lawitz E, et al. EASL Abstract O005.

18. GT1 Pts With NS5A Failure: Who Needs Resistance Testing?
If previous failure of any NS5A inhibitors (including DCV + SOF, LDV/SOF, OMV/PTV/RTV + DSV) and minimal liver disease, deferral preferred pending further data
If cirrhosis or other need for urgent treatment, test for NS3 and NS5A RAVs
Applies to genotype 1a and 1b HCV infection
NS3 and NS5A testing not required for:
Previous failure of NS3/4A PIs (including simeprevir, boceprevir, telaprevir)
Previous failure of NS5B inhibitors (sofosbuvir)
Tx-naive pts (unless considering SMV + SOF in cirrhotic GT1a)
AASLD, American Association for the Study of Liver Diseases; DCV, daclatasvir; DSV, dasabuvir; GT, genotype; IDSA, Infectious Diseases Society of America; LDV, ledipasvir; OMV, ombitasvir; PTV, paritaprevir; RAV, resistance associated variant; RBV, ribavirin; RTV, ritonavir; SMV, simeprevir; SOF, sofosbuvir; Tx, treatment.
AASLD/IDSA/IAS-USA. HCV Guidance.

19. Selecting Treatment Based on Resistance Testing Results
If genotype 1a or 1b HCV infection and previous failure with any NS5A inhibitors and cirrhotic or other need for urgent treatment:
RAV Testing Result
Retreatment Regimen
Duration
No NS5A RAVs
Ledipasvir/sofosbuvir + ribavirin
24 wks
NS5A but no NS3 RAVs
Simeprevir + sofosbuvir + ribavirin
NS5A and NS3 RAVs
Retreatment in a clinical trial setting
HCV, hepatitis C virus; RAV, resistance associated variant.
AASLD/IDSA/IAS-USA. HCV Guidance.

20. Is Ribavirin Required for Pts With Cirrhosis?
Integrated analysis of > 500 pts with cirrhosis treated with LDV/SOF ± RBV
Treatment-experienced pts had previously received HCV PI
Although NS5A resistance not measured, RBV overcomes shorter treatment duration in patients with HCV cirrhosis and prior treatment failure
SVR12, %
Total
(N = 513)
Treatment Naive
(n = 161)
Treatment Experienced
(n = 352)
Overall 96 98 95
12 wks ± RBV 97 94
24 wks ± RBV 99
Without RBV
With RBV
12 wks without RBV 92 90
12 wks with RBV
24 wks without RBV
24 wks with RBV
100
HCV, hepatitis C virus; LDV, ledipasvir; PI, protease inhibitor; RAV, resistance associated variant; RBV, ribavirin; SOF, sofosbuvir; SVR, sustained virologic response.
Reddy KR, et al. Hepatology. 2015;62:79-86.

21. Is Ribavirin Required for Pts With Cirrhosis and NS5A RAVs?
Integrated analysis of > 500 pts with cirrhosis treated with LDV/SOF ± RBV
Treatment experienced patients had previously received HCV PI
SVR12, % (n/N)18
With NS5A RAVs
Without NS5A RAVs
Overall
91 (86/94)
98 (407/417)
12 wks without RBV
88 (23/26)
95 (86/91)
12 wks with RBV
94 (32/34)
97 (164/169)
24 wks without RBV
85 (17/20)
100 (113/113)
24 wks with RBV
100 (14/14)
100 (44/44)
HCV, hepatitis C virus; LDV, ledipasvir; PI, protease inhibitor; RAV, resistance associated variant; RBV, ribavirin; SOF, sofosbuvir; SVR, sustained virologic response.
Reddy KR, et al. Hepatology. 2015;62:79-86.

22. Personal Recommendations for Resistance in GT3 and GT4 HCV Infection
Genotype 3
Treatment failures on daclatasvir should be tested for NS5A RAVs
BOSON: Adding pegIFN to SOF/RBV appears to help overcome virologic failure due to resistance in GT3[1]
Improved SVR12 vs SOF/RBV alone in both treatment-naive and treatment-experienced pts, with or without cirrhosis
Genotype 4
Resistance testing should be performed if considering retreatment after LDV/SOF failure
Use SMV/SOF/RBV for NS5A RAVs
GT, genotype; HCV, hepatitis C virus; pegIFN, peginterferon; RAV, resistance associated variant; RBV, ribavirin; SMV, simeprevir; SOF, sofosbuvir; SVR, sustained virologic response.
1. Foster GR, et al. EASL Abstract LO5.

23. Summary
Baseline RAVs (especially NS5A) are present in treatment-naive pts
Treatment-emergent RAVs (including multidrug-resistant RAVs) seen in treatment failure and in all DAA classes and rarely with SOF
NS3 RAVs have low replication efficacy and disappear over 9-18 mos
If considering SMV + SOF: In treatment-naive and treatment-experienced pts with both genotype 1a HCV infection and compensated cirrhosis, ensure no Q80K
NS5A treatment-emergent RAVs persistent and a clinical challenge
If failure with any NS5A inhibitors (including DCV + SOF, LDV/SOF, OMV/PTV/RTV + DSV), and treatment is urgent, test for NS3 and NS5A RAVs
Use SMV + SOF + RBV if NS5A but no NS3 RAVs
Use LDV/SOF + RBV if no NS5A RAVs
Treat in clinical trial if both NS5A and NS3 RAVs present
Resistance testing may be of benefit in treatment failures
DAA, direct-acting antiviral; DCV, daclatasvir; DSV, dasabuvir; HCV, hepatitis C virus; LDV, ledipasvir; OMV, ombitasvir; PTV, paritaprevir; RAV, resistance associated variant; RTV, ritonavir; SMV, simeprevir; SOF, sofosbuvir.