Baseline and treatment failure resistance analysis in HCV GT1 patients treated with first and second

generation direct acting antiviralsYael Gozlan1, Roy Moscona1, Avia Rakovsky1, Rachel Shirazi1, Arig Kabat1, Ella

Veitzman2, Tania Berdichevski2, Peretz Weiss2, Oranit Cohen-Ezra2, Yoav Luria3, Ina Gapnowitch3, Oren Shibolet4 , Ehud Zigmond4 , Eli Zuckerman5, Marius

Brown6, Michal Cohen-Naftali6, Amir Shlomai6, Michal Carmiel7, Rawi Hazan8, Ella Mendelson1, Orna Mor1, Ziv Ben Ari2

1Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat- Gan, 2Liver Disease Center, Sheba Medical Center, Ramat- Gan, 3Liver unit, Shaare Zedek Medical Center, Jerusalem, 4Department of Gastroenterology, Tel-Aviv Medical Center, 5Liver Unit, Carmel Medical Center, Haifa, 6Liver Institute, Beilinson Medical Center, Petah- Tikva, 7Liver unit, Western

Galilee Hospita, Nahariya, 8Liver unit, Haemek Medical Center

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Background

Treatment with the 2nd generation direct acting antivirals, DAAs, (e.g. Paritaprevirr/ombitasvir/dasabuvir, grazoprevir/elbasvir, simeprevir/sofosbuvir, daclatasvir/sofosbuvir, ledipasvir/sofosbuvir with or w/o ribavirin) usually results in ≥90% SVR in HCV patients

Pre-existing resistance associated substitutions (RASs) may influence SVR rates depending on DAA combination, treatment duration, virus genotype and subtype and clinical parameters like e.g. cirrhosis

Also, RASs emerging during therapy could abrogate subsequent therapies

RASs-

resistance associated

substitutions

RAVs-

resistance associated

variants

RAPs-

resistance associated

polymorphisms

RAMs-

resistance associated mutations

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Aims

RASs of GT1 at baseline• Assess the frequency of NS3 and NS5A RASs at baseline, before any DAA

treatment

• Evaluate the impact of baseline RASs on 2nd generation DAA treatment outcome.

RASs of GT1 at treatment failure• Failures of 1st generation DAAs

• Failures of 2nd generation DAAs

Lontok et al., Hepatology 2015

Clinically relevant RASs to protease inhibitors

No info on grazoprevir

1a, red; 1b, blue

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Clinically relevant RASs to NS5A inhibitors

Lontok et al., Hepatology 2015

1a, red; 1b, blue

No info on elbasvir

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Methods

• NS3 and NS5A RASs from GT1 naïve (n=248) , BOC or TLV treatment failures (n=44) and 2nd generation treatment failures (n=14) were assessed by population sequencing. Interpretation was done with Geno2Pheno.

• RASs conferring >2-fold change in drug susceptibility and that were found to be clinically relevant (based on Lontok et al 2015) were considered for baseline analysis

NS3:

NS5A:

• RASs conferring >2 for change in susceptibility of the administered drugs were considered at failure (only treatment related RASs were considered)

V36 T54 V55 Y56 Q80 S122 I132 R155 A156 D168 V170

M28 Q30 L31 H58 Y93

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Study Cohort(samples collected between August 2012 and May 2016)

CharacteristicsNumber

of Patients

Sequences from patients

NS3 NS5A

Baseline, before DAA treatment 248 241 174SVR12 and baseline clinically relevant RASs 144 144 144DAA failures (n=58)

BOC or TLV failures 44 44PTVr/OMV/DSV failures 7 7 7GRV/EBV failures 1 1 1SOF/LDV or SOF/SMV failures 4 4 3DCV/ASV, SMV failures 2 2 1

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Baseline clinically relevant NS3 RASs (n=241)

4%

0%3%

1% 1% 1% 1% 1%

34%

5% 5%3%

17%

2%

5%

2%0%

0%

5%

10%

15%

20%

25%

30%

35%

40%

All RASs 36 54 55 80 122 155 168 170

Pre

vale

nce

NS3 RASs

1b 1a

V36M (1a)

T54S (1a)

T54S (1b)

V55A (1b)

Q80K (1a)

Q80K (1b)

S122G (1b)

R155K (1a)

R155K (1b)

D168E (1a)

V170A (1b)

BOC 3 2 3 3 5 7.9

TLV 7

SMV 11 8 0.5 86 32

ASV 2 1 3 1 21 58

PRV 2 37 14

VNV >1000

Mean Fold-Change in Resistance Compared to Wild-Type Replicon

34% GT1a patients (20/59 ) with NS3 RASs

4% GT1b patients (7/182 ) with NS3 RASs

Lontok et al., Hepatology 2015

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Baseline clinically relevant NS5A RASs (n=174)

17%

1%

7%

10%

15%

11%

4%

0%0%

5%

10%

15%

20%

All RASs 28 31 93

Pre

vale

nce

NS5A RASs

1b 1a

M28V (1a) L31M (1a) L31M (1b) Y93H (1b)

DCV 105 3 12

LDV 554

OBV 58 77

Mean Fold-Change in Resistance Compared to Wild-Type Replicon

17% GT1b patients (25/147 ) with NS5A RASs

15% GT1a patients (4/27) with NS5A RASs

Lontok et al., Hepatology 2015

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Effect of treatment relevant baseline RASs on SVR12 rates in GT1 carriers (n=144)

N=12 N=102 N=3 N=4 N=3 N=17

14% (20/144) of patients had treatment relevant baseline RASs

12/12

Patients not reaching SVR12 (n=3) PTVr/OMV/DSV SMV/SOF;LDV/SOF;DCV/SOF;DCV GRV/EBV

Virological failure 0 0 1Discontinuation due to reasons other than virological failure 2 1 0

95%100% 100%

80%

98% 98%

80%

100%

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

Total PTVr/OMV/DSV SMV/SOF;LDV/SOF;DCV/SOF;DCV GRV/EBV

SVR

12

rat

e (

%)

With baseline RASs Without RASs

NS3:Q80K (SMV)NS5A:31M (DCV,LDV)

NS3:155K,168E,122G (PTV)NS5A:31M,93H (OMV)

NS5A:31M,93H (EBV)

12/12 102/104 3/3 4/5 4/5 15/15

The only virological failure (GRV/EBV) had NS5A 31M RAS at baseline and 31M+93H RASs at failure

19/20 121/124

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1st generation DAA failures: Boceprevir and telaprevir failures (n=44)

34%

5% 5% 3%

17%

2%5%

2% 0%

50%

25% 25%

0%

10%

20%

30%

40%

50%

60%

RA

Ss

freq

uen

cy

DAA naïve

BOC/TLV failure

4%

0%

3%

1% 1% 1% 1% 1%

8%

3%

5%

0%

1%

2%

3%

4%

5%

6%

7%

8%

RA

Ss

freq

uen

cy

DAA naïve

BOC/TLV failure

GT1a GT1b

- Double mutations were calculated as 2 separate mutations. Therefore the frequency of RASs is not identical to the rate of patients with RASs.- One of the GT1a PIs failures was erroneously reported and treated as 1b

25% GT1a patients PI failures (1/4) with RASs 8% GT1b patients PI failures (3/40) with RASs

EC50 fold change 3 2 3 3-11 0.5 5->1000 96-373 8 60 3 3 3-11 0.5 3->1000 159-3100 8

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2nd generation DAAs failures (n=14)Serial

numberPatient number Age Sex

Place of birth

Genotype Treatment NS3 RAS

NS5A RAS Explanation >=2 RASs

1 243907 60.8 F Romania 1b

PTVr/OMV/DSV+/-RBV

168V 93H RAS explain failure 1

2 243943 43.7 M FSU 1b 168V 93H RAS explain failure 1

3 244590 52 M FSU 1b 80R 58S,93H RAS explain failure 1

4 245089 67.6 F FSU 1b none none no RAS

5 245641 45.11 F unknown 1b 168V 58S,93H RAS explain failure 1

6 245285 49.6 F FSU 1b none 93H RAS explain failure 0

1 244182 36.6 M Latvia 1bSOF/LDV

54S,55I 93H RAS explain failure 1

2 244345 71 M Israel 1b none 93H RAS explain failure 0

1 243169 53.1 F FSU 1b SOF/SMV 168V noneRAS possibly due to previous TLV treatment failure 0

2 243990 74.6 F Romania 1b NONE no RAS

1 241895 63.1 M Romania 1b GRV/EBV none 31M,93H RAS explain failure 1

2 244306 64.3 F FSU 1b SMV none nd no RAS

3 245113 44.11 M Israel 1a DCV/ASV 36M, 80K 31M RAS explain failure 1

4 243951 unknown F unknown 1b DCV nd none no RAS

64% of 2nd generation DAA failures had RASs

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Frequency of RASs increases in failures of 2nd generation DAAs

42 3

3

12 1

7

BASELINE PI FAILURES 2ND GENERATION FAILURES

SAM

PLE

S W

ITH

RA

S

# of samples with >=2 RASs # of samples with 1 RASNS3 NS5A

D168V (x90-x3100 fold change) 31M, 93H (x4000 fold change)

V36M (x2-x80 fold change) P58S, Y93H (x1600-x5000 fold change)

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Conclusions

• Sequencing NS3 or NS5A or NS5B genes is recommended for accurate G1 subtyping, especially in cases of previous subtyping by HCV 5’UTR or in unresolved G1 subtypes

• Systematic resistance testing prior to 2nd generation DAA therapy is currently not mandatory (except Q80K prior to SMV). However, NS5A baseline RASs may reduce SVR12 rates.

• 1st generation NS3 therapy failures are associated with the emergence of specific NS3 RASs (e.g. 168V) that affect subsequent NS3 based treatment

• RASs are highly frequent in patients failing 2nd generation DAAs and the rate of >2 RASs per virus increases significantly

• Therefore- NS3 and NS5A resistance testing at treatment failure is highly recommended to guide best DAA combinations and duration. Also, storing baseline samples for future use (e.g. for comparing baseline to treatment failure RASs) is recommended.

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ThanksHIV and Hepatitis Reference Center, Central virology Laboratory, MOH:

Marina Wax,

Zehava Yossefi,

Daniela Ram

Liver Disease Center, Sheba Medical Center:

Avishag Hassid,

Keren Tsaraf,

Shani Dor-hai,

Marina Balkarey

Virology laboratories:

Yonat Shemer (Infectious Diseases Institute, Ben-Gurion University of the Negev),

Zipi Kra-Oz (Virology Laboratory, Rambam Medical Center),

Licita Schreiber (Maccabi HealthCare Services),

Pninit Shaked (Microbiology and immunology laboratory, Carmel Medical Center),

Merav Strauss (Microbiology laboratory, Haemek Medical Center)

Liver unit, Rabin Medical Center:

Yael Harif

HIV and Hepatitis Reference Center