Hepatitis C: Retreatment and resistance

Will Irving

University of Nottingham

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Viral resistance

RAV Resistance associated variant

RAS Resistance associated substitution

Viral mutations which make the virus less susceptible to treatment

Pre-existing RAS polymorphisms

Treatment Emergent RAS selected by treatment

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Resistance: Principles

• Monotherapy will result in selection of mutations which enhance replication in presence of drug – Darwinian selection

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Resistance: data interpretation

• Resistance data are difficult to present and difficult to interpret (!)

• RAS may be specific to • A whole drug class

• Individual specific drugs

• Genotype specific

• Sub-genotype specific

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Lontok et al. Hepatology 2015; 62: 1623-1632

Gt 1a

Gt 1b

Gt 3

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Resistance: Principles

• Monotherapy will result in selection of mutations which enhance replication in presence of drug – Darwinian selection

• Resistance is NOT all or none – hence “fold-resistance”

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AASLD HCV Guidance – Resistance Primer https://www.hcvguidelines.org/evaluate/resistance ESCMID eLibrary

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Presentation title - edit in Header and Footer

Clinically relevant NS5A resistance-associatedsubstitutions (RASs)

Sorbo et al Drug Resist Update 37: 17 2018 ESCMID eLibrary

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Resistance testing: How?

• Sequencing of relevant sections of the genome

• Standard PCR-based – Sanger – sequencing• Also known as Population sequencing

• Technically straightforward, may labs capable

• Will only detect populations present at >20%

• Next generation sequencing (aka deep seq)• Can detect minority species down to 1%

• Technically very exacting, and requires considerable bioinformatics expertise to interpret the data

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UK NS5a RAS prevalence data (Dr D Bradshaw, Public Health England)• 635 pre-treatment samples NS5a sequenced

Number %

≥ 1 NS5A RAS

Overall 104 16.4

Treatment-naive* 74 14.6

Treatment-experienced‡ 22 25.9

Prior PEG/RBV 5 13.2

DAAs: Non-NS5A inhibitor containing 3 17.6

DAAs: NS5A inhibitor containing 11 50.0

Regimen unknown 3 37.5

≥ 2 NS5A RASs 17 2.7 ESCMID eLibrary

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Prevalence of HCV NS5A RASs at positions 28, 30, 31, 58 or 93

11 Surveillance of resistance to HCV NS5A inhibitors

0

1

2

3

4

5

6

7

8

9

10

M28 Q30 L31 H58 Y93

% o

f sa

mp

les

con

tain

ing

mu

tati

on

Treatment history not known

Prior DAA: NS5Ai

Prior DAA: non NS5Ai

Prior PEG/RBV

Treatment-naïve

V (47)T (6)

AV, AT (1)

R (18)H (10)L (1)

H (10)C, N (4)

S (3)FHL (1)

M (10) D (3)ADP, DN, R (1)

Brackets denote total number ESCMID eLibrary

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Resistance testing: How?

• Sequencing identifies possible RAS but doesn’t give any information about their effect on drug sensitivity

• In vitro susceptibility testing• Difficult to do

• Introduce specific mutations into replicon system and test effect of different drug concentrations on viral replication

• Correlation between in vitro data and in vivo significance is not perfect!

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Resistance testing: Why?

• Knowledge of RAS may influence clinical management:

(1) Alter duration of therapy

(2) Add ribavirin

(3) Choose particular DAA regimen (for retreatment, see later)

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SVR12 rates for HCV genotype 1a−infected patients with or without NS5A RASs across different elbasvir and grazoprevir

(Zepatier) regimens

14 Surveillance of resistance to HCV NS5A inhibitors

98

70

99

61

100

56

100 100

0

20

40

60

80

100

441/450 39/56 132/133 11/18 56/56 5/9 67/67 6/6

All 12W no RBV All 12W + RBV 16 or 18W no RBV 16 or 18W + RBV

Sust

ain

ed

vir

olo

gic

resp

on

se (

%)

Any RAS

No RAS

Komatsu et al Gastroenterology 152: 586 2017 ESCMID eLibrary

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ZEPATIER

• Data sheet for Genotype 1a• “ZEPATIER for 16 weeks should be considered in patients

with …… specific NS5A polymorphisms causing at least a 5-fold reduction in activity of Elbasvir to minimise the risk of treatment failure

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Resistance testing: When?

• Universal testing of all patients pre-treatment• This is the model for HIV

• BUT – SVR rates approach 100% for most patients on most regimens

• There are NO recommendations for this

• Selective• Only test those patients where knowledge of the results may influence clinical

management

• But which patients are those?

• Learned Society Recommendations

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AASLD September 2017:https://www.hcvguidelines.org/evaluate/resistance

Geno 3 patients; Sof/Dac or Sof/Vel; TE or cirrhosis; if Y93H present add weight-based ribavirin

TE = Treatment experiencedTN = Treatment naive

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EASL Recommendations April 2018:Article in press, Journal of Hepatology

Access to reliable HCV resistance testing is limited and there is no consensus on the techniques, interpretation and reporting of these tests.

Testing for HCV resistance prior to treatment is not recommended

Applies also to treatment-experienced patients – defined as patients who were previously treated with PEG/RBV; PEG/RBV/SOF; SOF/RBV

? Of value in patients who have failed DAA therapy? ESCMID eLibrary

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Patients who have failed DAA-containing therapy: Re-treatment• Does it work?

• Is resistance testing helpful?

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Retreatment: Does it work?

Bourliere M et al. NEJM June 2017;376: 2134-46

Wyles D et al. Hepatology Feb 2018; 67: 514-523

Poordad F et al. Hepatology April 2018;76: 1253-60 ESCMID eLibrary

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Polaris-1 and Polaris-4 trials NEJM June 2017;376: 2134-46

• Polaris-1 - Patients TE with NS5a inhibitors n = 264• Pts treated with Sof/Vel/Vox 12 weeks

• Polaris 4 – Patients TE with NS3/NS5b inhibitors n = 333• Pts treated with Sof/Vel/Vox 12 weeks OR Sof/Vel 12 weeks

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Polaris 1

• TE with NS5a inhibitors

• Overall SVR 96%

• Geno 3 SVR 95%

• No cirrhosis 99%

• Cirrhosis 93%

• 83% had NS3/NS5a RAS SVR 97%

• 17% had no RAS SVR 98%

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Polaris-4

• TE with NS3/NS5b inhibitors

• Overall SVR:

• S/V/V 98% versus S/V 90%

• S/V/V – geno not important

• S/V/V cirrhosis not important

• NS3/NS5a RAS had no effect

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Surveyor-II Part 3 studyWyles D et al. Hepatology Feb 2018; 67: 514-523

• Genotype 3 patients , previous Rx = PEG/RBV or Sof/RBV +/- PEG

• i.e. previous NS3 or NS5a treated patients were excluded

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7 of 8 patients with baseline Y93H achieved SVR ESCMID eLibrary

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Magellan-1 Part 2 studyPoordad F et al. Hepatology April 2018;76: 1253-60

• Pts with g1, 4, 5, 6

• Only 14% had cirrhosis

• Past treatment with NS5a and or NS3 inhibitor (didn’t include any Zepatier or Sof-Vel failures)

• Retreatment with Gle-Pib for 12 or 16 weeks

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Magellan-1 Part 2 study: Results• Gle-Pib 12 weeks n = 44 SVR 89%

• Gle-Pib 16 weeks n = 47 SVR 91%

• Baseline RAS SVR• None or NS3 only n=32 100%

• NS5a alone n=47 12 weeks 83% 16 weeks 96%

• NS3 and NS5a n=9 12 weeks 80% (4/5) 16 weeks 25% (1/4)

• Conclusion• 16 weeks Gle-Pib achieved high rates of SVR in g1 patients who had

previously failed NS5a and/or NS3 inhibitor DAA regimens

EASL 2018 recommendations: “The MAGELLAN-1 trial showed that the combination of Gle and Pib does not have a high enough barrier-to-resistance to achieve optimal SVR rates in patients previously exposed to an NS5A inhibitor.” ESCMID eLibrary

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Real-World data:Halfon et al J Hep 2018; 68: 595-76 centres France

24 patients, 20 with NS5a RAS, 96% SVR

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Halfon et al J Hep 2018; 68: 595-7

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EASL recommendations for retreatment (Apr 18)

Patients without cirrhosis or with compensated cirrhosis who failed after a DAA (PI and/or NS5A inhibitor)-containing regimen should be retreated with Sof/Vel/Vox for 12 weeks ….

HCV resistance testing prior to retreatment in patients who failed after any of the DAA-containing treatment regimens is useful to guide retreatment ……

If there are predictors of lower response (advanced liver disease, multiple courses of DAA-based treatment, complex NS5A RAS profile), …. (use) the combination of sofosbuvir plus the fixed-dose combination of glecaprevir and pibrentasvir for 12 weeks

In very difficult-to-cure patients (patients with NS5A RASs who failed twice to achieve SVR after aregimen including a PI and/or an NS5A inhibitor), the combination of Sof/Vel/Vox, or the triple combination of Sof + Gle-Pib can be administered for 12 weeks with weight-based RBV and/or treatmentduration can be prolonged to 16 to 24 weeks ESCMID eLibrary

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Factors influencing response to DAAs

• Genotype

• Cirrhosis

• Prior treatment experience

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How diverse is HCV?

Smith et al, Hepatology 2014

• 7 distinct genotypes

(1-7) - differ by >30%

• 84 subtypes (e.g. 1a, 1b etc) – differ by >15%

• quasispecies – differ by <15%

gt1

gt6

gt2

gt7

gt3

gt5

gt4

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Numbers of HCV genotypes and subtypes

Genotype No. of subtypesUnassigned

isolates

gt1 13 7

gt2 15 8

gt3 8 1

gt4 18 10

gt5 1 0

gt6 28 16

gt7 1 0

Total 84 42

There are also 9 recombinant HCV genomes (6x gt2/gt1; 1x gt2/gt5; 2x gt2/gt6) ESCMID eLibrary

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The gap in HCV genomic data in LMICs

Niebel et al., Lancet Gastro and Hepatol 2017

NS3 sequences

NS5A sequences

NS5B sequences

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447

AH D-Ia D-Ib LCS-I

LCS-II

D-II D-III

1 21310129 250 342 356

Posn of NS5A RAS

HCV GtSubjects/

ReferenceDAA Rx

1o Rx

Outcome

2o Rx

OutcomeTime 28 29 30 31 32 58 93

Gt1a Gt1a Ref M P Q L P H Y

Gt1b Gt1b Ref L P R L P P Y

Gt1l

P1SOF/LDV/

RbnResp-Rel Resp-Rel

Pre-Rx M P R M P P Y

Post-Rx M P R M P P Y

P2 SOF/DCV Resp-Rel Resp-RelPre-Rx M P Q M P P Y

Post-Rx NA

P3SOF/LDV/

RbnResp-Rel Resp-Rel

Pre-Rx M P R M P P Y

Post-Rx M P R M P P Y

NHE England Early Access Programme: Decompensated patients. Pre- and post-Rx sequences for gt1l patients

NS5A DAAbinding

Posn. 28 29 30 31 32 33 34 35

GT1a M P Q L P G I P

58

H

93

Y

Filipe et al., J Hepatol 2017 ESCMID eLibrary

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Posn of NS5A RAS

HCV GtSubjects/

ReferenceDAA Rx

1o Rx

Outcome

2o Rx

OutcomeTime 28 29 30 31 32 58 93

Gt1a Gt1a Ref M P Q L P H Y

Gt1b Gt1b Ref L P R L P P Y

Gt1l

P1SOF/LDV/

RbnResp-Rel Resp-Rel

Pre-Rx M P R M P P Y

Post-Rx M P R M P P Y

P2 SOF/DCV Resp-Rel Resp-RelPre-Rx M P Q M P P Y

Post-Rx NA

P3SOF/LDV/

RbnResp-Rel Resp-Rel

Pre-Rx M P R M P P Y

Post-Rx M P R M P P Y

Pre- and post-Rx sequences for gt1l patients

Posn of NS5A RASNS5A DAA

(fold resistance)

28 29 30 31 32 LDV DCV Vel

Gt1awt M P Q L P 1 1 1

Gt1amut M P R M P >23,400 >4,452 200

Wyles et al., J Hepatol 2013 ESCMID eLibrary

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Posn of NS5A RAS

HCV GtSubjects/

ReferenceDAA Rx

1o Rx

Outcome

2o Rx

OutcomeTime 28 29 30 31 32 58 93

Gt1a Gt1a Ref M P Q L P H Y

Gt1b Gt1b Ref L P R L P P Y

Gt1l

P1SOF/LDV/

RbnResp-Rel Resp-Rel

Pre-Rx M P R M P P Y

Post-Rx M P R M P P Y

P2 SOF/DCV Resp-Rel Resp-RelPre-Rx M P Q M P P Y

Post-Rx NA

P3SOF/LDV/

RbnResp-Rel Resp-Rel

Pre-Rx M P R M P P Y

Post-Rx M P R M P P Y

Gt4a Gt4a ref V P L M P P Y

Gt4r

P4 SOF/LDV Non-RespNot

re-treated

Pre-Rx M P R M P P Y

Post-Rx M P R M P P Y

P5SOF/LDV/

RbnResp-Rel

Not

re-treated

Pre-Rx M P R L P P Y

Post-Rx M P R L P P H

Pre- and post-Rx sequences for gt1l and gt4r patients

Filipe et al., J Hepatol 2017 ESCMID eLibrary

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How variable are the DAA resistance sites in gt1l and gt4r?

NS5A 28 29 30 31 32

Gt1a (n=4983) M (96%) P (100%) Q (96%) L (99%) P (100%)

Gt1b (n=4706) L (99%) P (100%) R (92%) L (96%) P (100%)

Gt1l (n=12)M P

R (n=5)M P

Q (n=6)

T (n=1) P Q M P

Aranday-Cortes et al., unpublished ESCMID eLibrary

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How variable are the DAA resistance sites in gt1l and gt4r?

NS5A 28 29 30 31 32

Gt1a (n=4983) M (96%) P (100%) Q (96%) L (99%) P (100%)

Gt1b (n=4706) L (99%) P (100%) R (92%) L (96%) P (100%)

Gt1l (n=12)M P

R (n=5)M P

Q (n=6)

T (n=1) P Q M P

Gt4r (n=27)

n=3 M P R M P

n=4 V P R M P

n=9 M P R L P

n=8 V P R L P

n=2 M P R V P

n=1 I P R L P ESCMID eLibrary

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Genotype Frequency Percentage (100%)

1 8 12.7

1a 4 6.3

1b 6 9.5

1c 1 1.6

1e 2 3.2

1g 1 1.6

1l 3 4.8

2r 1 1.6

3a 5 7.9

3h 1 1.6

4b 2 3.2

4f 2 3.2

4g 1 1.6

4k 3 4.8

4m 1 1.6

4r 16 25.4

4v 5 7.9

5a 1 1.6

Total 63 100.0

Percentage Genotype Distribution

Genotypes 1a, 1b and 3a account for only 23/63 (37%) of samples from UK patients born in Africa

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African unassigned gt1 isolates that did not respond to DAAs

gt1agt1b

2 patients of African origin, failed DAA therapy

Leitch et al., unpublished ESCMID eLibrary

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Overall summary

• Expect 95% or greater HCV-infected patients to achieve SVR

on first treatment

• Resistance testing is indicated in some specific

circumstances (eg pre-Zepatier) - AASLD

• Resistance testing should be restricted to those patients

who have failed DAA-containing regimens - EASL

• Patients who have failed DAA regimens can be retreated

with high SVR rates

• Incomplete record of HCV diversity could influence selection

of DAAs used in certain global regions

• Rare subtypes in some ethnic groups may be problematic to

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Acknowledgements

UK NS5a resistance prevalence dataDr Dan Bradshaw Public Health EnglandDr Tamyo Mbisa

Rare subtype dataProf John McLaughlan Centre for VirusDr Carol Leitch for Research, GlasgowDr Ana Felippe University

Kazeem Adeboyejo University of Nottingham

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