virological assessment of patients candidate to...
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![Page 1: Virological assessment of patients candidate to DAAregist2.virology-education.com/2015/13EU/03_Svicher.pdf(log 1w 4w 5w 6w 1 2 3 4 5 6 7 LLOQ (12 IU/ml) HCV-RNA IU/ml) Non Responder](https://reader031.vdocuments.us/reader031/viewer/2022011913/5fb21455d16f761b4c194a6f/html5/thumbnails/1.jpg)
Virological assessment of patients candidate to DAA
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• Italian male patient • Diagnosis of chronic HCV infection in 1994 • Genotype 1b defined in 1998 • Non-responder to IFN+RBV
• He developed follicular lymphoma
Patients’ characteristics
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Day 0 Jan 2014
1w 4w 5w 6w
1
2
3
4
5
6
7
LLOQ (12 IU/ml)
HC
V- R
NA
(log
IU/m
l)
Asunaprevir + Daclatasvir + RBV (compassionate use)
Non Responder to SOC
HCV genotype: 1b (performed in 1998) Sex: M Follicular Lymphoma
ALT = 337U/L
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Chamaya et al., Hepatology 2012
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1w 4w 5w 6w
1
2
3
4
5
6
7
LLOQ (12 IU/ml)
HC
V- R
NA
(log
IU/m
l)
Non Responder to SOC
HCV genotype: 1b (performed in 1998) Sex: M Follicular Lymphoma
Day 0 Jan 2014
Asunaprevir + Daclatasvir + RBV (compassionate use)
ALT = 337U/L
![Page 6: Virological assessment of patients candidate to DAAregist2.virology-education.com/2015/13EU/03_Svicher.pdf(log 1w 4w 5w 6w 1 2 3 4 5 6 7 LLOQ (12 IU/ml) HCV-RNA IU/ml) Non Responder](https://reader031.vdocuments.us/reader031/viewer/2022011913/5fb21455d16f761b4c194a6f/html5/thumbnails/6.jpg)
1w 4w 5w 6w
1
2
3
4
5
6
7
LLOQ (12 IU/ml)
HC
V- R
NA
(log
IU/m
l)
Non Responder to SOC
HCV genotype: 1b (performed in 1998) Sex: M Follicular Lymphoma
Day 0 Jan 2014
Asunaprevir + Daclatasvir + RBV (compassionate use)
ALT = 337U/L
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1w 4w 5w 6w
1
2
3
4
5
6
7
LLOQ (12 IU/ml)
HC
V- R
NA
(log
IU/m
l)
Non Responder to SOC
HCV genotype: 1b (performed in 1998) Sex: M Follicular Lymphoma
Day 0 Jan 2014
Asunaprevir + Daclatasvir + RBV (compassionate use)
ALT = 337U/L
![Page 8: Virological assessment of patients candidate to DAAregist2.virology-education.com/2015/13EU/03_Svicher.pdf(log 1w 4w 5w 6w 1 2 3 4 5 6 7 LLOQ (12 IU/ml) HCV-RNA IU/ml) Non Responder](https://reader031.vdocuments.us/reader031/viewer/2022011913/5fb21455d16f761b4c194a6f/html5/thumbnails/8.jpg)
Day 0 Jan 2014
1w 4w 5w 6w
1
2
3
4
5
6
7
LLOQ (12 IU/ml)
HC
V- R
NA
(log
IU/m
l)
Asunaprevir + Daclatasvir + RBV (for compassionate use)
Non Responder to SOC
HCV genotype: 1b (performed in 1998) Sex: M Follicular Lymphoma
GRT after 5 weeks of therapy A genotypic resistance test was performed in our laboratory…
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• Sequencing of NS3 and NS5a for: - genotype re-assessment by phylogenetic analysis - drug resistance detection
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By phylogenetic analysis, the sample was classified as genotype 4 subtype d (instead of genotype 1B)
Clade 4d
This result was afterwards confirmed by Abbott RealTime-HCV Genotype II
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Day 0 Jan 2014
1w 4w 5w 6w
1
2
3
4
5
6
7
LLOQ (12 IU/ml)
HC
V- R
NA
(log
IU/m
l)
Asunaprevir + Daclatasvir + RBV (for compassionate use)
GRT after 5 weeks of therapy NS3 Resistance Mutations: Q41Q/R, D168V NS5A Resistance Mutation: L28V, M31M/V, Y93H/Y
GRT at Baseline NS3 Resistance Mutations: none NS5A Resistance Mutation: none
Detection of drug resistance mutations in both NS3 and NS5a at week 5 of therapy, not present at baseline
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Protease Inhibitor Resistance
HCV DRUG, Forum for Collaborative HIV Research, April 2014
paritaprevir/r
Boceprevir
Telaprevir
Simeprevir
Faldaprevir
Asunaprevir
Paritaprevir
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HCV DRUG, Forum for Collaborative HIV Research, April 2014
NS5a Inhibitor Resistance Daclatasvir
Ledipasvir
Ombitasvir
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High world-wide prevalence of NS5A RAVs in NS5a inhibitor naive patients
NS5A population-sequencing analysis was performed in > 3000 patients across 14 countries.
The circulation of NS5A RAVs in some European Countries was estimated with a prevalence ranging from 7% to 17% in GT-1a and from 9% to 13% in GT-1b.
Svarovskaia E.S., EASL 2015
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NS5A RAVs change from one type to another over time and appear to be much more persistent
Among 43 GT-1a patients analyzed 48 weeks after failure to 3D +/- RBV: • Most still presented NS5A RAVs (100% in
GT-1a patients conpleting treatment as recommended by guidelines)
Krishnan P et al., EASL 2015
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The issue of HCV genotyping…..
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Consequences of HCV variability at population level: HCV genotypes
hivforum.org
31%–33% nucleotide difference among the 7 known HCV genotypes and 20%–25% among the nearly 67 HCV subtypes (Smith et al., 2014).
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Genotype 1 is by far the most frequent genotype in chronically infected patients worldwide as well as in Europe
Esteban JI et al J Hepatol 2008;48:148-162
3a
1b
1b
1b
2
1a
1a 3a
2
2 1b
1b
1b 1b
1b
1b
1b 1b
1a 3a
1a 3a
1a 3a
1a 3a
1a 3a
1a 3a
1a 3a
4 4
4
1a
2
4 3a
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Treatment Failure =
Failure to Cure HCV infection =
There remains hepatocytes in the liver that are infected with wt and/or resistant HCV viruses when treatment is
stopped
A correct determination of HCV-genotype is mandatory prior to treatment initiation
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Treatment recommendations for HCV-infected patients with chronic hepatitis C and compensated cirrhosis (including naïve and previous Peg/RBV failures)
EASL Recommendations on Treatment of Hepatitis C 2015, J Hepatol 2015
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Treatment recommendations for HCV-infected patients with chronic hepatitis C without cirrhosis
(including naïve and previous Peg/RBV failures)
EASL Recommendations on Treatment of Hepatitis C 2015, J Hepatol 2015
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Trugene HCV Genotyping assay Direct sequencing INNO-LiPA HCV 1.0 Reverse hybridization INNO-LiPA HCV 2.0 Reverse hybridization Abbott RealTime HCV Genotype II assay Real time PCR
Target Regions: HCV 5’ UTR, CORE & NS5B region
5’ UTR 3’ UTR
• Several commercial assays are available for determining genotype/subtype
• All assays target the 5’NCR gene for genotypes 1-6, in addition, the 2 assays more used in diagnostics, Abbott and INNO-LiPA-HCV-2.0, target also the NS5B and the core gene, respectively, providing additional information also in subtyping: for genotype 1 (1a/1b, both), and for all genotypes (only Innolipa)
Several commercial assays are available for determining genotype/subtype
![Page 23: Virological assessment of patients candidate to DAAregist2.virology-education.com/2015/13EU/03_Svicher.pdf(log 1w 4w 5w 6w 1 2 3 4 5 6 7 LLOQ (12 IU/ml) HCV-RNA IU/ml) Non Responder](https://reader031.vdocuments.us/reader031/viewer/2022011913/5fb21455d16f761b4c194a6f/html5/thumbnails/23.jpg)
Trugene HCV Genotyping assay Direct sequencing INNO-LiPA HCV 1.0 Reverse hybridization INNO-LiPA HCV 2.0 Reverse hybridization Abbott RealTime HCV Genotype II assay Real time PCR
Target Regions: HCV 5’ UTR, CORE & NS5B region
5’ UTR 3’ UTR
• Several commercial assays are available for determining genotype/subtype
• All assays target the 5’NCR gene for genotypes 1-6, in addition, the 2 assays more used in diagnostics, Abbott and INNO-LiPA-HCV-2.0, target also the NS5B and the core gene, respectively, providing additional information also in subtyping: for genotype 1 (1a/1b, both), and for all genotypes (only Innolipa)
Several commercial assays are available for determining genotype/subtype
Even newest commercial-assays may miss a precise determination of HCV-genotype
in 9-10% of cases!
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HCV genotyping
NS3 sequencing + phylogenetic analysis Innolipa or Abbott assay
Analysis in 343 patients candidate to DAA therapy
Ceccherini-Silberstein F. et al, Hepatology 2015
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HCV genotyping
NS3 sequencing + phylogenetic analysis Innolipa or Abbott assay
Analysis in 343 patients candidate to DAA therapy
HCV-sequencing and commercial-assays were concordant in 91.84% of cases analysed
Ceccherini-Silberstein F. et al, Hepatology 2015
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• The sequencing approach allows to assign HCV genotype/subtype in all patients with a previous result of ‘mixed’ or ‘indeterminate’ HCV-genotype/subtype by commercial assays
We reanalyzed genotype data by phylogenetic analysis of 343 HCV-infected patients candidate to DAA-treatment, who performed a genotypic-resistance-test between 2011 and 2014. To confirm the appropriate genotype allocation, HCV-sequencing was performed by home-made protocols, specific for each genotype, on NS3-protease (95% samples), together with/in alternative to NS5A (9%) and/or NS5B (14%).
Ceccherini-Silberstein F. et al, Hepatology 2015
Patients (N) Patients (%)
Genotype/subtype confirmed 315 91.84%
Mixed/Indeterminate genotypes 8 2.33%
Genotype 1 with no subtype 6 1.75%
Discordant genotypes 4 1.17%
Genotype 1 with discordant subtype 10 2.91%
4.08%
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In addition….
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HCV genotyping by
Innolipa/Abbot (year of genotyping) NS3 sequencing Abbott
2013/2014 1a (unknown) 2c -
1b (1993) 2c 2 1b (1994) 4d -
2a/2c (2005) 1b 1b
• 4.1% (14/343) patients showed a discordant genotype or subtype according to direct-sequencing
Innolipa/Abbott Sequencing
1a=5 1g=1 1b=4
1b=4 1a=4 Indeterminate/1a =1 1g=1
Ceccherini-Silberstein F. et al, Hepatology 2015
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HCV genotyping by
Innolipa/Abbot (year of genotyping) NS3 sequencing Abbott
2013/2014 1a (unknown) 2c -
1b (1993) 2c 2 1b (1994) 4d -
2a/2c (2005) 1b 1b
Innolipa/Abbott Sequencing
1a=5 1g=1 1b=4
1b=4 1a=4 Indeterminate/1a =1 1g=1
Ceccherini-Silberstein F. et al, Hepatology 2015
This suggests the importance to test again HCV genotype when the first version of
commercial assays were used
• 4.1% (14/343) patients showed a discordant genotype or subtype according to direct-sequencing
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How to manage this patient according to the new genotype (4d) and drug resistance mutations
in both NS3 and NS5a?
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Post-treatment virological issues
Currently, there is no data to firmly support retreatment recommendations, which must be based on indirect evidence (HCV genotype, known resistance
profiles of the administered drugs …) (EASL HCV Clinical Practice Guidelines 2015).
– Clinically meaningful NS5B RAVS have been exceptionally reported with sofosbuvir, and they rapidly disappeared after treatment cessation. Thus, retreatment strategies should include sofosbuvir
– NS3 RAVs can persist for several months (also as minority species)
– NS5A RAVs may persist for YEARS (or even forever?). Check the presence (and type) of NS5A RAVs before starting a second all-oral DAA regimen including an NS5A inhibitor!
Can UDPS provide an added value in the setting of re-treatment with the same drug class?
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Day 0 Jan 2014
1w 4w 5w 6w
1
2
3
4
5
6
7
LLOQ (12 IU/ml)
HC
V- R
NA
(log
IU/m
l)
Asunaprevir + Daclatasvir + RBV (for compassionate use)
GRT after 5 weeks of therapy NS3 Resistance Mutations: Q41Q/R, D168V NS5A Resistance Mutation: L28V, M31M/V, Y93H/Y
GRT at Baseline NS3 Resistance Mutations: none NS5A Resistance Mutation: none
How to manage this patient?
This patient achieved SVR12 after SOF+PEG+RBV therapy
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• Re-treatment issue: - may UDPS provide an added value compared to population sequencing to check for the absence of drug resistance mutations?
• HCV genotype assignment: - May the sequencing approach provide an added value in the setting of mixed/indeterminate results by commercial assays? • Genotypic testing at baseline (not only for Q80K in NS3)
Points to discuss: