Virological assessment of patients candidate to DAA

Virological assessment of patients candidate to DAA

Patients characteristics Italian male patient Diagnosis of chronic HCV infection in 1994 Genotype 1b defined in 1998 Non-responder to IFN+RBV He developed follicular lymphoma

HCV genotype: 1b (performed in 1998) Sex: M Non Responder to SOC Follicular Lymphoma Asunaprevir + Daclatasvir + RBV (compassionate use) 7 6 ALT = 337U/L HCV- RNA (log IU/ml) 5 4 3 2 1 LLOQ (12 IU/ml) Day 0 Jan 2014 1w 4w 5w 6w

Chamaya et al., Hepatology 2012

HCV genotype: 1b (performed in 1998) Sex: M Non Responder to SOC Follicular Lymphoma 7 6 Asunaprevir + Daclatasvir + RBV (compassionate use) ALT = 337U/L HCV- RNA (log IU/ml) 5 4 3 2 1 LLOQ (12 IU/ml) Day 0 Jan 2014 1w 4w 5w 6w

HCV genotype: 1b (performed in 1998) Sex: M Non Responder to SOC Follicular Lymphoma 7 6 Asunaprevir + Daclatasvir + RBV (compassionate use) ALT = 337U/L HCV- RNA (log IU/ml) 5 4 3 2 1 LLOQ (12 IU/ml) Day 0 Jan 2014 1w 4w 5w 6w

HCV genotype: 1b (performed in 1998) Sex: M Non Responder to SOC Follicular Lymphoma 7 6 Asunaprevir + Daclatasvir + RBV (compassionate use) ALT = 337U/L HCV- RNA (log IU/ml) 5 4 3 2 1 LLOQ (12 IU/ml) Day 0 Jan 2014 1w 4w 5w 6w

HCV genotype: 1b (performed in 1998) Sex: M Non Responder to SOC Follicular Lymphoma 7 6 Asunaprevir + Daclatasvir + RBV (for compassionate use) GRT after 5 weeks of therapy A genotypic resistance test was performed in our laboratory HCV- RNA (log IU/ml) 5 4 3 2 1 LLOQ (12 IU/ml) Day 0 Jan 2014 1w 4w 5w 6w

Sequencing of NS3 and NS5a for: - genotype re-assessment by phylogenetic analysis - drug resistance detection

By phylogenetic analysis, the sample was classified as genotype 4 subtype d (instead of genotype 1B) This result was afterwards confirmed by Abbott RealTime-HCV Genotype II Clade 4d

Detection of drug resistance mutations in both NS3 and NS5a at week 5 of therapy, not present at baseline 7 6 Asunaprevir + Daclatasvir + RBV (for compassionate use) GRT at Baseline NS3 Resistance Mutations: none NS5A Resistance Mutation: none HCV- RNA (log IU/ml) 5 4 3 2 LLOQ (12 IU/ml) GRT after 5 weeks of therapy NS3 Resistance Mutations: Q41Q/R, D168V NS5A Resistance Mutation: L28V, M31M/V, Y93H/Y 1 Day 0 Jan 2014 1w 4w 5w 6w

HCV DRUG, Forum for Collaborative HIV Research, April 2014 Boceprevir Protease Inhibitor Resistance Telaprevir Simeprevir Faldaprevir Asunaprevir Paritaprevir paritaprevir/r

NS5a Inhibitor Resistance Daclatasvir Ledipasvir Ombitasvir HCV DRUG, Forum for Collaborative HIV Research, April 2014

High world-wide prevalence of NS5A RAVs in NS5a inhibitor naive patients 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. NS5A population-sequencing analysis was performed in > 3000 patients across 14 countries. Svarovskaia E.S., EASL 2015

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

The issue of HCV genotyping..

Consequences of HCV variability at population level: HCV genotypes 31% 33% nucleotide difference among the 7 known HCV genotypes and 20% 25% among the nearly 67 HCV subtypes (Smith et al., 2014). hivforum.org

Genotype 1 is by far the most frequent genotype in chronically infected patients worldwide as well as in Europe 3a 1a 1b 3a 4 3a 2 1a 1b 1a 1b 3a 1b 1a 3a 1a 1b 3a 1a 1b 3a 2 1a 1b 3a 1b 1a 4 1a 3a 1b 2 2 4 1b 3a 4 1a 1b Esteban JI et al J Hepatol 2008;48:148-162

A correct determination of HCV-genotype is mandatory prior to treatment initiation 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

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

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

Several commercial assays are available for determining genotype/subtype 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) Target Regions: HCV 5 UTR, CORE & NS5B region 5 UTR 3 UTR 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

Several commercial assays are available for determining genotype/subtype 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) Even newest Target commercial-assays Regions: HCV 5 UTR, CORE & NS5B region may miss a precise determination of HCV-genotype in 9-10% of cases! 5 UTR 3 UTR 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

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

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

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 Patients (N) Patients (%) Genotype/subtype confirmed 315 91.84% Mixed/Indeterminate genotypes 8 2.33% Genotype 1 with no subtype 6 1.75% 4.08% Discordant genotypes 4 1.17% Genotype 1 with discordant subtype 10 2.91% 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

In addition.

4.1% (14/343) patients showed a discordant genotype or subtype according to direct-sequencing Innolipa/Abbot (year of genotyping) HCV genotyping by 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

4.1% (14/343) patients showed a discordant genotype or subtype according to direct-sequencing Innolipa/Abbot (year of genotyping) HCV genotyping by NS3 sequencing Abbott 2013/2014 1a (unknown) 2c - This suggests 1b (1993) the importance 2c to test again 2 HCV 1b genotype (1994) when the 4d first version of - 2a/2c commercial (2005) assays 1b were used 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

How to manage this patient according to the new genotype (4d) and drug resistance mutations in both NS3 and NS5a?

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?

How to manage this patient? 7 6 Asunaprevir + Daclatasvir + RBV (for compassionate use) GRT at Baseline NS3 Resistance Mutations: none NS5A Resistance Mutation: none HCV- RNA (log IU/ml) 5 4 3 2 1 LLOQ (12 IU/ml) GRT after 5 weeks of therapy NS3 Resistance Mutations: Q41Q/R, D168V NS5A Resistance Mutation: L28V, M31M/V, Y93H/Y This patient achieved SVR 12 after SOF+PEG+RBV therapy Day 0 Jan 2014 1w 4w 5w 6w

Points to discuss: 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) Re-treatment issue: - may UDPS provide an added value compared to population sequencing to check for the absence of drug resistance mutations?