Showing posts with label Resistant–Associated Variants. Show all posts
Showing posts with label Resistant–Associated Variants. Show all posts

March 6, 2014

Antiviral therapy of hepatitis C in 2014: Do we need resistance testing?

Antiviral Research
Available online 25 February 2014
In Press, Uncorrected ProofNote to users

Commentary

Maximilian David Schneider, Christoph Sarrazin

Highlights

  • Hepatitis C virus resistance-associated variants (RAVs) pre-exist in quasispecies and can be selected under drug exposure.
  • NS3/4A protease inhibitors and NS5a inhibitors have a low genetic barrier to resistance and a high level of cross-resistance.
  • No significant resistance concerns have been observed for nucleoside polymerase inhibitors.
  • Resistance testing can be useful in special cases, such as DAA-experienced patients, HCV-subtype 1a.
  • Combination therapy with different classes of DAA can overcome antiviral resistance in the future.

Abstract

The treatment of chronic hepatitis C has fundamentally changed since the approval of the first direct-acting antivirals (DAA) in 2011. In addition to telaprevir and boceprevir, in 2014 two new NS3 protease inhibitors (simeprevir and faldaprevir), one non-nucleoside polymerase inhibitor (sofosbuvir) and one NS5a replication complex inhibitor (daclatasvir) have expanded the treatment options for chronic hepatitis C. Resistance-associated variants (RAV) are naturally produced during the HCV life cycle. The frequency of RAVs within HCV quasispecies mainly depends on their replicational fitness. Variants conferring resistance to nucleos(t)ide analogues have not been detected, and the majority of NS3 protease-resistant variants are present at low frequencies (0.1–3%) before initiation of DAA-based therapies. However, the Q80K variant conferring resistance to simeprevir has been observed in 9–48% of untreated HCV genotype 1a-infected patients, leading to reduced SVR rates. Resistant variants are detectable in the majority of patients with treatment failure to NS3 protease inhibitor- or NS5a inhibitor-based antiviral therapy. Long-term follow-up studies by population-based sequence analysis have shown the disappearance of resistant variants in the majority of patients, with median times to loss of mutations of 4–64 weeks. For the nucleotide analogue sofosbuvir, the emergence of the S282T resistant variant has been observed only in single patients, with reversion to wild-type within several weeks. Data are sparse on retreatment of patients with the same DAA or the same class of DAAs. However, retreatment with a different class of DAAs after failure of NS3 protease inhibitor-based therapy has been successful in small studies. This article forms part of a symposium in Antiviral Research on “Hepatitis C: next steps toward global eradication.”

Keywords: Hepatitis C virus; Direct-acting antivirals; Drug resistance; Sequencing

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December 17, 2013

Naturally occurring resistance mutations to inhibitors of HCV NS5A region and NS5B polymerase in DAA treatment-naive patients

Virology Journal 2013, 10:355 doi:10.1186/1743-422X-10-355

Stefania Paolucci (s.paolucci@smatteo.pv.it)
Loretta Fiorina (loretta75@libero.it)
Bianca Mariani (b.mariani@smatteo.pv.it)
Roberto Gulminetti (r.gulminetti@smatteo.pv.it)
Stefano Novati (s.novati@smatteo.pv.it)
Giorgio Barbarini (g.barbarini@smatteo.pv.it)
Raffaele Bruno (r.bruno@smatteo.pv.it)
Fausto Baldanti (f.baldanti@smatteo.pv.it)

ISSN 1743-422X

Article type Research
Submission date 23 September 2013
Acceptance date 3 December 2013
Publication date 17 December 2013

Article URL http://www.virologyj.com/content/10/1/355
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Abstract

Background

Direct-acting antiviral (DAA) agents target HCV proteins; some of these have already been approved for the treatment of HCV infection, while others are in development. However, selection of DAA-resistant viral variants may hamper treatment. The aim of this study was to illustrate potential natural DAA-resistance mutations in the HCV NS5A and NS5B regions of HCV genotypes 1a and 1b from DAA-naïve patients.

Methods

Direct sequencing of HCV NS5A and NS5B regions was performed in 32 patients infected with HCV genotype 1a and 30 patients infected with HCV genotype 1b; all subjects were naïve to DAAs.

Results

In genotype 1a strains, resistance mutations in NS5A (M28V, L31M and H58P) were observed in 4/32 (12.5%) patients, and resistance mutations in NS5B (V321I, M426L, Y448H, Y452H) were observed in 4/32 (12.5%) patients. In genotype 1b, resistance mutations in NS5A (L28V, L31M, Q54H, Y93H and I280V) were observed in 16/30 (53.3%) patients, while resistance mutations in NS5B (L159F, V321I, C316N, M426L, Y452H, R465G and V499A) were observed in 27/30 (90%) patients.

Conclusions

Mutations conferring DAA resistance were detected in NS5A and NS5B of HCV genotypes 1a and 1b from DAA-naïve patients. Although some mutations confer only a low level of resistance, the presence at baseline of mutated HCV variants should be taken into consideration in the context of DAA therapy.

Keywords Hepatitis C virus, HCV baseline resistance, NS5A and NS5B genes, DAA inhibitors

Background

Hepatitis C virus (HCV) is classified into six genotypes (1–6) and more than 100 subtypes. The most common genotypes in Western countries are 1a and 1b [1]. Peginterferon/ribavirin (PegIFN/RBV) for the treatment of HCV infection is burdened by adverse reactions in at least 10% of patients [2]. Moreover, a sustained virological response is achieved in only 50% of patients infected with HCV genotype 1 [3]. PegIFN/RBV treatment failure is mainly attributed to its low efficacy against genotypes 1 and 4, but also, to some extent to its side effects [3,4]. Recently developed direct-acting antiviral agents (DAAs) are predicted to have a major impact both in combination with PegIFN/RBV, as well as in IFN-free regimens and telaprevir and boceprevir have now been approved as standard of care treatment [5]. Targets for DAA include HCV NS3 protease, NS5B polymerase and NS5A protein which are essential for virus replication. [6-12].

Nevertheless, the combination of a high HCV replication rate, the low fidelity of HCV polymerase and selective pressures by the immune system and drug treatment lead to the in vivo development of viral quasispecies with high sequence diversity among various genotypes and subtypes [13,14] with the potential accumulation of virus variants showing mutations with varying degrees of resistance to DAAs [11-13,15-22], even in the absence of pre-existing drug-exposure [17,23-26]. In particular, natural changes in HCV NS5A and NS5B amino acids (aa) associated with reduced drug susceptibility have been observed in treatment naïve patients [17,27,28].

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July 3, 2013

Selection of Resistant–Associated Variants to the NS5A Inhibitor Daclatasvir: Revenge of the Hepatitis C Virus

Gastroenterology
Volume 145, Issue 1 , Pages 247-249, July 2013

Alessio Aghemo, Massimo Colombo

First Division of Gastroenterology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy

published online 31 May 2013.

Philip S. Schoenfeld, Section Editor, John Y. Kao, Associate Section

Full Text

Karino Y, Toyota J, Ikeda K, et al. Characterization of virologic escape in hepatitis C virus genotype 1b patients treated with the direct-acting antivirals daclatasvir and asunaprevir. J Hepatol 2012 Nov 22 [Epub ahead of print].

Selection of resistant hepatitis C virus (HCV) strains to directly acting antivirals (DAA) was among the main concerns during the initial drug development process for telaprevir (TVR) and boceprevir (BOC; J Hepatol 2012;56 Suppl 1:S88–100). In phase I and II studies both first-generation NS3 protease inhibitors (PI) were associated with rapid development of HCV resistance in monotherapy studies, as well as in ribavirin (Rbv)-free treatment regimens (N Engl J Med 2009;360:1827–1838; Lancet 2010;376:705–716). These alarming figures were, however, rapidly counterbalanced by some key concepts that were learned from phase II and III studies. First, we understood that not only pegylated interferon (PegIFN) and Rbv were essential components of first-generation PI regimens, but also that selection of resistant HCV strains was the direct consequence of the inability of PegIFN/Rbv to suppress replication of minority resistant variants that are already present in most, if not all, HCV genotype 1 patients (Gastroenterology 2012;142:1369–1372). Second, through long-term follow-up studies of patients with a treatment failure to TVR/BOC, we recognized that a restoration to wild type HCV happens in ≤90% of patients after a 2-year off-treatment period (Gastroenterology 2012;142:1369–1372). From a clinical standpoint, this means that patients responding poorly to PegIFN/Rbv are those more prone to develop DAA resistance, and that these HCV resistant strains are unlikely to impair efficacy of future anti-HCV regimens that will be based on drugs targeting different and multiple key steps in HCV replication (Hepatology 2013 Mar 6 http://dx.doi.org/10.1002/hep.26371).

However, less is known about the clinical significance of HCV resistance to future treatment options. Indeed, treatment of HCV patients will be revolutionized by the advent of IFN-free regimens, that are currently in phase II–III development and that have been shown to be highly effective independent of HCV genotype (Hepatology 2013 Mar 6 http://dx.doi.org/10.1002/hep.26371). The rationale of IFN-free regimens is to combine drugs targeting different steps of HCV replication process, with the ultimate aim to suppress viral replication and allow clearance of infected hepatocytes. The first proof that this was possible came from 2 small studies that showed the combination of PI asunaprevir (ASV), and the NS5A inhibitor daclatasvir (DCV) resulted in high sustained virologic response (SVR) rates in Japanese patients and in US patients infected with HCV genotype 1b (N Engl J Med 2012;366:216–224; Hepatology 2012;55:742–748). In the study by Karino et al, the authors report on the characterization of virologic escape in Japanese HCV genotype 1b patients who previously failed (n = 21) or were ineligible/intolerant to PegIFN/Rbv (n = 22), who received treatment with a 24-week course of ASV plus DCV (J Hepatol 2012 http://dx.doi.org/10.1016/j.jhep.2012.11.012). In this phase IIa study, the authors performed population sequencing and clonal analysis sequencing of HCV at baseline, and during virologic breakthrough or posttreatment relapse. Interestingly, all cases of viral breakthrough (n = 3) and posttreatment relapse (n = 4) occurred in the ineligible/intolerant subpopulation. Noncompliance to treatment was not the apparent cause of these failures, because adherence by pill count was high in 6 of the 7 patients; in the lone nonadherent patient who relapsed posttreatment, the serum concentrations of ASV/DCV were considered optimal. All 3 patients with a virologic breakthrough had a moderate-to-high level of DCV resistant variants at baseline. However, the presence of DCV or ASV resistant-associated variants (RAVs) at baseline was not a strong predictor of treatment failure, because only 2 of the 11 patients with baseline RAVs experienced a posttreatment relapse. The most interesting and somewhat worrisome finding of the study, however, relies on the long-term virologic characterization of patients with a failure to ASV/DCV. The authors followed patients for 48 weeks after treatment completion and thus were able to report on HCV sequencing data performed for a prolonged off-treatment period. The 3 breakthroughs were characterized at the time of virologic failure by high level RAVs to both DCV (6467- to 65,000-fold) and ASV (120- to 280-fold), in all 3 patients the NS5A RAVs persisted through the 48 week follow-up period, whereas in 2 out of 3 patients the NS3 RAVS were replaced by wild-type virus. In the 4 patients with posttreatment relapse, a high level of RAVs to both ASV/DCV were found at the time of virologic relapse. However in the 48-week follow-up period, 3 out of 4 patients (75%) reverted to wild-type HCV at the NS5A region, whereas NS3 RAVs were not detectable in any patient at the week 36 follow-up visit. In summary, Karino et al demonstrate that virologic failure to ASV/DCV in HCV-1b patients is characterized by selection of RAVs to both DAA compounds. However, although NS3 RAVS failed to persist in most patients during follow-up, the NS5A RAVs were in all cases still detectable up to 48 weeks after treatment completion.

Comment

IFN-free regimens are the future of anti-HCV treatment, because their advent will provide significant benefits from clinical and epidemiologic points of view (J Viral Hepat 2012;19:449–464). If these regimens are affordable for national healthcare systems, it is probable that large chunks of HCV patients that are currently excluded from treatment for contraindications or are unwilling to start an IFN-based regimen for tolerability reasons will finally receive an effective antiviral treatment. Moreover, the availability of effective and tolerable treatments should also increase the number of HCV patients who are diagnosed and eventually referred to a specialist, hence eliminating 1 of the key limiting factors that precludes access to therapy nowadays (J Hepatol 2012;57:1326–1335). Although some issues, especially the affordability of these regimens, might preclude the fulfillment of these scenarios, it is projected that in 2015 the first IFN-free regimens will become commercially available. Phase II studies have convincingly demonstrated that by combining 2 or 3 DAAs for 12–24 weeks, up to 80%–90% of HCV-1 genotype patients can achieve an SVR (Hepatology 2013 Mar 6 http://dx.doi.org/10.1002/hep.26371). These mesmerizing figures have been only partially confirmed by real-life experiences or by studies enrolling more difficult to cure patients, where SVR rates have been slightly lower. Whether this is directly caused by clinical or epidemiologic factors such as advanced liver disease, virus subtype, ethnicity, or adherence remains unknown. The obvious question that follows these results is this: Why do patients fail an IFN-free regimen? Is this owing to selection for RAVs? Until now, RAVs have not played a clinically meaningful role in the treatment of hepatitis C for several reasons. First, there is no stable genetic reservoir for HCV and hence RAVs are not archived. Second, most resistant variants to TVR/BOC are unfit in terms of their replication capacity and failure to persist. The study by Karino et al confirms this for the second generation of PI such as ASV, because NS3 RAVs reverted to wild type in 6 out of 7 cases (85%) during the 48-week follow-up period. However, this was not the case for NS5A RAVs that persisted in all patients with an on-treatment viral breakthrough. This shows that high level NS5A RAVS that are selected during treatment are relatively fit in terms of replication capacity and might persist for a long period of time after treatment discontinuation. The clinical implications of this finding are currently hard to foresee, because one would expect wild-type HCV, which has emerged as the most fit to replicate over a long evolutionary period, would slowly return to be the dominant viral strain in all patients over time (Best Pract Res Clin Gastroenterol 2012;26:487–503). Still, the selection of a replication fit RAV could be problematic in terms of spread of the disease, as in theory new HCV cases could circulate dominant RAVs that will impair efficacy of future treatment options. Moreover, these RAVs might be clinically relevant in cases where viral replication is the direct cause of the disease, such as in post-liver transplant patients who develop fibrosing cholestatic hepatitis C.

When interpreting the findings by Karino et al, we need to remember that the study was conducted in a highly selected group of HCV-1b genotype patients without cirrhosis, who do not reflect the current epidemiology of HCV infection in most developed countries (J Hepatol 2011;55:245–264). Once these IFN regimens are moved into more difficult to cure subgroups of patients, like those with the HCV-1a subtype, advanced fibrosis or cirrhosis or HIV co-infection, the rate of RAVs selection might be further magnified. These subgroups of patients present a challenge not only as a consequence of impaired efficacy of some IFN-free regimens in the HCV-1a subtype, but also in terms of safety in patients with advanced fibrosis/cirrhosis and adherence in patients receiving multiple concomitant medications that might cause significant drug–drug interactions. Obviously, these are the worst-case scenarios, and to date we have no data to be sure that they will actually happen. Indeed the DAA combination used by Karino et al, a second wave PI plus an NS5A inhibitor, is now considered suboptimal as it features 2 drugs with low genetic barrier to resistance especially in patients with HCV-1a genotype. The optimal IFN-free regimen should in theory combine a drug with potent antiviral activity (PI or NS5A inhibitor) with a drug with high genetic barrier to resistance (NS5B Nucleoside inhibitor). However, some studies have shown that extremely high SVR rates can be obtained by combining a PI an NS5A inhibitor and an NS5B non-nucleoside inhibitor with or without Rbv (Hepatology 2013 Mar 6 http://dx.doi.org/10.1002/hep.26371). This demonstrates that matching an NS5A with a high genetic barrier DAA or with 2 low genetic barrier DAAs, should minimize the risk of selection of resistant viral strains. This seems especially true when an NS5A inhibitor is combined with an NS5B nucleoside inhibitor, which to date seems like the most well-tolerated IFN-free DAA regimen in terms of pill burden.

NS5B nucleoside inhibitors are characterized by a high barrier to resistance because the S282T mutation associated with decreased susceptibility to this class of compounds dramatically reduces HCV replication capacity (N Engl J Med 2013;368:34–44). This means that this mutation is very rarely found as a pretreatment naturally occurring variant and is also seldom found at the time of relapse (Hepatology 2012;56 Suppl 1:A551). In the context of this DAA combination, the finding by Karino et al, that viral breakthrough emerged only in intolerant/ineligible to PegIFN/Rbv patients could be clinically relevant. There is no clear-cut explanation for this, but the most reasonable is to attribute this finding to impaired adherence in this category of patients. The authors were quick to show that compliance with treatment, assessed through pill count, was high in the current study, but it is well known from the experience with chronic hepatitis B patients that compliance to simple and tolerable regimens is not as high as expected in real life (J Hepatol 2011;54:12–18). If these data were to be confirmed, they could suggest that in patients where optimal adherence can be problematic to achieve, a combination of only 2 DAAs that includes an NS5A inhibitor, could be suboptimal in terms of SVR rates and lead to selection of NS5A RAVs.

It is too early to draw sound clinical recommendations from the findings of the study by Karino et al, because many studies investigating IFN-free regimens are currently ongoing and we do not have solid data on resistance profiles yet; still, we think that overall Karino et al's data support a cautious approach towards future therapeutic regimens for HCV infection. Clearly, SVR rates will be increased by IFN-free regimens, and tolerability will be greatly improved compared with any PegIFN/Rbv-containing regimen, but the selection of durable resistant variant strains might be problematic, especially in some categories of patients. This piece of information not only needs to be taken into consideration when clinicians consider treatment deferral until the availability of IFN-free regimens for their patients, but should also probably be part of the informed deferral process that some consider a moral requirement for entry in the HCV treatment warehouse (Hepatology 2012;56:1591–1592).

PII: S0016-5085(13)00785-3

doi:10.1053/j.gastro.2013.05.028

© 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.

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