Management of patients with hepatitis C virus resistance–associated variants to NS5A inhibitors: Where are we now?

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Abbreviations

BL

baseline

DAA

direct‐acting antiviral

GT

genotype

HCV

hepatitis C virus

NS

nonstructural

RAV

resistance‐associated variant

SVR

sustained virologic response

TEV

treatment‐emergent resistance‐associated variant

The hepatitis C virus (HCV) gene is an enveloped and single‐stranded RNA.1 Its 9.6 kb of genomic code provides instructions for the formation of an approximately 3000–amino acid polyprotein flanked by a highly conserved internal ribosome entry site. This HCV polyprotein is further cleaved into four structural and six nonstructural (NS) proteins through the actions of proteolytic enzymes.2 The viral RNA‐dependent polymerase, which comprises the catalytic core of the virus's replication machinery, is encoded by NS5B (Fig. 1).1 Furthermore, the serine protease that carries out the post‐translational processing of the NS proteins, together with its cofactor NS4A, at the NS3/NS4A, NS4A/NS4B, NS4B/NS5A, and NS5A/NS5B junctions are encoded by the N‐terminal domain of the NS3 protein.3 Therefore, the major targets of direct‐acting antivirals (DAAs) include highly selective inhibitors of NS5A, NS5B (both nucleoside and non‐nucleoside analogs), and NS3/NS4A.4 Figure 1 shows the currently approved protease, polymerase, and NS5A inhibitors used as part of a multitargeted approach to HCV treatment. Unfortunately, the development of resistance variants (referred to as resistance‐associated variants [RAVs]) to first‐generation DAAs quickly became apparent.5, 6, 7, 8, 9 More recently, RAVs against NS5A inhibitors have been characterized.10, 11, 12, 13, 14

Figure 1.

Multitargeted approach to HCV treatment based on the structure of the HCV protein. Adapted from McGovern et al.1 Abbreviation: UTR, untranslated region.

Prevalence of Baseline RAVs and Effects on Sustained Virologic Response Rates

Many clinicians cringe at the suggestion of complicating HCV therapy, because simplicity is the current theme. However, not all patients achieve sustained virologic response (SVR) with the all‐oral regimens. Clinicians need to know some of the reasons they may fail. Recent studies have identified the relative prevalence of RAVs and the relationship between specific RAVs and SVR rates. The results of three studies detected baseline (BL) NS5A RAVs in 12% to 18% of patients never previously exposed to an NS5A inhibitor (Table 1).10, 11, 12 A phase 3 study (UNITY‐1)15 examined the effect of BL RAVs on the response to a fixed‐dose combination of daclatasvir, asunaprevir, and beclabuvir in HCV genotype (GT) 1 patients with cirrhosis. NS5A RAVs were more problematic in GT 1a–infected patients than in those with GT 1b.11 Specifically, the fixed‐dose combination of daclatasvir, asunaprevir, and beclabuvir achieved SVR at week 12 (SVR12) in fewer patients with GT 1a (89%) than GT 1b (98%). Relapse was the most common reason for virologic failure (5%) and was primarily observed in GT 1a–infected patients. Further analysis showed that 34 GT 1a–infected patients (11%) had a BL NS5A RAVs, and only 74% of these patients achieved SVR12; in comparison, 100% SVR12 was observed in 17/106 (16%) of GT 1b–infected patients with this specific RAV.11

Table 1.

Percentage of Patients with BL RAVs and Numbers of Patients with Specific RAVS by HCV GT 1 Status

Study (ref)	% of patients with BL RAVs	No. of GT 1a patients with specific RAVs	No. of GT 1b patients with specific RAVs
Black et al. 2015a (12)	NS5A = 12  GT 1a = 11  GT 1b = 15 NS3‐30  GT 1a = 45  GT 1b = 8	NS5A  M28T/V/A = NR  Q30E/H/R/G/K/L/D = NR  L31M/V/F = NR  H58D = NR  Y93C/H/N/S = NR	NS5A  L28T/V/A = NR  R30E/H/G/K/L/D = NR  L31M/V/F = NR  H58D = NR  Y93C/H/N/S = NR
Krishnan et al. 2015b (14)	NR	NS3  R155K = 9  D168A/F/H/I/L/N/T/V/Y = 43  D168V = 35 NS5A  M28A/T/V = 20  Q30E/K/R = 29  Y93H = 0 NS5B  C316Y = 2  M414I/T = 3  S556G/R = 23	NS3  R155K = 0  D168A/F/H/I/L/N/T/V/Y = 4  D168V = 3 NS5A  M28A/T/V = 0  Q30E/K/R = 0  Y93H = 2 NS5B  C316Y = 1  M414I/T = 1  S556G/R = 1
Reddy et al. 2015c (11)	Overall = 13  GT 1a = 11  GT 1b = 16	M28: L/I/T/V = 26 Q30: H/R = 6 L31: M = 4 Y93: C/H = 2	L28: M/V = 2 R30::Q = 4 L31: I/M = 4 Y93: H = 9
Sarrazin et al. 2015c (10)	Overall = 18  GT 1a = 13  GT 1b = 25	L31M = 14 K24R = 10 M28T = 3 Y93H = 1 Y93F = 1 H58D = 1 Q30R = 1 Q30H = 1	Y93: H = 32 L31M = 12 L31l = 2 L31F = 1
Wyles et al. 2015c (13)	Overall = 16  GT 1a = NR  GT 1b = NR	NR	NR

^aThe types of NS3 BL RAVs assessed were reported, but not by patient GT; BL NS5A RAVs assessed based on GT 1a and GT 1b were reported, but not the number of patients with each.

^bBL RAVs not reported; numbers of patients reflects number of patients with virologic failures.

^cOnly BL NS5A RAVs reported.

Abbreviations: BL, baseline; GT, genotype; NR, not reported; RAVs, resistance‐associated variants.

The results of two additional studies indicated that although the majority of patients with BL NS5A RAVs achieved SVR12 (91%) or SVR24 (82%), respectively, baseline RAVs did have an impact on SVR.10, 12 In a recent study examining the efficacy of ledipasvir/sofosbuvir, the reduced SVR12 rate was limited to a small group of treatment‐experienced cirrhotic patients with GT 1a and BL NS5A RAVs that conferred a >100‐fold shift in the half‐maximal effective concentration.10 In the C‐WORTHY study, the presence of BL NS5A RAVs was associated with lower SVR24 in GT 1a–infected patients (69% versus 96% in patients with and without BL NS5A RAVs, respectively), but had no impact on efficacy in GT 1b–infected patients treated with the combination of grazoprevir and elbasvir.12 Although baseline RAVs are found in both subtypes, the impact appears to be more significant with GT 1a.

RAVs as Possible Reasons for Treatment Failure

Almost all patients treated with DAA regimens attain undetectable viral load on therapy. As a result, viral kinetics are not very useful in predicting outcome of treatment. The results of two recent studies suggested that failure to achieve SVR with DAA therapy was usually due to relapse, and that RAVs were almost universal in patients who relapsed following exposure to NS5A inhibitors.13, 14 In a study that assessed NS5A RAVs in patients who had virologic failure on ledipasvir regimens, 16% had detectable BL NS5A RAVs; however, 99% had NS5A RAVs at virologic failure.13 The other study was a long‐term follow‐up of treatment‐emergent resistance‐associated variants (TEVs) in NS3, NS5A, and NS5B with paritaprevir/ritonavir‐, ombitasvir‐, and dasabuvir‐based regimens.14 Study results from a pooled analysis of 2510 patients with virologic failure revealed that 97% of GT 1 patients achieved SVR12. Of the 2.9% (74/2510) of patients who failed treatment, 67 (91%) were infected with GT 1a and 7 (9%) were infected with GT 1b. Post‐treatment monitoring of NS5A TEVs revealed that they were still detected in 97% (68/70) and 96% (49/51) of treatment failures at post‐treatment weeks 24 and 48, respectively.14

An attempt to ascertain whether longer treatment duration using the same regimen could overcome RAVs was disappointing. The experiment was designed to enroll the patients who failed after 8 or 12 weeks of ledipasvir/sofosbuvir‐based regimens and retreat with ledipasvir/sofosbuvir for 24 weeks resulting in 71% SVR12.16 Unfortunately, the presence of certain NS5A RAVs, such as at the 93 locus, or the presence of more than one variant, led to SVR rates of <50%.16 Ribavirin was not used in this study; however, data derived from other studies suggest that the inclusion of ribavirin in patients with BL NS5A RAVs may minimize treatment failure.10

It is important to understand the long‐term implications of NS5A RAVs. One previously mentioned study13 demonstrated the persistence of NS5A RAVS in >95% and in 86% of patients through weeks 48 and 96, respectively. The aforementioned study that focused on the long‐term follow‐up of TEVs in NS3, NS5A, and NS5B with paritaprevir/ritonavir‐, ombitasvir‐, and dasabuvir‐based regimens also found that unlike RAVs to protease inhibitors, the RAVs against NS5A were very fit, and that 96% of them were detected 48 weeks after treatment.14 Collectively, these data demonstrate that NS5A RAVs can persist for >96 weeks after treatment in patients who relapse.

Implications and Recommendations for Practitioners

Clinicians were hopeful that a single therapy for HCV would soon be here and all patients would respond. However, this is not yet the case, and some patients do fail therapy. Our collective goal must focus on how to then treat that group. We do know that almost all patients who fail to achieve SVR will have resistant variants, and if treatment involved NS5A agents, these patients will have long‐lived RAVs, most likely for years. The screening of all patients who previously failed a regimen containing an NS5A inhibitor is recommended when considering retreatment with a regimen containing an NS5A inhibitor. It is not a matter of if a RAV will be found, because that is almost a given. The specific RAV and the number of RAVs are critical in determining if the patient can be retreated with an NS5A again. The likelihood of SVR can range from 30% to 100% if retreated with a regimen containing an NS5A, depending on these specifics. To further complicate the issue, not all NS5A agents have the same liability to the same RAVs, making it even more critical to know what variants are present. Commercial assays for NS3, NS5A, and NS5B variants are now available. Although not a current practice recommendation, given the foreseen increase in multitargeted therapies, the presence of BL variants will most certainly impact treatment selection in the future if differences in SVR can be demonstrated. Next‐generation NS5A agents may confer higher barriers of resistance to RAVs as compared to current NS5A inhibitors. The recommendations in this article may indeed change as newer agents enter the arena. Several DAA failure trials will be underway in the near future, and will govern how these emerging difficult‐to‐treat populations will be managed.