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Management of Hepatitis C Infection

Stefan Zeuzem, MD
Program Director
Jordan J. Feld, MD, MPH
Hemant Shah, MD, MScCH HPTE
Released: June 17, 2019

Drug Resistance

The development of DAAs has been a major therapeutic advance in the treatment of HCV infection, but it has also introduced new challenges. True viral resistance to peginterferon and ribavirin has not been described (although host resistance to interferon is well characterized). By contrast, RAS have been identified for all DAAs and have been shown to emerge rapidly with the use of DAA monotherapy. This section will discuss issues relating to the prevention and management of drug resistance to DAAs.

For information on resistance associated with specific agents, see individual drug entries in Types of Therapy.

Mechanisms of Resistance. Because of the high replication rate and error-prone nature of the HCV RNA polymerase, in theory, every possible single and double mutation across the HCV genome is produced every day in an infected, untreated person.[137] As a result, DAA-resistant virus exists before patients are exposed to therapy. DAAs select for resistant virus; they do not create resistant virus. Virus resistant to DAAs is present at very low levels at baseline because resistance mutations typically reduce viral fitness. Wild-type HCV replicates more successfully than resistant virus and outgrows resistant quasispecies in the absence of drug pressure. Once a DAA is initiated, replication of wild-type virus is inhibited, but resistant virus continues to grow and, over time, becomes the dominant viral population. It is for this reason that DAA monotherapy is ineffective and DAAs are always used with other agents. With combination therapy, the different agents are collectively able to suppress both wild-type and resistant virus. This premise is reliant on all components of the regimen providing antiviral activity. For example, in poorly interferon-responsive patients treated with a protease inhibitor plus peginterferon/ribavirin, the virus is effectively exposed to protease inhibitor (functional) monotherapy, leading to the rapid emergence of protease inhibitor–resistant virus.

Resistance Associated Variants. HCV differs from HIV and HBV in its inability to “archive” resistant variants. HIV inserts viral RNA into the host genome and, hence, resistant virus will persist for at least the lifespan of infected cells and may well survive cell division. Similarly, HBV has a long-lived nuclear form of the virus known as covalently closed circular, or cccDNA, that also persists in the nucleus of the infected hepatocyte long term. The consequence of these nuclear reservoirs of HBV or HIV infection is that once drug-resistant virus has emerged, it is stored in these long-lasting reservoirs even after treatment is stopped. Retreatment then leads to rapid reemergence of the resistant variant. Unlike HIV and HBV, however, HCV has an entirely cytoplasmic lifecycle with no known long-lasting nuclear or other reservoir.[138] Theoretically, therefore, once a protease inhibitor is stopped, protease inhibitor–resistant HCV may slowly decrease back to baseline levels.

The rapidity with which resistant virus “disappears” will depend on the fitness of resistant virus compared with wild-type virus. If resistant virus has improved its fitness through compensatory mutations, it may compete favorably with wild-type virus, even in the absence of drug pressure, and persist long term. As a result, it is critical to stop a failing regimen as soon as virologic failure is detected to prevent the development of resistant virus with improved fitness. This is the rationale behind the futility or stopping rules for first-generation protease inhibitors, and these should be followed carefully when using these drugs.

Protease Inhibitors
Once protease inhibitor–resistant virus reaches detectable levels, continuing protease inhibitor therapy is of very limited value and may, in fact, be harmful. If protease inhibitor therapy is continued in the presence of resistant variants, the resistant virus may continue to evolve to improve its replicative fitness. Development of compensatory mutations may reverse fitness deficits. Compensatory mutations allow resistant virus to increase its fitness over time, possibly even to levels comparable to that of wild-type virus. The greater the fitness of resistant virus, the longer it will persist once the protease inhibitor is stopped. Persistence of protease inhibitor–resistant virus may limit future therapeutic options and may pose a significant public health risk if it is transmitted to protease inhibitor–naive individuals.[138]

However, long-term follow-up of patients who failed to achieve SVR on telaprevir-based triple therapy in phase III trials suggests that resistant virus is not detected in most such individuals several months after therapy is stopped.[139-141] Among 126 telaprevir-treated patients without SVR and with population sequencing data available in the EXTEND study, 85% of patients no longer had detectable resistant variants at 29 months of follow-up.[139] In an analysis of patients who did not achieve SVR in phase III studies with boceprevir, 53% of patients had detectable RAS. After a follow-up of 6-14 months, 23% of patients still had detectable RAS by population sequencing.[142] Although these findings are encouraging, it is important to note that population sequencing only detects viral variants that constitute at least 20% of the viral population. This means that a proportion of patients still had at least 20% resistant virus more than 2 years after the removal of therapy. Although in other patients resistance was “undetectable,” it may not have been truly absent but rather below the limit of detection of the assay (ie, resistant variants formed less than 20% of the viral population). Rates of resistance to boceprevir and telaprevir differ according to HCV subgenotype, with higher rates and longer posttreatment persistence of RAS observed in genotype 1a vs genotype 1b infection.[143]

In one study, 9 patients from early trials of telaprevir monotherapy were retreated with telaprevir combination therapy.[144] All had resistance at the end of their first course of treatment as the dominant viral species. By population sequencing, none had detectable variants prior to restarting telaprevir-based therapy. Eight of 9 patients suppressed virus to undetectable levels with combination therapy. The 1 patient with viral breakthrough had a resistant variant that differed from that seen in his first course of treatment. Although these data are certainly encouraging and support the notion that archiving of resistance does not occur with HCV, more data will clearly be required before retreatment with protease inhibitors can be recommended for previous protease inhibitor–treatment failures.

Sofosbuvir
As noted above, the S282T mutation associated with high-level sofosbuvir resistance markedly limits the replication fitness of the virus, and therefore rarely emerges during first-line sofosbuvir therapy and is likely to return to extremely low levels in the absence of drug pressure. This creates a scenario in which patients who relapse after sofosbuvir-based therapy can likely be treated again with a sofosbuvir-containing regimen.

A proof of concept was shown in a patient in the LONESTAR trial.[145] In this study, 1 patient relapsed after treatment with a combination of sofosbuvir and ledipasvir (NS5A inhibitor). At relapse, sequencing identified both the S282T sofosbuvir signature mutation and multiple NS5A-resistance mutations. At the first positive HCV test after therapy, the S282T variant accounted for 91% of the viral population. On retesting 2 weeks later, the S282T was still present but only at 9% of the population, suggesting that in the absence of selection pressure, it had been largely outgrown by wild-type virus. This patient was then retreated with sofosbuvir and ledipasvir with ribavirin for 24 weeks and achieved SVR. This case illustrates the poor fitness of the S282T mutant, which will hopefully make resistance to sofosbuvir and other nucleotide analogue polymerase inhibitors much less of concern than with other DAA classes. The S282T variant is susceptible to other classes of DAAs as well.

Findings from a prospective phase II trial indicate that sofosbuvir-based therapy remains effective after failure of a sofosbuvir-containing regimen. In this study, 98% (50/51) of patients with genotype 1 HCV infection who experienced previous treatment failure on a sofosbuvir-based regimen achieved SVR following 12 weeks of ledipasvir/sofosbuvir plus ribavirin.[146] The single patient who experienced virologic relapse proved to have genotype 3a HCV infection and was enrolled as a result of incorrect genotyping. This study demonstrates that sofosbuvir resistance is unlikely to persist off therapy, and patients who experience treatment failure with a sofosbuvir-based regimen can be effectively retreated with another sofosbuvir-based regimen. However, in patients who fail ledipasvir/sofosbuvir, retreatment may be less straightforward. In a small, open-label study, 41 patients who relapsed after receiving ledipasvir/sofosbuvir treatment for 8 or 12 weeks were retreated with ledipasvir/sofosbuvir for 24 weeks.[31] Overall, 71% achieved SVR. However, the outcome of therapy was highly dependent on the presence and number of NS5A RAS after initial treatment. Patients with no RAS at the start of retreatment had an SVR12 rate of 100%, whereas the SVR12 rate was only 69% in those with 1 baseline RAV and fell to 50% (7 of 14) in those with 2 or more NS5A RAS. Notably, of the 12 patients who did not achieve SVR, variants associated with sofosbuvir resistance were found in 4 patients (33%). Two had detectable S282T variants, 1 had L159F, and 1 had both S282T and L159F. This study suggests that sofosbuvir-resistant variants may be more likely to emerge in the setting of preexisting RAS to another class (in this case NS5A). Whether the addition of ribavirin or a third DAA to this combination would have been more successful is currently unknown.

The results of an open-label, nonrandomized trial evaluating retreatment with intensified sofosbuvir-based regimens in patients with genotype 2 or 3 HCV infection who experienced virologic relapse after receiving sofosbuvir and ribavirin in phase III clinical trials also demonstrated promising outcomes. Patients enrolled in the study were retreated with either sofosbuvir plus peginterferon alfa 2a/ribavirin for 12 weeks (n = 34) or sofosbuvir plus ribavirin for 24 weeks (n = 73) based on investigator discretion.[147] At the time of reporting, SVR12 rates (available for 62% of the enrolled population) were 92% with 12-week, peginterferon-containing therapy and 63% with 24 weeks of interferon-free retreatment. Among patients with cirrhosis, SVR12 rates were 88% (n = 8) and 47% (n = 15), respectively. Both regimens were generally well tolerated with no discontinuations for adverse events.

NS5A Inhibitors
NS5A RAS are very fit and compete well with wild-type virus. As such, they are often found at baseline in patients who have not been exposed to NS5A inhibitors in the past. Most studies have found that NS5A RAS are present in 10-20% of genotype 1 HCV–infected treatment-naive patients at baseline. The significance of baseline NS5A RAS for treatment response depends on the regimen used and is an evolving area. In patients with genotype 1b HCV treated with asunaprevir and daclatasvir in the HALLMARK DUAL trial, 20%% of patients had baseline NS5A RAS and only 39% of those patients achieved SVR12 compared with 92% in the patients without RAS at baseline.[148] In addition, the presence of NS5A RAS at baseline is associated with reduced SVR12 rates to elbasvir/grazoprevir in patients with genotype 1a HCV infection.[124,126]

When NS5A inhibitors are combined with sofosbuvir, the importance of baseline NS5A RAS is less clear. Although initial reports suggested that baseline NS5A resistance was not an important predictor of treatment failure in the ION studies of ledipasvir/sofosbuvir, more careful analysis showed that patients with genotype 1a HCV with baseline RAS had a slightly lower SVR rate than those without RAS.[149] The effect was much less pronounced in genotype 1b HCV–infected patients and was largely overcome with either extension of therapy to 24 weeks or the addition of ribavirin. The prevalence of RAS is also relevant. Low-level RAS detected only by deep sequencing may have much less impact than RAS that represent a significant proportion of the circulating quasispecies and can be detected by population sequencing. The effect of baseline RAS was much greater in patients treated with ledipasvir/sofosbuvir in those with > 15% prevalence than in those who had only low-level (1%) RAS detected.

Most patients who fail a regimen containing an NS5A inhibitor will have detectable RAS after treatment. Because of their high fitness level, these RAS may persist long term. Of patients who failed a course of therapy with ledipasvir (without sofosbuvir), 98% (63 of 64) had detectable NS5A RAS at the time of treatment failure.[150] In follow-up, 86% had persistent NS5A RAS 96 weeks after stopping ledipasvir. These data highlight that once NS5A RAS are selected, they are likely to persist long term. The latest HCV management guidance from the AASLD/IDSA recommends that pretreatment testing for NS5A inhibitor RAS be conducted in specific populations defined by HCV genotype, treatment experience, cirrhosis status, and the regimen under consideration (Table 39).[54] In these populations, pretreatment testing results may modify HCV management by altering therapy selection, duration, or ribavirin inclusion.

Table 39. NS5A Pretreatment Testing Recommendations

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