Direct-acting Antiviral Treatment Failure Research Articles

A Systematic Review on the Evolution of Natural Mutation-dependent Antiviral Drug Resistance in Hepatitis C Virus (HCV) Genotypes Prevalent in Saudi Arabia: A Genomic and Therapeutic Perspective

Background: The characterization of resistance-associated amino acid substitution (RAAS) in direct-acting antivirals (DAA) molecular targets could reshape the treatment strategy for HCV infection. Hence, this review aimed to provide evidence on the impact of the RAASs on DAA treatment for HCV. <P> Methods: PRISMA model was followed for the literature survey and evaluation (sources: PubMed, Sci-Hub, and Google Scholar). RAASs in DAA target proteins and their locations were mapped on 3-D proteins using two reference protein sequences: NS3/ID: AAA72945.1 and NS5A/NS5B/ID: NP_671491.1. NCBI-Basic Local Alignment Tool, UniProt and AlphaFold2/MMSeqs2, PyMol, and R-base/R-studio were used for alignment, retrieval of protein sequences, 3-D protein structure modeling, visualization of locations of RAASs, and diagrammatic representations, respectively. <P> Results: Genotype 4 afterwards genotype 1 was the most prevalent in Saudi Arabia. L2003M, Y2065N, M2000T, L2003V, and Q2002H RAASs were anti-NS5A inhibitor. NS5A-Q2002H was anti-daclatasvir in genotype 4. NS5A-Y2065H and NS5B-S2702T in genotype 1 were antisofosbuvir- resistant. NS3-A1182V, NS3-Q1106K/R, and NS3-T1080S RAASs exhibited resistance to double antivirals. NS3-D1194A RAAS was a multi-drug resistant variant (against 3 DAAs). NS3- V1062A, NS3-D1194G, NS3-D1194E/T, NS3- S1148R, NS3-V1196A, NS3-V1062LNS3-S1148A, and NS3-S1148G RAASs in genotype 1 were single drug-resistant variants. NS3- S1148R and NS3- S1148A in genotypes 2 and 5 were anti-simeprevir-resistant variants. <P> Conclusions: An array of identified RAASs, RAAS-dependent DAA treatment failure, and recommended combination DAA therapy in such clinical scenarios of RAASs are the significant outcomes of this research. RAAS-linked in vitro and in vivo resistance profiling at genotype/sub-genotype level will be crucial in treatment choice and for future DAA design strategies.

A randomized-controlled trial of SOF/VEL/VOX with or without ribavirin for retreatment of chronic hepatitis C

The combination of sofosbuvir, velpatasvir and voxilaprevir (SOF/VEL/VOX) is recommended retreatment for patients with hepatitis C virus (HCV) infection who failed previous direct-acting antiviral (DAA) treatment. However, whether ribavirin further increases the therapeutic efficacy of SOF/VEL/VOX retreatment remains unclear. We aimed to test this hypothesis by a randomized controlled trial. We randomly assigned 315 patients with DAA treatment failure from 5 Egyptian sites into two groups. Group A (n=158) received SOF/VEL/VOX for 12 weeks, and group B (n=157) received SOF/VEL/VOX + weight-based ribavirin for 12 weeks. Therapeutic efficacy was defined as SVR12 (undetectable HCV RNA 12 weeks after treatment completion). Safety and tolerability were evaluated by monitoring treatment-related adverse events (AEs) and laboratory abnormalities. Seventeen patients in each group were lost to follow-up. SVR12 rates by intention-to-treat (ITT) were 87.3% (138/158), and by per-protocol analysis, 97.8% (138/141) in group A; and 87.9% (138/157) and 98.5% (138/140) in group B (p=NS for ITT and PP). Males comprised 53.9% of group A, and 57.1% in group B (p=0.58), with mean ages of 51.8 and 47.3 years in group A and B, respectively. Both regimens were well-tolerated, with no deaths and only one serious AE (anemia) in group B requiring ribavirin discontinuation. Fifty-five patients in group A vs. 77 in group B experienced any adverse events (p=0.002). This randomized controlled trial showed equal, high efficacy of both regiments in retreating previous DAA failures, although ribavirin was associated with more adverse events. Therefore SOF/VEL/VOX monotherapy should be the preferred retreatment strategy. HCV treatment guidelines recommend retreating DAA treatment failures with the combination of sofosbuvir, velpatasvir and voxilaprevir (SOF/VEL/VOX) for 12 weeks. However, whether ribavirin exerts an additional/synergistic effect remains unclear. The present study confirmed that SOF/VEL/VOX without ribavirin is the best regimen for retreating DAA treatment failures, and thus will help clinicians caring for patients who are not cured with a first course of DAA therapy. CLINCIALTRIALS. NCT04695769.

Characterization of multi-DAA resistance using a novel hepatitis C virus genotype 3a infectious culture system.

The high HCV infection cure rates achieved with direct-acting antiviral (DAA) treatments could be compromised in the future by the emergence of antiviral resistance. Thus, it is essential to understand the viral determinants that influence DAA resistance, which is most prevalent in genotype 3. We aimed at studying how resistance to protease-, NS5A-, and NS5B-inhibitors influences the activities of glecaprevir/pibrentasvir, sofosbuvir/velpatasvir, and sofosbuvir/velpatasvir/voxilaprevir in cell culture, and how the HCV genome adapts to selective pressure by successive rounds of treatment failure. A previously developed in vivo infectious cDNA clone of strain S52 (genotype 3a) was adapted to efficiently replicate and propagate in human hepatoma cells (Huh7.5) using 31 adaptive substitutions. DAA escape experiments resulted in the selection of S52 variants with decreased drug susceptibility (resistance), which was linked to the emergence of known resistance-associated substitutions (RASs). NS5A-inhibitor resistance was sufficient to promote treatment failure with double-DAA but not triple-DAA regimens. Enhanced viral fitness associated with the selection of sofosbuvir resistance accelerated escape from DAAs. After serial DAA treatment failure, HCV genetic evolution led to a complex genome-wide network of substitutions, some of which coevolved with known RASs. Baseline NS5A-RAS can compromise the efficacy of double-DAA pangenotypic regimens for HCV genotype 3, and enhanced viral fitness can accelerate treatment failure. Persistence of RASs after successive treatment failure is facilitated by the remarkable evolutionary capacity and plasticity of the HCV genome. Proof-of-concept for the potential development of multi-DAA resistance is shown.

Artificial intelligence predicts direct-acting antivirals failure among hepatitis C virus patients: A nationwide hepatitis C virus registry program.

Despite the high efficacy of direct-acting antivirals (DAAs), approximately 1-3% of hepatitis C virus (HCV) patients fail to achieve a sustained virological response. We conducted a nationwide study to investigate risk factors associated with DAA treatment failure. Machine-learning algorithms have been applied to discriminate subjects who may fail to respond to DAA therapy. We analyzed the Taiwan HCV Registry Program database to explore predictors of DAA failure in HCV patients. Fifty-five host and virological features were assessed using multivariate logistic regression, decision tree, random forest, eXtreme Gradient Boosting (XGBoost), and artificial neural network. The primary outcome was undetectable HCV RNA at 12 weeks after the end of treatment. The training (n=23,955) and validation (n=10,346) datasets had similar baseline demographics, with an overall DAA failure rate of 1.6% (n=538). Multivariate logistic regression analysis revealed that liver cirrhosis, hepatocellular carcinoma, poor DAA adherence, and higher hemoglobin A1c were significantly associated with virological failure. XGBoost outperformed the other algorithms and logistic regression models, with an area under the receiver operating characteristic curve of 1.000 in the training dataset and 0.803 in the validation dataset. The top five predictors of treatment failure were HCV RNA, body mass index, α-fetoprotein, platelets, and FIB-4 index. The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the XGBoost model (cutoff value=0.5) were 99.5%, 69.7%, 99.9%, 97.4%, and 99.5%, respectively, for the entire dataset. Machine learning algorithms effectively provide risk stratification for DAA failure and additional information on the factors associated with DAA failure.

Evaluation of machine learning algorithms for predicting direct-acting antiviral treatment failure among patients with chronic hepatitis C infection

Despite the availability of efficacious direct-acting antiviral (DAA) therapy, the number of people infected with hepatitis C virus (HCV) continues to rise, and HCV remains a leading cause of liver-related morbidity, liver transplantation, and mortality. We developed and validated machine learning (ML) algorithms to predict DAA treatment failure. Using the HCV-TARGET registry of adults who initiated all-oral DAA treatment, we developed elastic net (EN), random forest (RF), gradient boosting machine (GBM), and feedforward neural network (FNN) ML algorithms. Model performances were compared with multivariable logistic regression (MLR) by assessing C statistics and other prediction evaluation metrics. Among 6525 HCV-infected adults, 308 patients (4.7%) experienced DAA treatment failure. ML models performed similarly in predicting DAA treatment failure (C statistic [95% CI]: EN, 0.74 [0.69–0.79]; RF, 0.74 [0.69–0.80]; GBM, 0.72 [0.67–0.78]; FNN, 0.75 [0.70–0.80]), and all 4 outperformed MLR (C statistic [95% CI]: 0.51 [0.46–0.57]), and EN used the fewest predictors (n = 27). With Youden index, the EN had 58.4% sensitivity and 77.8% specificity, and nine patients were needed to evaluate to identify 1 DAA treatment failure. Over 60% treatment failure were classified in top three risk decile subgroups. EN-identified predictors included male sex, treatment < 8 weeks, treatment discontinuation due to adverse events, albumin level < 3.5 g/dL, total bilirubin level > 1.2 g/dL, advanced liver disease, and use of tobacco, alcohol, or vitamins. Addressing modifiable factors of DAA treatment failure may reduce the burden of retreatment. Machine learning algorithms have the potential to inform public health policies regarding curative treatment of HCV.

Long-term persistence of HCV resistance-associated substitutions after DAA treatment failure

Data on the long-term persistence of HCV resistance-associated substitutions (RASs) after treatment with direct acting antivirals (DAAs) are limited. This study evaluated the persistence of NS3, NS5A and NS5B RASs for up to 5 years after the end of treatment (EOT). We included samples from n=678 patients with a HCV GT (genotype) 1 or 3 infection and virologic DAA treatment failure collected in the European Resistance Database. NS3, NS5A and NS5B were sequenced and clinical parameters were evaluated. A total of 242 patients with HCV GT1a (36%), 237 with GT1b (35%) and 199 (29%) with GT3 and a DAA failure were included. After protease inhibitor failure, the frequencies of NS3 RASs were 40-90% after end of treatment (EOT) and RASs disappeared rapidly in GT1b and GT3 after follow-up month 3 (FU3), while in GT1a RASs were stable (≥ 60%) due to Q80K. The SOF-resistant NS5B RAS S282T was only found in individual GT3a patients. Non-nucleoside NS5B RASs were frequent in GT1 (56-80%) and decreased to 30% in GT1a but persisted in GT1b. NS5A RASs were very common in all GTs after NS5A inhibitor failure (88-95%), and even after FU24 their frequency was 65% and higher. However, RASs in GT1b had a stable course, while RASs in GT1a and GT3 declined slightly after FU24 (GT1a, 68%; GT1b, 95%; GT3, 65%), mainly due to the slow decline of high-level resistant Y93H. We found that low to medium-level RASs persisted, while high-level resistant RAS disappeared over time. Different patterns of RAS persistence according to HCV subtype could have implications for retreatment with first generation DAAs and for global HCV elimination goals. The long-term persistence of RASs after DAA failure is largely unknown. RASs in NS3 (with exception of Q80K) and S282T in NS5B generally declined rapidly. NS5A RASs persisted beyond two years after end of treatment, with a slight decrease in GT1a and GT3 compared to GT1b. The different patterns of RAS persistence could be of importance for re-treatment especially in countries with limited medical resources.

Safety and efficacy of sofosbuvir–velpatasvir–voxilaprevir for re-treatment of chronic hepatitis C virus infection in patients with previous direct-acting antiviral treatment failure in Rwanda (SHARED-3): a single-arm trial

Hepatitis C virus (HCV) genotype 4 non-a/d subtypes, which frequently have NS5A resistance-associated substitutions, are highly prevalent in sub-Saharan Africa. These subtypes, particularly genotype 4r, have been associated with higher rates of failure of treatment regimens containing the NS5A inhibitors ledipasvir or daclatasvir, which are the most accessible direct-acting antivirals in low-income countries. Clinical evidence regarding the efficacy of re-treatment options for these subtypes is limited. We aimed to evaluate the safety and efficacy of sofosbuvir-velpatasvir-voxilaprevir for the treatment of adults in Rwanda with chronic HCV infection, predominantly of genotype 4, and a history of direct-acting antiviral treatment failure. In this single-arm prospective trial, we enrolled adults (aged ≥18 years) with a HCV RNA titre of at least 1000 IU/mL, and a documented history of direct-acting antiviral failure. Patients were assessed for eligibility at a single study site after referral from hospitals with HCV treatment programmes throughout Rwanda, and participants for whom sofosbuvir-ledipasvir treatment had failed in the previous SHARED trial were also included. Participants with decompensated liver disease or hepatitis B virus co-infection were excluded. Participants were treated once daily with an oral fixed-dose combination tablet containing sofosbuvir (400 mg), velpatasvir (100 mg), and voxilaprevir (100 mg) for 12 weeks. The primary endpoint was the proportion of participants with a sustained virological response 12 weeks after completion of treatment (SVR12) in the intention-to-treat population. Viral sequencing of NS3, NS5A, and NS5B genes was done at baseline in all participants and at end of follow-up (week 24) in participants with treatment failure. The study is registered with ClinicalTrials.gov (NCT03888729) and is completed. Between Sept 23, 2019, and Jan 10, 2020, 49 individuals were screened and 40 participants were enrolled. 20 (50%) were female, 20 (50%) were male, median age was 63 years (IQR 56-68), and median HCV viral load was 6·2 log10 IU/mL (5·8-6·5) at baseline. The genotype subtypes identified were 4r (18 [45%] participants), 4k (six [15%]), 4b (five [13%]), 4q (four [10%]), 4l (two [5%]), 4a (one [3%]), 4m (one [3%]), and 3h (one [3%]). One (3%) genotype 4 isolate could not be subtyped, and one (3%) isolate was of unknown genotype. All successfully sequenced isolates (33 [83%]) had at least two NS5A resistance-associated substitutions and 25 (63%) had three or more. 39 (98% [95% CI 87-100]) participants had SVR12. Seven (18%) participants had a total of ten grade 3, 4, or 5 adverse events, including three (8%) cases of hypertension, and one (3%) case each of cataract, diabetes, gastrointestinal bleeding, joint pain, low back pain, vaginal cancer, and sudden death. Four of these events were categorised as serious adverse events resulting in hospitalisation. The one sudden death occurred at home from an unknown cause 4 weeks after the completion of treatment. No serious adverse event was determined to be related to the study drug or resulted in treatment discontinuation. A 12 week course of sofosbuvir-velpatasvir-voxilaprevir is safe and efficacious for the re-treatment of individuals infected with HCV genotype 4 non-a/d subtypes with frequent baseline NS5A resistance-associated substitutions, following failure of previous direct-acting antiviral treatment. Improved affordability and access to sofosbuvir-velpatasvir-voxilaprevir in regions with these subtypes is crucial. Gilead Sciences.

Machine learning algorithms for predicting direct-acting antiviral treatment failure in chronic hepatitis C: An HCV-TARGET analysis.

We aimed to develop and validate machine learning algorithms to predict direct-acting antiviral (DAA) treatment failure among patients with HCV infection. We used HCV-TARGET registry data to identify HCV-infected adults receiving all-oral DAA treatment and having virologic outcome. Potential pretreatment predictors (n=179) included sociodemographic, clinical characteristics, and virologic data. We applied multivariable logistic regression as well as elastic net, random forest, gradient boosting machine (GBM), and feedforward neural network machine learning algorithms to predict DAA treatment failure. Training (n=4894) and validation (n=1631) patient samples had similar sociodemographic and clinical characteristics (mean age, 57 years; 60% male; 66% White; 36% with cirrhosis). Of 6525 HCV-infected adults, 95.3% achieved sustained virologic response, whereas 4.7% experienced DAA treatment failure. In the validation sample, machine learning approaches performed similarly in predicting DAA treatment failure (C statistic [95% CI]: GBM, 0.69 [0.64-0.74]; random forest, 0.68 [0.63-0.73]; feedforward neural network, 0.66 [0.60-0.71]; elastic net, 0.64 [0.59-0.70]), and all four outperformed multivariable logistic regression (0.51 [0.46-0.57]). Using the Youden index to identify the balanced risk score threshold, GBM had 66.2% sensitivity and 65.1% specificity, and 12 individuals were needed to evaluate to identify 1 DAA treatment failure. Over 55% of patients with treatment failure were classified by the GBM in the top three risk decile subgroups (positive predictive value: 6%-14%). The top 10 GBM-identified predictors included albumin, liver enzymes (aspartate aminotransferase, alkaline phosphatase), total bilirubin levels, sex, HCV viral loads, sodium level, HCC, platelet levels, and tobacco use. Machine learning algorithms performed effectively for risk prediction and stratification of DAA treatment failure.

Clinical efficacy of Direct Acting Antivirals (DAAs) for Treatment of Recurrent Hepatitis C Virus infection After Liver Transplantation

Abstract BACKGROUND &amp; AIMS Recurrent hepatitis C virus (HCV) infection of transplanted liver allografts is universal in patients with detectable HCV viremia at the time of transplantation. Directacting antiviral (DAA) therapy has been adopted as the standard of care for recurrent HCV infection in the post-transplant setting. However, there are insufficient data regarding its efficacy in liver transplant (LT) recipients with a history of hepatocellular carcinoma (HCC), and the risk of HCC recurrence after DAA therapy is unknown. In this study, we aimed to demonstrate predictors of DAA treatment failure and HCC recurrence in LT recipients. METHODS A total of 106 LT recipients given DAAs for recurrent HCV infection from 2015 to 2019 were identified (68 with and 38 without HCC). Descriptive statistics and logistic regression models were used to estimate the multivariate odds ratios and respective 95% confidence intervals for predictors of treatment failure and HCC recurrence. RESULTS Six patients (6%) experienced DAA therapy failure and 100 (94%) had a sustained virologic response at follow-up week 12 (SVR12). A high alanine transaminase level &amp;gt;35 U/L at treatment week 4 was a significant predictor of treatment failure. DAA failure at follow-up week 12 was significantly associated with post-transplantation HCC recurrence, (odds ratio, 10.6 [95% confidence interval, 1.0-121.6]; P = .05). CONCLUSIONS DAAs are effective and safe in the treatment of recurrent HCV infection in LT recipients with history of HCC. Lack of SVR12 is a predictor of post-transplantation HCC recurrence.

Real-world re-treatment outcomes of direct-acting antiviral therapy failure in patients with chronic hepatitis C.

Direct-acting antiviral (DAA) drugs are associated with high (>95%) sustained virological response at 12 weeks (SVR12) in chronic hepatitis C (CHC) patients. There is a paucity of data regarding the characteristics and re-treatment outcomes of DAA treatment failure patients. In a retrospective analysis of the prospectively collected database, we assessed the outcomes of re-treatment among patients with previous DAA failure. Patients' characteristics, viral characteristics, including resistance-associated substitutions (RAS) in a subgroup of patients, SVR12, and clinical outcomes were studied. Of 40 patients with DAA failure, among whom 36 were retreated, mean age was 45.7 years, 63.9% (n = 23) were male, 63.9% (n = 23) had agenotype-3 infection and 63.9% (n = 23) were cirrhotic. The re-treatment regimens included a combination of pan-genotypic DAA, mainly sofosbuvir and velpatasvir with or without ribavirin. Three patients who declined retreatment and one who was still on treatment was excluded. For patients who completed re-treatment, SVR12 was 100% irrespective of genotypes. SVR12 among genotype 3 was 75% (15 of 20) when lost to follow-up was considered a treatment failure. Six patients died due to liver-related causes, including five (83.3%) with hepatocellular carcinoma. RAS analysis in 17 randomly selected patients did not reveal any dominant substitutions in NS5A or NS5B region affecting SVR12, though several novel mutations were observed. In conclusion, re-treatment of CHC patients with prior DAA failure using pan-genotypic DAA is associated with high SVR12 rates irrespective of genotype or the presence of RAS.

Global evolutionary analysis of chronic hepatitis C patients revealed significant effect of baseline viral resistance, including novel non-target sites, for DAA-based treatment and retreatment outcome.

Direct-acting antivirals (DAAs) have proven highly effective against chronic hepatitis C virus (HCV) infection. However, some patients experience treatment failure, associated with resistance-associated substitutions (RASs). Our aim was to investigate the complete viral coding sequence in hepatitis C patients treated with DAAs to identify RASs and the effects of treatment on the viral population. We selected 22 HCV patients with sustained virologic response (SVR) to match 21 treatment-failure patients in relation to HCV genotype, DAA regimen, liver cirrhosis and previous treatment experience. Viral-titre data were compared between the two patient groups, and HCV full-length open reading frame deep-sequencing was performed. The proportion of HCV NS5A-RASs at baseline was higher in treatment-failure (82%) than matched SVR patients (25%) (p= .0063). Also, treatment failure was associated with slower declines in viraemia titres. Viral population diversity did not differ at baseline between SVR and treatment-failure patients, but failure was associated with decreased diversity probably caused by selection for RAS. The NS5B-substitution 150V was associated with sofosbuvir treatment failure in genotype 3a. Further, mutations identified in NS2, NS3-helicase and NS5A-domain-III were associated with DAA treatment failure in genotype 1a patients. Six retreated HCV patients (35%) experienced 2nd treatment failure; RASs were present in 67% compared to 11% with SVR. In conclusion, baseline RASs to NS5A inhibitors, but not virus population diversity, and lower viral titre decline predicted HCV treatment failure. Mutations outside of the DAA targets can be associated with DAA treatment failure. Successful DAA retreatment in patients with treatment failure was hampered by previously selected RASs.

Clinical efficacy of direct-acting antiviral therapy for recurrent hepatitis C virus infection after liver transplantation in patients with hepatocellular carcinoma.

BACKGROUNDRecurrent hepatitis C virus (HCV) infection of transplanted liver allografts is universal in patients with detectable HCV viremia at the time of transplantation. Direct-acting antiviral (DAA) therapy has been adopted as the standard of care for recurrent HCV infection in the post-transplant setting. However, there are insufficient data regarding its efficacy in liver transplant (LT) recipients with a history of hepatocellular carcinoma (HCC), and the risk of HCC recurrence after DAA therapy is unknown.AIMTo demonstrate predictors of DAA treatment failure and HCC recurrence in LT recipients.METHODSA total of 106 LT recipients given DAAs for recurrent HCV infection from 2015 to 2019 were identified (68 with and 38 without HCC). Descriptive statistics and logistic regression models were used to estimate the multivariate odds ratios and respective 95% confidence intervals for predictors of treatment failure and HCC recurrence.RESULTSSix patients (6%) experienced DAA therapy failure post-LT and 100 (94%) had a sustained virologic response at follow-up week 12. A high alanine transaminase level > 35 U/L at treatment week 4 was a significant predictor of treatment failure. Relapse to pre-LT DAA therapy is a predictor of post-LT HCC recurrence, P = 0.04. DAA relapse post-LT was also associated with post-transplantation HCC recurrence, P = 0.05.CONCLUSIONDAAs are effective and safe in the treatment of recurrent HCV infection in LT recipients with history of HCC. Relapse to pre- and post-LT DAA therapy is associated with post-transplantation HCC recurrence.

Real-word efficacy of sofosbuvir, velpatasvir plus ribavirin therapy for chronic hepatitis patients who failed to prior DAA therapy with NS5A-P32 deletion mutated HCV infection.

The hepatitis C virus (HCV) NS5A-P32 deletion (P32del) confers potent resistance to NS5A inhibitors. Chronic hepatitis C patients in whom NS5A-P32del variants had emerged during prior direct-acting antiviral (DAA) therapy with an NS5A inhibitor show poor response to DAA retreatment. Here, we report three patients with HCV NS5A-P32del infection who were treated with sofosbuvir, velpatasvir plus ribavirin (SOF/VEL + RBV) in a real-world setting. The patients developed HCV NS5A-P32del, L31F + P32del, or L31V + P32del variants following failure of daclatasvir plus asunaprevir (DCV/ASV) therapy. One of the patients failed to respond to subsequent DCV/ASV and beclabuvir therapy, and the remaining two patients failed to respond to subsequent glecaprevir and pibrentasvir therapy. All three patients completed 24-week SOF/VEL + RBV therapy. Serum HCV RNA became negative at the end of the therapy in all three patients. Two patients with NS5A-P32del and NS5A-L31F + P32del achieved sustained virological response 12weeks after completion of treatment (SVR12), but HCV relapsed in the remaining NS5A-L13V + P32del patient. Direct sequence analysis detected no additional variants within either the NS5A or NS5B regions at the time of relapse. In conclusion, three patients with prior NS5A-P32del-associated DAA treatment failure received 24weeks of SOF/VEL + RBV therapy, and two of the patients achieved SVR12.

Resistance-associated substitutions (RASs) to HCV direct-acting antivirals (DAAs) at baseline of treatment in thalassemia patients: a referral center study.

Patients with thalassemia major are at high risk of hepatitis C through blood transfusion from donors infected by hepatitis C virus (HCV). The use of direct-acting antiviral (DAA) therapy against such HCV infections has increased in different populations. However, resistant viral variants can affect treatment outcomes, and therefore improved surveillance strategies are needed. Accordingly, we aimed to evaluate resistance-associated substitutions (RASs) to HCV DAAs at the baseline of treatment in thalassemia patients in a referral center. Out of 89 thalassemia patients who suffered from HCV infection and were referred to our center between 2016 and 2017, 43 underwent further analysis of the HCV nonstructural proteins NS5A and NS5B using polymerase chain reaction (PCR) sequencing methods. Unique primers were designed using bioinformatics software for separate detection of HCV subtypes 1a, 3a, and 1b. Detection of RASs was performed based on previously published literature. Statistical analysis was carried out using SPSS version 19. The participants, 60.4% (26/43) of whom were male, had a mean age ± standard deviation (SD) of 33.0 ± 5.0years. HCV subtype 1a was found in 27 cases, 3a in 13, and 1b in three. In HCV subtype 1a there were 163 mutations in NS5A and 212 mutations in NS5B. The frequency of RASs was 20.9% (8 RASs in 9 patients), including M28V and H58P in subtype 1a, L28M, R30Q, C316N, and C316S in subtype 1b, and S24F in subtype 3a. Statistically, the subtype 1b and a higher mutation rate in NS5A were associated with RASs (p-value < 0.05). The emergence of natural RASs to HCV DAAs serves as a warning of the risk of drug resistance in response to the broad usage of antivirals. However, relapses in these DAA-treated HCV-infected thalassemia patients are rarely reported. Our findings indicate that the prevalence of RASs prevalence at baseline was 20.9% in these patients, and this calls for extrapolation to a larger population study, as highlighted in other studies, with larger sample sizes, high-throughput methods, and follow-up in order to fully evaluate treatment outcomes in RASs-detected individuals. Optimized therapeutic strategies, particularly in complex, difficult-to-cure patients, can effectively prevent DAA treatment failure as a result of selection for RASs.

Incidence of HCC recurrence after DAA treatment for HCV in a multicentre Italian cohort study

AbstractBackground and aimThe present real‐life multicentre, prospective study aims to investigate the effects of direct‐acting antivirals (DAAs) in HCV patients with a previous successfully treated hepatocellular carcinoma (HCC), in terms of neoplastic recurrence and sustained virological response (SVR) rates.MethodsFrom March 2015 to March 2017, all consecutive HCV patients with a previous successfully treated HCC who underwent DAA therapy were enrolled. Neoplastic recurrence was used as the primary outcome, whereas the secondary outcomes were patient characteristics predicting HCC recurrence. Cumulative probabilities of recurrence were extracted from time‐to‐event curves based on the Kaplan‐Meier method. Hazard ratios with 95% confidence intervals were estimated using univariate and multivariate Cox regressions.ResultsA total of 101 patients were enrolled: 83% of them were in Child‐Pugh class A, 88% had a history of HCC BCLC stage 0/A and 91.1% achieved SVR. The median time from the last successful HCC treatment to DAA start was 10.1 months [IQR: 5.6‐16.7]. Thirty‐one HCC recurrences were observed from DAA start (median follow‐up: 31.7 months). The incidence rate of recurrence was 20.5/100 person‐years. The 6‐, 12‐ and 24‐months HCC recurrence rates from the last HCC treatment were 1%, 8.9% and 25.6% respectively. DAA treatment failure, higher level of total bilirubin, higher BMI and higher level of AFP were significantly associated with higher risk of HCC recurrence in both univariate and Cox multivariate analysis.ConclusionsOur data suggest that the achievement of SVR and the absence of well‐known HCC risk factors reduce recurrence in patients who have taken DAAs.

NS5A resistance – associated substitutions in chronic hepatitis C patients with direct acting antiviral treatment failure in Turkey

ObjectivesChronic hepatitis C (CHC) is now a more curable disease with new direct acting antivirals (DAA). Although high sustained virologic response rates, failures still occur in DAA regimens. Our objective in this study was to characterize the real-life presence of clinically relevant resistance – associated substitutions (RASs) in the HCV NS5A gene in CHC patients whose DAA regimen has failed. MethodsThe study enrolled 53 CHC patients who experienced failure with DAA regimen as the prospective longitudinal cohort between 2017–2019. Genotypic resistance testing was performed via the viral population sequencing method and The Geno2pheno HCV tool was used for RAS analysis. ResultsThe most frequent failure category was relapse (88%) followed by non-responder (12%). For a total of 36% of patients, RASs was detected in NS5A, Y93H was the most detected RAS in GT1b infected patients (89%). ConclusionsThis study establishes an HCV failure registry for Turkey in which samples were combined with clinical, virologic and molecular data of adult patients whose DAA therapy failed. RASs can occur in CHC patients with DAA treatment failures. Evaluation of RAS after DAA failure is very important before re-treatment is initiated to prevent virologic failure.

Hepatocellular Carcinoma Is a Negative Predictor of Sustained Viral Response in Liver Transplant Recipients With Hepatitis C Treated With Direct-Acting Antivirals

IntroductionTreatment with direct-acting antivirals (DAA) for hepatitis C (HCV) in liver transplant (LTX) recipients is very effective, but some studies showed that the treatment effectiveness might be impaired in patients with hepatocellular carcinoma (HCC). The study aimed to evaluate the predictors of DAA treatment failure in LTX recipients. MethodsLiver biopsy was done before the treatment in 107 of the 120 patients included. All patients had an abdominal ultrasound and liver elastography performed before and after the therapy. Blood HCV polymerase chain reaction was done before; during; and at 4, 12, and 24 weeks after the treatment. ResultsOverall sustained viral response 24 weeks after treatment (SVR24) was 96%. There were 2 patients with HCC at the start of the DAA treatment and 3 cases of HCC recurrence during a 1-year follow-up. Treatment failure was observed in 1/115 (0.9%) patients without HCC and 4/5 (80%) with active HCC (P = .0001). Liver fibrosis and previous interferon treatment had no impact on treatment efficacy. Time to viremia elimination on treatment was shorter in the responder versus nonresponder group (28 vs 58 days, P = .03). ConclusionsHCC is a negative predictor of DAA therapy success in LTX recipients.

First Reported Treatment Failure in a Recipient of a Hepatitis C Viremic Heart Transplant

Cardiac transplant centers are now successfully utilizing hepatitis C virus (HCV) donor hearts to increase the availability of organs now that a curative treatment is available with direct acting antivirals (DAA). We present the first described case of DAA treatment failure in a patient who received an HCV donor, nucleic acid testing (NAT) positive heart. A 65-year-old male with a mixed cardiomyopathy underwent orthotopic heart transplant with an HCV+/NAT+ heart. He seroconverted within seven days of transplant, noted by a peak HCV viral load of 7.65 log IU/mL and genotype of 1a without resistance markers. Planned initial treatment with glecaprevir/pibrentasvir (G/P) was denied by insurance. After approval for and treatment with ledipasvir/sofosbuvir (L/S) for 8 weeks, the patient's viral load was initially undetectable. However, he developed recurrent viremia 6 months after treatment completion with an HCV load of 7.40 log IU/mL with NS5A resistance due to a Y93H mutation. He was subsequently initiated on sofosbuvir/velpatasvir/voxilaprevir (S/V/V) with persistent undetectable viral loads to date at 4 months. This is the first documented case of DAA treatment failure in a recipient of HCV+/NAT+ transplanted heart treated with L/S. This treatment failure was likely secondary to insufficient treatment duration. The ION-3 study demonstrated noninferiority for an 8 week treatment duration compared to 12 weeks of L/S, but at the cost of a higher relapse rate in the 8 week arm (5% vs 1%) associated with viral load of >6.78 log IU/mL. The Y93H mutation is more likely to reduce treatment efficacy in L/S as noted by a pooled resistance analysis compared to G/P, which has a failure rate of <1%. In our case, resistance may have been prevented by 12 weeks of L/S or initial use of G/P for 8 weeks, as supported by the ENDURANCE-1 trial. In the new era of HCV transplantation, selection of DAA and duration of treatment are critical. Awareness of the resistance development data is needed when selecting HCV treatment regimens.

Incidence and predictors of direct-acting antiviral treatment failure in Turkish patients with chronic hepatitis C genotype 1b infection.

Evaluation of the incidence and predictors of failure of direct-acting antiviral treatment for hepatitis C virus genotype 1b patients is important. Our retrospective cohort study assessed 172 Turkish patients who had received a full course of such treatment and could be checked for sustained virologic response. The overall treatment failure rate was 2.9% (5/172), all of whom relapsed. In three of these cases with sequencing data available, all had NS5A resistance-associated substitution. Multivariate analysis revealed that a 1 mg/dL increase in pre-treatment total bilirubin level was associated with a sevenfold increased likelihood of treatment failure. The baseline level of total bilirubin was the only significant independent predictor of direct-acting antiviral treatment failure.

Ribavirin induces hepatitis C virus genome mutations in chronic hepatitis patients who failed to respond to prior daclatasvir plus asunaprevir therapy.

Ribavirin (RBV) induces nucleotide (nt) substitutions in hepatitis C virus (HCV) genome nonstructural (NS) regions. Although emergence of drug resistance-associated variants is associated with direct-acting antiviral treatment failure, the effect of RBV on genome substitutions in such patients is unknown. Genotype 1b HCV subgenomic replicon cells were treated with RBV for 120 hours. Six patients with chronic genotype 1b with HCV-infected patients who failed to respond to prior daclatasvir plus asunaprevir (DCV/ASV) therapy were treated with 12 weeks of sofosbuvir and ledipasvir plus RBV after 4 weeks of RBV monotherapy. RBV-induced genome mutations in the HCV NS region (nt3493-9301) in replicon cells and in patients during 4 weeks of RBV monotherapy were analyzed by deep sequencing. RBV-associated G-to-A and C-to-U transitions increased in a dose-dependent manner in HCV replicon cells after the RBV treatment. In patients with prior DCV/ASV treatment failures, the median serum HCV RNA level was 6.25 ± 0.31 log IU/mL at the start of RBV therapy and decreased significantly to 5.95 ± 0.4 log IU/mL (P = .03) after 4 weeks of RBV monotherapy. Although predominant HCV genome substitutions rates were similar between nontreatment and RBV-treatment periods (0.042 and 0.031 per base pair, respectively; P = .248), the frequencies of G-to-A and C-to-U transitions significantly increased after RBV monotherapy. These transitions were enriched, particularly within the HCV NS3 region in all patients. RBV treatment induces G-to-A and C-to-U transitions in the HCV genome even in chronic patients with hepatitis C with prior DCV/ASV treatment failures.