Baseline and Breakthrough Resistance Mutations in HCV Patients Failing DAAs

Abstract

Sustained virologic response rates have increased dramatically following direct acting antiviral (DAA) therapy in chronic HCV infection. However, resistance-associated substitutions (RASs) may occur either prior to DAA or following drug exposure. The aim of this study was to determine RASs in DAA treatment-failing patients and the role of RASs in failure treatment. Six hundred and twenty HCV patients were evaluated. Direct sequencing of HCV genes was performed at breakthrough in all 31 patients failing DAAs, and in 19 baseline patients. Deep sequencing analysis was performed in 15/19 baseline patients. RASs were detected at breakthrough in 17/31 patients and at baseline in 11/19 patients, although, only 8/19 patients carried RASs associated with the prescribed regimen. Deep sequencing analysis showed RASs at baseline in 10/15 treatment-failing patients. No significant difference was observed with the Sanger sequencing. Treatment failure in the 14/31 patients without RASs was associated with suboptimal treatment. In 54.8% of treatment-failing patients one of the causes of failure might be the presence of RASs. In the majority of patients with RASs, mutations were present at baseline. Direct resistance test is advocated before treatment and at breakthrough in order to optimize retreatment regimens.

Detection of low-level HCV variants in DAA treated patients: comparison amongst three different NGS data analysis protocols

“…outcomes [11][12][13][14][15], as we also reported in our work. Therefore, detecting low-level RAS Y93H on the NS5A of Pt.2 at his baseline can be important to further stress the correlations, described by AADLS, between the presence of Y93H at the baseline in patients treated with sofosbuvir/velpatasvir and reduced SVR12 [4].…”

“…Current clinical guidelines state that only RAS present at frequencies above 15% need to be considered when choosing antiviral treatments [4] since polymorphisms associated with drug resistance have been also demonstrated by Sanger for higher represented viral variants [9,10]. However, the detection threshold is still debated as studies showed different results when mutations at a frequency below 15% are investigated [4, [11][12][13][14][15].…”

Epistatic Interactions in NS5A of Hepatitis C Virus Suggest Drug Resistance Mechanisms

“…For these drugs, not only is there different susceptibility among GTs, but also there is evidence of different resistance-associated-mutations (RAMs) development [ 7 , 9 ]. Importantly, NS5A RAMs have been described both before treatment (also called baseline) as well as after failure of NS5A inhibitors-containing therapies [ 10 , 11 , 12 , 13 , 14 , 15 ]. According to the current recommendations of the European Association for the Study of the Liver (EASL), resistance testing for NS5A inhibitors is subject to the availability of reliable tests, and the list of potential NS5A RAMs include several mutations in positions 28, 30, 31, 58, and 93 for GT-1a viruses and the mutation Y83H for the GT-3 viruses [ 10 ].…”

“…Q30R is known to confer resistance against multiple NS5A inhibitors for GT-1a viruses [ 16 , 17 , 23 , 24 , 25 ]. The substitution to a chemically similar lysine (K) has been observed to confer resistance both for GT-1a viruses [ 26 ] and for GT-3 viruses [ 11 ].…”

Baseline Amino Acid Substitutions in the NS5A ISDR and PKR Binding Domain of Hepatitis C and Different Fibrosis Levels and Levels of Development of Hepatocellular Carcinoma in Patients Treated with DAAs

“…Viral RNA was extracted from serum samples using the automatic Easy Mag extractor (Biomerieux, Lyon, France). HCV NS5A domain I (aa 1-406), NS3-protease (aa 1-181), and NS5B (aa 1-591) genes were amplified using a nested RT-PCR [17,18]. The amplified NS5A region Viruses 2020, 12, 255 3 of 10 included PKR-bd (from aa 237 to 302) and ISDR (from aa 237 to 302).…”