Amino Acid Substitutions in Genotype 3a Hepatitis C Virus Polymerase Protein Affect Responses to Sofosbuvir

Abstract

Background & aims: Sofosbuvir is a frequently used pan-genotype inhibitor of hepatitis C virus (HCV) polymerase. This drug eliminates most chronic HCV infections, and resistance-associated substitutions in the polymerase are rare. However, HCV genotype 3 responds slightly less well to sofosbuvir-based therapies than other genotypes. We collected data from England's National Health Service Early Access Program to search for virus factors associated with sofosbuvir treatment failure.

Methods: We collected patient serum samples and used the capture-fusion assay to assess viral sensitivity to sofosbuvir in 14 HCV genotype 3 samples. We identified polymorphisms associated with reduced response and created modified forms of HCV and replicons containing the substitutions of interest and tested their sensitivity to sofosbuvir and ribavirin. We examined the effects of these polymorphisms by performing logistic regression multivariate analysis on their association with sustained virologic response in a separate cohort of 411 patients with chronic HCV genotype 3 infection who had been treated with sofosbuvir and ribavirin, with or without pegylated interferon.

Results: We identified a substitution in the HCV genotype 3a NS5b polymerase at amino acid 150 (alanine [A] to valine [V]), V at position 150 was observed in 42% of patients) with a reduced response to sofosbuvir in virus replication assays. In patients treated with sofosbuvir-containing regimens, the A150V variant was associated with a reduced response to treatment with sofosbuvir and ribavirin, with or without pegylated interferon. In 326 patients with V at position 150, 71% achieved an sustained virologic response compared to 88% with A at position 150. In cells, V at position 150 reduced the response to sofosbuvir 7-fold. We found that another rare substitution, glutamic acid (E) at position 206, significantly reduced the response to sofosbuvir (8.34-fold reduction); the combinations of V at position 150 and E at position 206 reduced the virus response to sofosbuvir 35.77-fold. Additionally, in a single patient, we identified 5 rare polymorphisms that reduced sensitivity to sofosbuvir our cell system.

Conclusions: A common polymorphism, V at position 150 in the HCV genotype 3a NS5b polymerase, combined with other variants, reduces the virus response to sofosbuvir. Clinically, infection with HCV genotype 3 containing this variant reduces odds of sustained virologic response. In addition, we identified rare combinations of variants in HCV genotype 3 that reduce response to sofosbuvir.

Keywords: amino acid change; genetics; mutation; response to therapy.

Copyright © 2019 AGA Institute. Published by Elsevier Inc. All rights reserved.

Figures

Figure 1

SOF sensitivity in HCV genotype 3 treatment non-responders to direct-acting antiviral (DAA) therapy was assessed using the capture-fusion assay. Sera from patients with HCV genotype 3 (n = 14) who achieved SVR (blue) or relapsed (red) were used to assess sensitivity to SOF and RBV. Changes in HCV RNA for SOF and RBV in patients who achieved SVR (n = 4) (A, E) or relapsed are shown. Samples from patients who relapsed were further divided into 2 groups, depending on the assay outcome, those who were SOF- and RBV-sensitive (n = 4) (B, F) and insensitive (n = 6) (C, G). Data were summarized in (D; SOF) and (G; RBV) to show HCV RNA as a percentage of no drug treatment for a single dose of drug (0.25 μM of SOF and 0.75 μM of RBV). Graphs show mean ± SEM. P values were calculated using Kruskal-Wallis test. Drug sensitivity of each sample was assessed in quadruplicate for each concentration.

Figure 2

3-Dimensional model of the HCV polymerase NS5b (A, front; B, back; C, top) derived from the JFH-1 crystal structure with the location of the polymorphisms of interest shown in purple. The structure in the center represents a bound RNA strand. PDB crystal structure ID: 4WTG. Structure was annotated using the Chimera software. dNTP, deoxyribonucleotide triphosphate; dsRNA, double-stranded RNA.

Figure 3

Huh7.5-SEC14L2 cells transiently transfected (by electroporation) with luciferase-containing HCV (S52-replicon) constructs with the NS5b polymorphisms from patient 9 (see Table 1). Cells were treated with SOF for 72 hours and replication was determined by luciferase assay, normalized to a sample 4 hours post electroporation for each construct. As a control for SOF non-response, a replicon containing the S282T NS5b mutation was included. Panels A–E indicate the effect of the polymorphisms from patient 9 to SOF sensitivity. IC50 values with 95% CIs were calculated by determining the drug concentration that affected a 50% reduction in HCV RNA and are summarized in Table 2. Mean values per drug concentration are plotted ± SEM. The above is representative of at least 3 independent experiments.

Figure 4

Huh7.5-SEC14L2 cells were transiently transfected (by electroporation) with luciferase containing HCV (S52-replicon) with Wt, 150V, and 206E, individually and in combination. Cells were treated with SOF for 72 hours and HCV replication was measured using a luciferase assay and normalized to a sample 4 hours post electroporation for each construct. Panels A–C indicate the effect of the polymorphisms (A150V and K206E) from patients 10–14 on SOF sensitivity. IC50 values with 95% CIs were calculated by determining the drug concentration that affected a 50% reduction in replication. Mean values per drug concentration are plotted ± SEM. The above is representative of at least 3 independent experiments.

Figure 5

Sensitivity of HCV genotype 3 viruses to SOF, RBV, and DAC, comparison between the Wt and polymorphisms of interest. Huh7.5 SEC14L2 cells were infected with the indicated HCV genotype 3 viruses at an multiplicity of infection of 0.2 for 72 hours before treatment with serial dilutions of SOF (A), RBV (B), or DAC (C). After 24 hours of drug treatment, the cells were harvested (72 hours for RBV) and HCV quantified by reverse-transcription quantitative polymerase chain reaction. Concentration–response curves were calculated. IC50 values with 95% CIs were calculated by determining the drug concentration that affected a 50% reduction in HCV replication. Mean values per drug concentration are plotted ± SEM. Results show a mean of 2 independent experiments done in duplicate.

Supplementary Figure 1

Huh7.5 cells were incubated with a serial dilution of RBV for 72 hours in triplicate. AlamarBlue reagent was added for 3 hours and fluorescence intensity was assessed as a measure of cytotoxicity.

Supplementary Figure 2

(A) HCV genotype 1–7 amino acid sequences were aligned and the table shows the amino acid at the positions of interest and compared to the gt3a reference sequence. (B) Alignment of 1200 HCV genotype 3a sequences from the HCV-GLUE database identifying the minor variants at each position of interest. Legend designates the color code for each amino acid. (C) Analysis of the NS5b polymorphisms in the BOSON cohort, the prevalence of the NS5b polymorphisms was assessed from >500 viral sequencing samples obtained from the BOSON cohort. (D) Each mutation was tested to assess whether the frequency was significantly different between SVR and non-SVR samples. Frequencies were analyzed using Fisher’s exact test.

Supplementary Figure 3

Huh7.5-SEC cells transiently transfected (by electroporation) with luciferase containing HCV (S52-replicon) constructs with the indicated NS5b polymorphisms were assessed. Cells were treated with RBV for 72 hours and replication was measured using a luciferase assay, normalized to a sample 4 hours post electroporation for each construct. Panels A–E indicate the effect of the polymorphisms from patient 9 to RBV sensitivity. The above is representative of at least 3 independent experiments. Relative luciferase units (RLU).

Supplementary Figure 4

Huh7.5-SEC cells transiently transfected (by electroporation) with luciferase containing HCV (S52-replicon) constructs with the indicated NS5b polymorphisms were assessed. Cells were treated with RBV for 72 hours and replication was measured in a luciferase assay, normalized to a sample 4 hours post electroporation for each construct. Panels A–C indicate the effect of the polymorphisms from patients 10–14 on RBV sensitivity. The above is representative of at least 3 independent experiments. Relative luciferase units (RLU).

Supplementary Figure 5

Huh7.5-SEC14L2 cells transfected with the viral constructs were stained for the HCV NS5a protein (green) by immunofluorescence 7 days post transfection to confirm establishment of replication complexes. Mock transfected cells were included as a negative control.

Supplementary Figure 6

(A) Naïve Huh7.5-SEC14L2 cells were infected with Wt and DBN virus with the polymorphisms of interest at a multiplicity of infection of 0.05. Samples were taken at the indicated time points for quantification of HCV RNA by reverse-transcription quantitative polymerase chain reaction. Data presented are representative of 2 independent experiments and analyzed using a Mann-Whitney U test. Graph depicts mean ± SEM. (B, C) An equal inoculum of the Wt and mutant virus was used to infect the cells (multiplicity of infection = 0.03 median tissue culture infectious dose), the relative amounts of the competing viruses were determined by next-generation sequencing at 0, 24, 48, and 72 hours post infection and the percent of Wt (alanine at 150 or lysine at 206) is shown.