Pilot Sub-Study of the Effect of Hepatitis C Cure by Glecaprevir/Pibrentasvir on the Gut Microbiome of Patients with Chronic Hepatitis C Genotypes 1 to 6 in the Mythen Study

Abstract

In this small pilot sub-study, longitudinal gut microbiota composition changes, after successful treatment of hepatitis C virus (HCV) with the co-formulated glecaprevir/pibrentasvir (GLE/PIB), were analyzed before treatment (baseline) and 12 weeks post-treatment. Participating patients provided a fresh stool sample the week before their study visit, from which microbial DNA was extracted and sequenced for the 16S rRNA region in an Illumina MiSeq2 platform. Microbial and statistical analyses were conducted to determine the alpha-diversity (number of different taxa within a sample) and beta-diversity (number of overlapping taxa between samples). Stool samples from 58 patients were eligible for analysis. There were 27 patients with HCV genotype 1, 10 with genotype 2, 16 with genotype 3, and 5 with genotype 4. No statistically significant differences in gut microbiota diversity, species richness, or microbial community pattern were found at baseline and at post-treatment Week 12. Lack of statistically significant differences remained consistent in further analysis by demographic and baseline disease characteristics. Surprisingly, no statistically significant changes in alpha- and beta-diversity were seen in the microbiota after GLE/PIB treatment, though there was a trend toward less richness over time. Further investigation is needed into this unexpected outcome to better understand the role of HCV treatment and the gut microbiota.

Keywords: HCV; alpha-diversity; beta-diversity; direct-acting antivirals; gut microbiota.

Figure 1

Microbial differences before treatment (baseline) vs. SVR12 groups. Taxonomy profile of patients at baseline and 12 weeks after the end of the treatment are shown (A) at phylum level and (B) at family level. (C) Microbial clustering is shown based on generalized UniFrac metrics using fecal DNA samples at baseline and SVR12. Non-parametric analysis of variance (Adonis) was used to test significant differences between groups on the PCoA plot, with a result of p > 0.05. The ellipses represent a 95% CI surrounding each disease group. B = baseline; E = end of treatment; PC = principal component; PCoA = principal coordinate analysis; SVR12 = sustained virologic response 12 weeks after the end of the treatment.

Figure 2

Overall species richness comparison of before treatment (baseline) and SVR12 groups. In this analysis, p < 0.05 was considered significant. Box-and-whisker plots display quartiles and range. SVR12 = sustained virologic response 12 weeks after the end of the treatment.

Figure 3

Overall beta-diversity differences before treatment (baseline) vs. SVR12 groups by patient and HCV genotype. Notable outliers with considerable changes are circled in red. Examples of minimal change are circled in blue for comparison. Non-parametric analysis of variance (Adonis) was used to test significant differences between groups on the PCoA (principal coordinate analysis) plot with a result of p > 0.05. SVR12 = sustained virologic response 12 weeks after the end of treatment.