Fig. 5
From: Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus
Ultra-deep sequencing of four HCV samples derived from patients who failed directly-acting antiviral agents (DAAs) therapies. Viral RNAs from four HCV-infected patients, corresponding to G1a, G1b, G3a, and G4d (top headings) were used to amplify NS3- [PCR 1.1 (533 bp) in Fig. 2], NS5A- [PCR 2.1 (477 bp) in Fig. 2], and NS5B-coding regions [PCRs 3.1 (478 bp) and 3.2 (483 bp) in Fig. 2] using MiSeq platform. For each amplicon the number of cleaned reads (given in parenthesis), the list of amino acid substitutions, and their frequencies (percentage given following each amino acid substitution) are indicated. Failure occurred after the following treatments: ledipasvir/sofosbuvir/ribavirin (12 weeks), ledipasvir/sofosbuvir (12 weeks), daclatasvir/sofosbuvir/ribavirin (12 weeks), ledipasvir/sofosbuvir/ribavirin (12 weeks) for G1a, 1b, 3a, and 4d HCV-infected patients, respectively. Viral load was 6.9 × 104 IU/ml, 1.4 × 106 IU/ml, 7.6 × 105 IU/ml, and 6.3 × 104 IU/ml for G1a, 1b, 3a, and 4d HCV-infected patients, respectively. Substitutions written in red means that they are known to confer resistance to DAAs included in the treatment combinations. Distribution of haplotypes in the NS5A-coding region for the G1b patient is depicted in the box at the bottom to explain the difference between the frequency of an individual amino acid substitution (independently of the haplotypes that contain it) or the frequency of an haplotype that includes the same substitution in its constellation of substitutions