Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure

Abstract

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Amino acid substitutions associated with treatment failure of hepatitis C virus infection

“…These differences of distribution among the two genotypes are statistically significant (for T64A, p=0.03899 and p=5.89×10 −4 for the comparison between G1b and G1a or G3a, respectively; for R78K, S213C and A218S, p=2.2×10 −16 for the comparisons between G1a and G1b; for S231N and Q309R, p=3.4×10 −14 and p=5.9×10 −6 for the comparisons between G1a and G1b, respectively; proportion test). These results suggest that the HRSs display a certain degree of subtype specificity, as has been previously reported for RAS [6,9,10].…”

“…RAS identified by UDS have been recently described in a cohort of 220 HCV-infected patients failing DAA therapies [9]. To provide a broad picture of all substitutions identified in NS3 (within amino acids 32 to 179), NS5A (within amino acids 24 to 152) and NS5B (within amino acids 124 to 320) proteins in these patients (Table S1), we constructed a heat map representing the frequency of each substitution in each viral sample (Figure 1A).…”

“…Since HCV subtype can influence the response to treatment and RAS selection [9,10], it was interesting to explore if HCV subtype may also affect the types of HRSs found in the viral proteins. In NS5A, while T64A was present in patients infected with HCV of the three main viral genotypes (G1b, G1a and G3a), R78K was found mainly in G1a HCV-infected patients (Figure 2A).…”

“…Given the massive number of patients undergoing treatment worldwide, characterization of resistance-associated substitutions (RAS) has become part of HCV therapy management [5–8]. Selection of RAS associated with treatment failure is increasingly reported, concomitantly with the number of treated patients [9–13]. RAS can be also present in naïve patients who have not received DAA therapies, again as documented with several cohorts worldwide [14–18].…”

“…In a recent deep sequencing analysis of 220 subtyped HCV samples from infected patients who failed therapy, collected from 39 Spanish hospitals, we determined amino acid sequences of the DAA-target proteins NS3, NS5A and NS5B, by ultra-deep sequencing (UDS) of HCV patient samples, in search of RAS [9]. Interestingly, 18.6% of the patients that failed therapy did not include any substitutions that could be considered bona fide RAS, according to current guidelines [6].…”