Prevalence of Single and Multiple Natural NS3, NS5A and NS5B Resistance-Associated Substitutions in Hepatitis C Virus Genotypes 1–4 in Italy

Abstract

Natural resistance-associated substitutions (RASs) are reported with highly variable prevalence across different HCV genotypes (GTs). Frequency of natural RASs in a large Italian real-life cohort of patients infected with the 4 main HCV-GTs was investigated. NS3, NS5A and NS5B sequences were analysed in 1445 HCV-infected DAA-naïve patients. Sanger-sequencing was performed by home-made protocols on 464 GT1a, 585 GT1b, 92 GT2c, 199 GT3a, 16 GT4a and 99 GT4d samples. Overall, 20.7% (301/1455) of patients showed natural RASs, and the prevalence of multiclass-resistance was 7.3% (29/372 patients analysed). NS3-RASs were particularly common in GT1a and GT1b (45.2-10.8%, respectively), mainly due to 80K presence in GT1a (17%). Almost all GTs showed high prevalence of NS5A-RASs (range: 10.2–45.4%), and especially of 93H (5.1%). NS5A-RASs with fold-change >100x were detected in 6.8% GT1a (30H/R-31M-93C/H), 10.3% GT1b (31V-93H), 28.4% GT2c (28C-31M-93H), 8.5% GT3a (30K-93H), 45.5% GT4a (28M-30R-93H) and 3.8% GT4d (28V-30S-93H). Sofosbuvir RAS 282T was never detected, while the 159F and 316N RASs were found in GT1b (13.4–19.1%, respectively). Natural RASs are common in Italian patients infected with HCV-GTs 1–4. High prevalence of clinically-relevant RASs (such as Y93H) supports the appropriateness of HCV resistance-test to properly guide DAA-based therapy.

Hepatitis C virus genotype 1 infection: Prevalence of NS5A and NS5B resistance‐associated substitutions in naïve patients from Argentina

“…L159F and C316N were the most frequently identified NS5B substitutions at baseline. These findings appear to be in line with previous reports stating a high prevalence of L159F and C316N in Brazil (16%) and Italy (13%‐19%) . C316N and L159F were related to virologic failure after SOF/LDV and SOF/DCV treatment .…”

“…In the present study, RASs were present in 25.8% of the NS5A sequences analyzed from Buenos Aires, Argentina. Even when RASs frequencies informed in the literature comprise wide values ranging between less than 10% to more than 40%, the prevalence observed in this study is higher when compared to most regional and worldwide studies . Differences in sample characteristics such as cohort size, positions analyzed, applied detection methods, uncertainty about prior exposure to DAA, and acting viral genotypes/subtypes can affect the rate of RASs, hindering comparison among different studies.…”

“…Contrary to expectations, findings from this study show a similar prevalence of NS5A RASs in patients infected with HCV‐1a and HCV‐1b. Most previous studies report a higher NS5A RASs prevalence in HCV‐1b infected patients; other studies from Brazil had shown similar prevalence in both subtypes or even higher in HCV‐1a …”

Suboptimal SVR rates in African patients with atypical genotype 1 subtypes: Implications for global elimination of hepatitis C

“…17 This has been linked to the presence of an amino acid motif, MPRMP, at positions 28-32 of the NS5A gene that confers high-level resistance to DAAs in vitro. 18 Population-based studies to determine the frequency of unusual subtypes and the efficacy of DAA regimens against them, are urgently needed to formulate guidelines for treating HCV in Africa. 19 The corollary of these data, and the fact that in resource poor regions of Africa genotyping or full genome sequencing will not be available, is that second generation NS5A inhibitors should be preferred as first-line agents in the region.…”

A Prospective Italian Study on Baseline NS3 and NS5A Resistance to Direct-Acting Antivirals in a Real-World Setting of HIV-1/HCV Coinfected Patients and Association with Treatment Outcome

“…Natural RASs prevailed in NS3, with more occurring in GT1a (13/23) than GT3a (0/26) and GT4d (2/13). The prevalence of naturally occurring RASs in NS3 has been found to be 11.4-40% [12][13][14][15][16][17] depending on the HCV genotype investigated and geographic origin of the isolates. One recent study [18] of HIV-1/HCV-coinfected patients reported 38% of RASs in the NS3 domain.…”