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

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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.