Resistance analysis and treatment outcomes in hepatitis C virus genotype 3-infected patients within the Italian network VIRONET-C

Aim This study aimed to investigate the role of resistance-associated substitutions (RASs) to direct-acting-antivirals (DAAs) in HCV genotype 3 (GT3). Methods Within the Italian VIRONET-C network, a total of 539 GT3-infected patients (417 DAA-naïve and 135 DAA-failures, of them, 13 at both baseline and failure) were analysed. Sanger sequencing of NS3/NS5A/NS5B was performed following home-made protocols. Results The majority of patients were male (79.4%), 91.4% were injection drug users, 49.3% were cirrhotic and 13.9% were HIV co-infected. Phylogenetic analysis classified sequences as GT3a-b-g-h (98%-0.4%-0.2%-1.2%) respectively. Overall, 135 patients failed a DAA regimen: sofosbuvir (SOF)/daclatasvir (DCV) or velpatasvir (VEL)±ribavirin (RBV) (N = 91/15) and glecaprevir (G)/pibrentasvir (P) (N = 9). Moreover, 14.8% of patients were treated with suboptimal regimens for GT3: 3D ± RBV (Paritaprevir/r + Ombitasvir+Dasabuvir, N = 15), SOF + Simeprevir (SIM) (N = 1) or SOF/Ledipasvir (LDV) ± RBV (N = 4). RAS prevalence was 15.8% in DAA-naïve patients. At failure, 81.5% patients showed at least one RAS: 11/25 (44.0%) in NS3, 109/135 (80.7%) in NS5A, 7/111 (6.3%) in NS5B SOF-failures. In NS5A-failures, Y93H RAS was the most prevalent (68.5% vs 5.1% DAA-naïve, P < .001) followed by A30K (12.7% vs 2.8% in DAA-naïve, P < .001). Analysing baseline samples, a higher prevalence of NS5A-RASs was observed before treatment in DAA-failures (5/13, 38.5%) vs DAA-naïves (61/393, 15.5%, P = .04). Regarding 228 DAA-naïve patients with an available outcome, 93.9% achieved a SVR. Interestingly, patients with baseline Y93H and/or A30K had SVR rate of 72.2% vs 95.7% for patients without NS5A-RASs (P = .002). Conclusions In this real-life GT3 cohort, the majority of failures harboured resistant variants carrying NS5A-RASs, the most frequent being Y93H. The presence of natural NS5A-RASs before treatment was associated with failure. Further analyses are needed to confirm this observation, particularly for the new current regimens

THU-117-Evaluation of risk factors associated with failure to a first-line NS5A-containing regimen in HCV-infected patients naive to direct acting antivirals: Particular focus on natural resistance

Background and aims: This study aimed to evaluate the presence of natural resistance-associated- substitutions (RASs) and other pre-treatment risk-factors for failure in a large group of HCV-infected patients (pts) naive to direct-acting-antivirals (DAA) with an available outcome after their first-line NS5A inhibitor-containing regimen in Italy. Method: RASs in NS3/NS5A/NS5B (N = 1685/1497/1175) were analysed in 1947 DAA-naïve pts. Of them, 705 had an available outcome after a first-line NS5A-containing regimen recommended by the 2016/18 guidelines, with a baseline (BL) NS5A-test. HCV Sanger-sequencing was performed by home-made protocols. Potential differences between the sustained-virological-response (SVR) and virological-failure (VF) group were evaluated by Fisher’s exact test. A multivariable logistic-regression analysis was performed to define risk-factors associated to treatment-response. Results: Overall, 579/1947 (29.7%) pts showed at least one natural RASs, particularly NS5A-RAS was observed in 18.9% of pts. 705 pts (GT1a/b/g[200/214/1]-GT2a/c[84]-3a[141]-4a/d[65]) had an available outcome (656 with a SVR and 49 with a VF) after the following recommended NS5A- containing regimen: daclatasvir (DCV)/ledipasvir (LDV)/velpatasvir (VEL)+sofosbuvir (SOF)±ribavirin (RBV) (N = 125/130/161), 3D/2D (paritaprevir/ritonavir+ombitasvir ± dasabuvir)±RBV (N = 125/44), grazoprevir (GZR)+elbasvir (EBR)±RBV (N = 70), glecaprevir+pibrentasvir (G/P) (N = 50). By analysing retrospectively the BL samples, a higher prevalence of natural NS5A-RASs was observed before treatment in DAA-failures (18/49, 36.7%) vs SVR-pts (94/656, 14.3%; P < 0.001). Notably, ≥ 2 risk factors for failure were more frequently observed at BL among pts who experienced a VF to a DAA treatment (37/49, 75.5%) compared to those achieving SVR (295/656, 45.0%, P < 0.001). By multivariable logistic-regression high HCV-RNA, natural RAS, cirrhosis, previous IFN-failure were negatively associated with SVR (see figure). Interestingly, all 32 GT1-3 pts treated with G/P achieved SVR, with the exception of 1 GT3, who had a breakthrough and had at BL the NS5A RAS A30K and HCV-RNA > 800.000 IU/ml. All others were without (or only 1) risk-factor: notably none of them showed BL RASs regimen-related. Conclusion: The presence of specific pre-treatment risk-factor, such as RAS regimen-related, BL HCV-RNA > 800.000 IU/ml, cirrhosis and previous IFN-failure were associated with virological failure for some specific regimens and GTs

Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains

HIV-1 non-B subtypes/circulating recombinant forms (CRFs) are increasing worldwide. Since subtype identification can be clinically relevant, we assessed the added value in HIV-1 subtyping using updated molecular phylogeny (Mphy) and the performance of routinely used automated tools. Updated Mphy (2015 updated reference sequences), used as a gold standard, was performed to subtype 13,116 HIV-1 protease/reverse transcriptase sequences and then compared with previous Mphy (reference sequences until 2014) and with COMET, REGA, SCUEAL, and Stanford subtyping tools. Updated Mphy classified subtype B as the most prevalent (73.4%), followed by CRF02-AG (7.9%), C (4.6%), F1 (3.4%), A1 (2.2%), G (1.6%), CRF12-BF (1.2%), and other subtypes (5.7%). A 2.3% proportion of sequences were reassigned as different subtypes or CRFs because of misclassification by previous Mphy. Overall, the tool most concordant with updated Mphy was Stanford-v8.1 (95.4%), followed by COMET (93.8%), REGA-v3 (92.5%), Stanford-old (91.1%), and SCUEAL (85.9%). All the tools had a high sensitivity (\ue2\u89\ua598.0%) and specificity (\ue2\u89\ua595.7%) for subtype B. Regarding non-B subtypes, Stanford-v8.1 was the best tool for C, D, and F subtypes and for CRFs 01, 02, 06, 11, and 36 (sensitivity, \ue2\u89\ua592.6%; specificity, \ue2\u89\ua599.1%). A1 and G subtypes were better classified by COMET (92.3%) and REGA-v3 (98.6%), respectively. Our findings confirm Mphy as the gold standard for accurate HIV-1 subtyping, although Stanford-v8.1, occasionally combined with COMET or REGA-v3, represents an effective subtyping approach in clinical settings. Periodic updating of HIV-1 reference sequences is fundamental to improving subtype characterization in the context of an effective epidemiological surveillance of non-B strains