title: Ultradeep pyrosequencing of NS3 to predict response to triple therapy with protease inhibitors in previously treated chronic hepatitis C patients.
abstract: Despite the gain in sustained virological responses (SVR) provided by protease inhibitors (PIs), failures still occur. The aim of this study was to determine if a baseline analysis of the NS3 region using ultradeep pyrosequencing (UDPS) can help to predict an SVR. Serum samples from 40 patients with previously nonresponding genotype 1 chronic hepatitis C who were retreated with triple therapy, including a PI, were analyzed. Baseline UDPS of the NS3 gene was performed on plasma and peripheral blood mononuclear cells (PBMC). Mutations conferring resistance to PIs were sought. The overall diversity of the quasispecies was evaluated by calculating the Shannon entropy (SE). Resistance mutations were found in plasma and PBMC but were not discriminating enough to predict an SVR. NS3 quasispecies heterogeneity was significantly lower at baseline in patients achieving an SVR than in those not achieving an SVR (SE of 26.98 ± 16.64 × 10(-3) versus 44.93 ± 19.58 × 10(-3), P = 0.0047). With multivariate analysis, the independent predictors of an SVR were fibrosis of stage F ≤2 (odds ratio [OR], 13.3; 95% confidence interval [CI], 1.25 to 141.096; P < 0.03) and SE below the median (OR, 5.4; 95% CI, 1.22 to 23.87; P < 0.03). More than the presence of minor mutations at the baseline in plasma or in PBMC, the NS3 viral heterogeneity determined by UDPS is an independent factor for an SVR in previously treated patients receiving triple therapy that includes a PI.
authors.affiliation: Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France slarrat@chu-grenoble.fr.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Larrat
authors.affiliation: Laboratoire TIMC-IMAG/University of Grenoble Alpes/CNRS/UMR 5525, Grenoble, France.
authors.forename: Om
authors.initials: O
authors.lastname: Kulkarni
authors.affiliation: Genostar-Bioinformatics Solutions, Montbonnot Saint Martin, France.
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Claude
authors.affiliation: Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France.
authors.forename: Réjane
authors.initials: R
authors.lastname: Beugnot
authors.affiliation: Laboratoire TIMC-IMAG/University of Grenoble Alpes/CNRS/UMR 5525, Grenoble, France.
authors.forename: Michaël G B
authors.initials: MG
authors.lastname: Blum
authors.affiliation: Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France.
authors.forename: Katia
authors.initials: K
authors.lastname: Fusillier
authors.affiliation: Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Lupo
authors.affiliation: Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France.
authors.forename: Pauline
authors.initials: P
authors.lastname: Tremeaux
authors.affiliation: Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France.
authors.forename: Agnès
authors.initials: A
authors.lastname: Plages
authors.affiliation: Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France.
authors.forename: Alice
authors.initials: A
authors.lastname: Marlu
authors.affiliation: Floralis, Gieres, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Duborjal
authors.affiliation: Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Signori-Schmuck
authors.affiliation: Laboratoire TIMC-IMAG/University of Grenoble Alpes/CNRS/UMR 5525, Grenoble, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Francois
authors.affiliation: Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unité INSERM/University Grenoble Alpes U823, IAPC Institut Albert Bonniot, Grenoble, France.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Zarski
authors.affiliation: Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France.
authors.forename: Patrice
authors.initials: P
authors.lastname: Morand
authors.affiliation: Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unité INSERM/University Grenoble Alpes U823, IAPC Institut Albert Bonniot, Grenoble, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Leroy
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000998:Antiviral Agents / Q000627:therapeutic use*; D024882:Drug Resistance, Viral; D004359:Drug Therapy, Combination / Q000379:methods; D005260:Female; D014644:Genetic Variation; D019698:Hepatitis C, Chronic / Q000175:diagnosis / Q000188:drug therapy* / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D020125:Mutation, Missense; D011379:Prognosis; D011480:Protease Inhibitors / Q000627:therapeutic use*; D016879:Salvage Therapy / Q000379:methods; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D055815:Young Adult; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000998:Antiviral Agents; D011480:Protease Inhibitors; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases