title: Hepatitis E virus mutations associated with ribavirin treatment failure result in altered viral fitness and ribavirin sensitivity.
abstract: Ribavirin monotherapy is the preferred treatment for chronic hepatitis E, although occasional treatment failure occurs. We present a patient with chronic hepatitis E experiencing ribavirin treatment failure with a completely resistant phenotype. We aimed to identify viral mutations associated with treatment failure and explore the underlying mechanisms.
  
  
  
  Viral genomes were deep-sequenced at different time points and the role of identified mutations was assessed in vitro using mutant replicons, antiviral assays, cell culture of patient-derived virus and deep-sequencing.
  
  
  
  Ribavirin resistance was associated with Y1320H, K1383N and G1634R mutations in the viral polymerase, but also an insertion in the hypervariable region comprising a duplication and a polymerase-derived fragment. Analysis of these genome alterations in vitro revealed replication-increasing roles for Y1320H and G1634R mutations and the hypervariable region insertion. In contrast, the K1383N mutation in the polymerase F1-motif suppressed viral replication and increased the in vitro sensitivity to ribavirin, contrary to the clinical phenotype. Analysis of the replication of mutant full-length virus and in vitro culturing of patient-derived virus confirmed that sensitivity to ribavirin was retained. Finally, deep-sequencing of hepatitis E virus genomes revealed that ribavirin is mutagenic to viral replication in vitro and in vivo.
  
  
  
  Mutations Y1320H, G1634R and the hypervariable region insertion compensated for K1383N-associated replication defects. The specific role of the K1383N mutation remains enigmatic, but it appears to be of importance for the ribavirin resistant phenotype in this patient.
  
  
  
  Ribavirin is the most common treatment for chronic hepatitis E and is mostly effective, although some cases of ribavirin treatment failure have been described. Here, we report on a particular case of ribavirin resistance and investigate the underlying causes of treatment failure. Mutations in the viral polymerase, an essential enzyme for viral replication, appear to be responsible.
authors.affiliation: Rega Institute for Medical Research, Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium.
authors.forename: Yannick
authors.initials: Y
authors.lastname: Debing
authors.affiliation: Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI) (Inserm U1111, CNRS UMR 5308), Lyon, France; Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Ramière
authors.affiliation: Rega Institute for Medical Research, Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium.
authors.forename: Kai
authors.initials: K
authors.lastname: Dallmeier
authors.affiliation: Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13385 Marseille, France.
authors.forename: Géraldine
authors.initials: G
authors.lastname: Piorkowski
authors.affiliation: Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.
authors.forename: Mary-Anne
authors.initials: MA
authors.lastname: Trabaud
authors.affiliation: Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; Service d'Hépato-Gastroentérologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; INSERM U1052, CRCL (Centre de Recherche en Cancérologie de Lyon), Lyon, France.
authors.forename: Fanny
authors.initials: F
authors.lastname: Lebossé
authors.affiliation: Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI) (Inserm U1111, CNRS UMR 5308), Lyon, France; Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Scholtès
authors.affiliation: ViroScan3D, Trevoux, France.
authors.forename: Magali
authors.initials: M
authors.lastname: Roche
authors.affiliation: ViroScan3D, Trevoux, France; UMR CNRS 5557 UCBL USC INRA 1193 ENVL, Dynamique Microbienne et Transmission Virale, Lyon, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Legras-Lachuer
authors.affiliation: Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13385 Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: de Lamballerie
authors.affiliation: Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI) (Inserm U1111, CNRS UMR 5308), Lyon, France; Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France.
authors.forename: Patrice
authors.initials: P
authors.lastname: André
authors.affiliation: Rega Institute for Medical Research, Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium. Electronic address: johan.neyts@rega.kuleuven.be.
authors.forename: Johan
authors.initials: J
authors.lastname: Neyts
mesh_terms: D000998:Antiviral Agents; D024882:Drug Resistance, Viral; D016752:Hepatitis E virus; D006801:Humans; D009154:Mutation; D012254:Ribavirin; D017211:Treatment Failure; D014779:Virus Replication
chemical_list: D000998:Antiviral Agents; D012254:Ribavirin
keywords: Chronic hepatitis E; Fidelity; G1634R; Hepatitis E virus; Hypervariable region; RNA-dependent RNA polymerase; Resistance; Ribavirin