title: Diversity of 1,213 hepatitis C virus NS3 protease sequences from a clinical virology laboratory database in Marseille university hospitals, southeastern France.
abstract: Infection with hepatitis C virus (HCV) represents a major public health concern worldwide. Recent therapeutic advances have been considerable, HCV genotype continuing to guide therapeutic management. Since 2008, HCV genotyping in our clinical microbiology laboratory at university hospitals of Marseille, Southeastern France, has been based on NS3 protease gene population sequencing, to allow concurrent HCV genotype and protease inhibitor (PI) genotypic resistance determinations. We aimed, first, to analyze the genetic diversity of HCV NS3 protease obtained from blood samples collected between 2003 and 2013 from patients monitored at university hospitals of Marseille and detect possible atypical sequences; and, second, to identify NS3 protease amino acid patterns associated with decreased susceptibility to HCV PIs. A total of 1,213 HCV NS3 protease sequences were available in our laboratory sequence database. We implemented a strategy based on bioinformatic tools to determine whether HCV sequences are representative of our local HCV genetic diversity, or divergent. In our 2003-2012 HCV NS3 protease sequence database, we delineated 32 clusters representative of the majority HCV genetic diversity, and 61 divergent sequences. Five of these divergent sequences showed less than 85% nucleotide identity with their top GenBank hit. In addition, among the 294 sequences obtained in 2013, three were divergent relative to these 32 previously delineated clusters. Finally, we detected both natural and on-treatment genotypic resistance to HCV NS3 PIs, including a substantial prevalence of Q80K substitutions associated with decreased susceptibility to simeprevir, a second generation PI.
authors.affiliation: Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.
authors.forename: Hind
authors.initials: H
authors.lastname: Hajji
authors.affiliation: Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.|Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France.
authors.forename: Sarah
authors.initials: S
authors.lastname: Aherfi
authors.affiliation: Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Motte
authors.affiliation: IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Conception, Assistance Publique-Hôpitaux de Marseille, Marseille, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Ravaux
authors.affiliation: IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Nord, Marseille, France.
authors.forename: Saadia
authors.initials: S
authors.lastname: Mokhtari
authors.affiliation: Assistance Publique-Hôpitaux de Marseille, Hôpitaux Sud, Service de Médecine en milieu pénitentiaire, Centre pénitentiaire de Marseille, Marseille, France.
authors.forename: Jean-Marie
authors.initials: JM
authors.lastname: Ruiz
authors.affiliation: AP-HM Sainte-Marguerite, Service d'Immuno-hématologie clinique, Marseille, France.|Aix-Marseille University, INSERM, UMR 912 (SESSTIM), Marseille, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Poizot-Martin
authors.affiliation: Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Tourres
authors.affiliation: Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.
authors.forename: Natacha
authors.initials: N
authors.lastname: Tivoli
authors.affiliation: Service d'Hépato-Gastro-Entérologie, Centre Hospitalo-Universitaire Conception, Marseille, France.
authors.forename: René
authors.initials: R
authors.lastname: Gérolami
authors.affiliation: Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.|Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Tamalet
authors.affiliation: Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.|Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Colson
mesh_terms: D016000:Cluster Analysis; D024882:Drug Resistance, Viral; D005260:Female; D005602:France; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques; D016174:Hepacivirus / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000821:virology*; D006785:Hospitals, University; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D020125:Mutation, Missense; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
keywords: NS3 protease; diversity; genotype; hepatitis C virus; resistance mutations; therapy