title: Tracking HCV protease population diversity during transmission and susceptibility of founder populations to antiviral therapy.
abstract: Due to the highly restricted species-tropism of Hepatitis C virus (HCV) a limited number of animal models exist for pre-clinical evaluation of vaccines and antiviral compounds. The human-liver chimeric mouse model allows heterologous challenge with clinically relevant strains derived from patients. However, to date, the transmission and longitudinal evolution of founder viral populations in this model have not been characterized in-depth using state-of-the-art sequencing technologies. Focusing on NS3 protease encoding region of the viral genome, mutant spectra in a donor inoculum and individual recipient mice were determined via Illumina sequencing and compared, to determine the effects of transmission on founder viral population complexity. In all transmissions, a genetic bottleneck was observed, although diverse viral populations were transmitted in each case. A low frequency cloud of mutations (<1%) was detectable in the donor inoculum and recipient mice, with single nucleotide variants (SNVs) > 1% restricted to a subset of nucleotides. The population of SNVs >1% was reduced upon transmission while the low frequency SNV cloud remained stable. Fixation of multiple identical synonymous substitutions was apparent in independent transmissions, and no evidence for reversion of T-cell epitopes was observed. In addition, susceptibility of founder populations to antiviral therapy was assessed. Animals were treated with protease inhibitor (PI) monotherapy to track resistance associated substitution (RAS) emergence. Longitudinal analyses revealed a decline in population diversity under therapy, with no detectable RAS >1% prior to therapy commencement. Despite inoculation from a common source and identical therapeutic regimens, unique RAS emergence profiles were identified in different hosts prior to and during therapeutic failure, with complex mutational signatures at protease residues 155, 156 and 168 detected. Together these analyses track viral population complexity at high-resolution in the human-liver chimeric mouse model post-transmission and under therapeutic intervention, revealing novel insights into the evolutionary processes which shape viral protease population composition at various critical stages of the viral life-cycle.
authors.affiliation: Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Feodor-Lynen-Str. 7, 30625, Hannover, Germany.
authors.forename: Tanvi
authors.initials: T
authors.lastname: Khera
authors.affiliation: Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Feodor-Lynen-Str. 7, 30625, Hannover, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Todt
authors.affiliation: Laboratory of Liver Infectious Diseases, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium.
authors.forename: Koen
authors.initials: K
authors.lastname: Vercauteren
authors.affiliation: The School of Life Sciences and the NIHR Nottingham Digestive Diseases Biomedical Research Unit, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
authors.forename: C Patrick
authors.initials: CP
authors.lastname: McClure
authors.affiliation: Laboratory of Liver Infectious Diseases, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium.
authors.forename: Lieven
authors.initials: L
authors.lastname: Verhoye
authors.affiliation: Laboratory of Liver Infectious Diseases, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium.
authors.forename: Ali
authors.initials: A
authors.lastname: Farhoudi
authors.affiliation: Genome Analytics, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
authors.forename: Sabin
authors.initials: S
authors.lastname: Bhuju
authors.affiliation: Genome Analytics, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
authors.forename: Robert
authors.initials: R
authors.lastname: Geffers
authors.affiliation: Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France; Université de Strasbourg, Strasbourg, France; Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Baumert
authors.affiliation: Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Feodor-Lynen-Str. 7, 30625, Hannover, Germany.
authors.forename: Eike
authors.initials: E
authors.lastname: Steinmann
authors.affiliation: Laboratory of Liver Infectious Diseases, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium.
authors.forename: Philip
authors.initials: P
authors.lastname: Meuleman
authors.affiliation: Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Feodor-Lynen-Str. 7, 30625, Hannover, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Pietschmann
authors.affiliation: Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Feodor-Lynen-Str. 7, 30625, Hannover, Germany. Electronic address: richard.brown@twincore.de.
authors.forename: Richard J P
authors.initials: RJ
authors.lastname: Brown
mesh_terms: D000818:Animals; D000998:Antiviral Agents / Q000627:therapeutic use; D004195:Disease Models, Animal; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics*; D006526:Hepatitis C / Q000188:drug therapy / Q000635:transmission* / Q000821:virology; D006801:Humans; D051379:Mice; D009154:Mutation; D011480:Protease Inhibitors / Q000008:administration & dosage / Q000627:therapeutic use; D017422:Sequence Analysis, DNA; D012697:Serine Endopeptidases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D017361:Viral Nonstructural Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000998:Antiviral Agents; D011480:Protease Inhibitors; D012697:Serine Endopeptidases; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
keywords: Founder populations; HCV protease; Longitudinal evolution; RAS emergence; Transmission