title: Cross-genotype characterization of genetic diversity and molecular adaptation in hepatitis C virus envelope glycoprotein genes.
abstract: Investigation of the mechanisms underlying hepatitis C virus (HCV) envelope glycoprotein gene evolution will greatly assist rational development of broadly neutralizing antibody-based vaccines or vaccine components. Previously, comprehensive cross-genotype evolutionary studies of E1E2 have not been possible due to the paucity of full-length envelope gene sequences representative of all major HCV genotypes (1-6) deposited in international sequence databases. To address this shortfall, a full-length E1E2 clone panel, corresponding to genotypes of HCV that were previously under-represented, was generated. This panel, coupled with divergent isolates available via international sequence databases, was subjected to high-resolution methods for determining codon-substitution patterns, enabling a fine-scale dissection of the selective pressures operating on HCV E1E2. Whilst no evidence for positive selection was observed in E1, the E2 protein contained a number of sites under strong positive selection. A high proportion of these sites were located within the first hypervariable region (HVR1), and statistical analysis revealed that cross-genotype adaptive mutations were restricted to a subset of homologous positions within this region. Importantly, downstream of HVR1, a differential genotype-specific distribution of adaptive mutations was observed, suggesting that subtly different evolutionary pressures shape present-day genotype diversity in E2 outside HVR1. Despite these observations, it is demonstrated that purifying selection due to functional constraint is the major evolutionary force acting on HCV E1E2. These findings are important in the context of neutralizing-antibody vaccine targeting, as well as in contributing to our understanding of E1E2 function.
authors.affiliation: The University of Nottingham, Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Division of Microbiology and Infectious Diseases, Queens Medical Centre, A Floor, West Block, Nottingham NG7 2UH, UK.
authors.forename: Richard J P
authors.initials: RJP
authors.lastname: Brown
authors.affiliation: The University of Nottingham, Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Division of Microbiology and Infectious Diseases, Queens Medical Centre, A Floor, West Block, Nottingham NG7 2UH, UK.
authors.forename: Alexander W
authors.initials: AW
authors.lastname: Tarr
authors.affiliation: The University of Nottingham, Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Division of Microbiology and Infectious Diseases, Queens Medical Centre, A Floor, West Block, Nottingham NG7 2UH, UK.
authors.forename: C Patrick
authors.initials: CP
authors.lastname: McClure
authors.affiliation: The University of Nottingham, Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Division of Microbiology and Infectious Diseases, Queens Medical Centre, A Floor, West Block, Nottingham NG7 2UH, UK.
authors.forename: Vicky S
authors.initials: VS
authors.lastname: Juttla
authors.affiliation: The University of Nottingham, Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Division of Microbiology and Infectious Diseases, Queens Medical Centre, A Floor, West Block, Nottingham NG7 2UH, UK.
authors.forename: Nader
authors.initials: N
authors.lastname: Tagiuri
authors.affiliation: The University of Nottingham, Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Division of Microbiology and Infectious Diseases, Queens Medical Centre, A Floor, West Block, Nottingham NG7 2UH, UK.
authors.forename: William L
authors.initials: WL
authors.lastname: Irving
authors.affiliation: The University of Nottingham, Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Division of Microbiology and Infectious Diseases, Queens Medical Centre, A Floor, West Block, Nottingham NG7 2UH, UK.
authors.forename: Jonathan K
authors.initials: JK
authors.lastname: Ball
mesh_terms: D000595:Amino Acid Sequence; D014644:Genetic Variation; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology; D019698:Hepatitis C, Chronic / Q000821:virology; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D014759:Viral Envelope Proteins / Q000737:chemistry / Q000235:genetics*
chemical_list: C087035:E1 protein, Hepatitis C virus; D014759:Viral Envelope Proteins; C091015:glycoprotein E2, Hepatitis C virus