title: Molecular footprints reveal the impact of the protective HLA-A*03 allele in hepatitis C virus infection.
abstract: OBJECTIVE
  CD8 T cells are central to the control of hepatitis C virus (HCV) although the key features of a successful CD8 T cell response remain to be defined. In a cohort of Irish women infected by a single source, a strong association between viral clearance and the human lecucocyte (HLA)-A*03 allele has been described, and the aim of this study was to define the protective nature of the associated CD8 T cell response.
  
  
  METHODS
  A sequence-led approach was used to identify HLA-A*03-restricted epitopes. We examine the CD8 T cell response associated with this gene and address the likely mechanism underpinning this protective effect in this special cohort, using viral sequencing, T cell assays and analysis of fitness of viral mutants.
  
  
  RESULTS
  A strong 'HLA footprint' in a novel NS3 epitope (TVYHGAGTK) was observed. A lysine (K) to arginine (R) substitution at position 9 (K1088R) was seen in a significant number of A*03-positive patients (9/12) compared with the control group (1/33, p=0.0003). Threonine (T) was also substituted with alanine (A) at position 8 (T1087A) more frequently in A*03-positive patients (6/12) compared with controls (2/33, p=0.01), and the double substitution of TK to AR was also observed predominantly in HLA-A*03-positive patients (p=0.004). Epitope-specific CD8 T cell responses were observed in 60% of patients three decades after exposure and the mutants selected in vivo impacted on recognition in vitro. Using HCV replicons matched to the viral sequences, viral fitness was found to be markedly reduced by the K1088R substitution but restored by the second substitution T1087A.
  
  
  CONCLUSIONS
  It is proposed that at least part of the protective effect of HLA-A*03 results from targeting of this key epitope in a functional site: the requirement for two mutations to balance fitness and escape provides an initial host advantage. This study highlights the potential protective impact of common HLA-A alleles against persistent viruses, with important implications for HCV vaccine studies.
authors.affiliation: Department of Clinical Medicine, Trinity College Dublin, St James' Hospital, Dublin, Ireland. kfitzmau@tcd.ie
authors.forename: Karen
authors.initials: K
authors.lastname: Fitzmaurice
authors.forename: Danijela
authors.initials: D
authors.lastname: Petrovic
authors.forename: Narayan
authors.initials: N
authors.lastname: Ramamurthy
authors.forename: Ruth
authors.initials: R
authors.lastname: Simmons
authors.forename: Shazma
authors.initials: S
authors.lastname: Merani
authors.forename: Silvana
authors.initials: S
authors.lastname: Gaudieri
authors.forename: Stuart
authors.initials: S
authors.lastname: Sims
authors.forename: Eugene
authors.initials: E
authors.lastname: Dempsey
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Freitas
authors.forename: Susan
authors.initials: S
authors.lastname: Lea
authors.forename: Susan
authors.initials: S
authors.lastname: McKiernan
authors.forename: Suzanne
authors.initials: S
authors.lastname: Norris
authors.forename: Aideen
authors.initials: A
authors.lastname: Long
authors.forename: Dermot
authors.initials: D
authors.lastname: Kelleher
authors.forename: Paul
authors.initials: P
authors.lastname: Klenerman
mesh_terms: D000328:Adult; D000483:Alleles; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology*; D015331:Cohort Studies; D018983:DNA Footprinting; D018274:Electroporation; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry / Q000276:immunology*; D005260:Female; D056084:Genetic Fitness / Q000276:immunology; D015791:HLA-A3 Antigen / Q000235:genetics / Q000276:immunology*; D006526:Hepatitis C / Q000276:immunology*; D006801:Humans; D016056:Immunodominant Epitopes / Q000276:immunology; D014176:Protein Biosynthesis / Q000276:immunology; D016415:Sequence Alignment
chemical_list: D018984:Epitopes, T-Lymphocyte; C487960:HLA-A*03 antigen; D015791:HLA-A3 Antigen; D016056:Immunodominant Epitopes