Abstract

Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. Here we use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals who were chronically infected with HCV, predominantly genotype 3. We show that both alleles of genes encoding human leukocyte antigen molecules and genes encoding components of the interferon lambda innate immune system drive viral polymorphism. Additionally, we show that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific amino acid residue in the HCV NS5A protein. These findings highlight the interplay between the innate immune system and the viral genome in HCV control.

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Acknowledgements

We thank Gilead Sciences for providing samples and data from the BOSON clinical study for use in these analyses. We also thank HCV Research UK (funded by the Medical Research Foundation) for their assistance in handling and coordinating the release of samples for these analyses.

This work was funded by a grant from the Medical Research Council (MRC) (MR/K01532X/1; to the STOP-HCV Consortium). The work was supported by Core funding to the Wellcome Trust Centre for Human Genetics provided by the Wellcome Trust (090532/Z/09/Z; C.C.A.S. and R.B.). E.B. is funded by the MRC as an MRC Senior Clinical Fellow and received additional support from the NIHR Oxford BRC and the Oxford Martin School. M.A.A. is funded by the Oxford Martin School. G.C. is funded by the BRC of the Imperial College NHS Trust. P.K. is funded by the Oxford Martin School, the NIHR Oxford BRC, the Wellcome Trust (109965MA) and the US National Institutes of Health (U19AI082630). J.M. has funding support from the MRC (MC.UU.12014/1) and the Medical Research Foundation (C0365). C.C.A.S. is funded by Wellcome Trust grant 097364/Z/11/Z. G.M. is funded by Wellcome Trust grant 100956/Z/13/Z.

Author information

Author notes

    • M Azim Ansari
    •  & Vincent Pedergnana

    These authors contributed equally to this work.

Affiliations

  1. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

    • M Azim Ansari
    • , Vincent Pedergnana
    • , Camilla L C Ip
    • , Gilean McVean
    • , Amy Trebes
    • , Paolo Piazza
    • , Chris C A Spencer
    •  & Rory Bowden
  2. Oxford Martin School, University of Oxford, Oxford, UK.

    • M Azim Ansari
  3. Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK.

    • M Azim Ansari
    • , Camilla L C Ip
    • , Andrea Magri
    • , Annette Von Delft
    • , David Bonsall
    • , David Smith
    • , Eleanor Barnes
    • , Emma Hudson
    • , Paul Klenerman
    • , Jane McKeating
    •  & Peter Simmonds
  4. School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

    • Nimisha Chaturvedi
    • , Istvan Bartha
    •  & Jacques Fellay
  5. Department of Statistics, University of Oxford, Oxford, UK.

    • George Nicholson
    •  & Chris Holmes
  6. Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.

    • Gilean McVean
  7. Wright–Fleming Institute, Imperial College London, London, UK.

    • Graham Cooke
  8. Queen Mary University of London, London, UK.

    • Graham R Foster
  9. MRC–University of Glasgow Centre for Virus Research, Glasgow, UK.

    • John McLauchlan
    •  & Emma Thomson
  10. University of Nottingham, Queen's Medical Centre, Nottingham, UK.

    • Jonathan Ball
    • , Neil Guha
    •  & William Irving
  11. Gilead Sciences, Inc., Foster City, California, USA.

    • Diana Brainard
    • , Benedetta Massetto
    •  & John McHutchison
  12. Conatus Pharmaceuticals, San Diego, California, USA.

    • Gary Burgess
  13. University of Dundee, Ninewells Hospital and Medical School, Dundee, UK.

    • John Dillon
  14. Hepatitis C Trust, London, UK.

    • Charles Gore
    •  & Rachel Halford
  15. Gilead Sciences, Middlesex, UK.

    • Cham Herath
  16. BC Centre for Excellence in HIV–AIDS, St. Paul's Hospital, Vancouver, British Columbia, Canada.

    • Anita Howe
  17. University of Southampton, Southampton, UK.

    • Salim Khakoo
  18. Janssen Diagnostics, Beerse, Belgium.

    • Diana Koletzki
  19. University of California, San Diego, La Jolla, California, USA.

    • Natasha Martin
  20. Public Health England, London, UK.

    • Tamyo Mbisa
  21. London School of Hygiene and Tropical Medicine, London, UK.

    • Alec Miners
  22. OncImmune Limited, Nottingham City Hospital, Nottingham, UK.

    • Andrea Murray
  23. Merck and Company, Inc., Kenilworth, New Jersey, USA.

    • Peter Shaw
  24. Medivir AB, Huddinge, Sweden.

    • Paul Targett-Adams
  25. University of Bristol, Clifton, UK.

    • Peter Vickerman
  26. University of Oxford, Oxford, UK.

    • Nicole Zitzmann

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  1. STOP-HCV Consortium

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Contributions

M.A.A. and V.P. contributed equally to this work, and E.B. and C.C.A.S. jointly supervised this research. M.A.A., V.P., E.B. and C.C.A.S. conceived and designed the experiments; M.A.A., V.P., C.L.C.I., A.M., D.B., A.V.D., D.S., N.C., I.B., A.T. and P.P. performed the experiments; M.A.A., V.P., A.M., N.C., I.B., G.N. and C.C.A.S. performed the statistical analysis; M.A.A., V.P., A.M., D.B., P.K., E.B. and C.C.A.S. analyzed the data; C.L.C.I., G.N., A.V.D., D.B., D.S., G.M., A.T., P.P., J.F. and J.M. contributed reagents, materials and analysis tools; and M.A.A., V.P., J.F., G.C., G.R.F., E.H., J.M., P.S., R.B., P.K., E.B. and C.C.A.S. wrote the paper.

Competing interests

G.R.F. has received grants from, consulted for, has been a speaker at or has been on the advisory board of AbbVie, Alcura, Bristol-Myers Squibb, Gilead, Janssen, GlaxoSmithKline, Merck, Roche, Springbank, Idenix, Tekmira and Novartis. G.M. is a partner in Peptide Groove LLP, which commercializes the HLA*IMP software used for HLA imputation.

Corresponding authors

Correspondence to Eleanor Barnes or Chris C A Spencer.

Integrated supplementary information

Supplementary figures

  1. 1.

    Ancestry stratifies patterns of human genetic variations.

  2. 2.

    Virus whole-genome phylogeny labeled by self-reported ethnicity for all patients.

  3. 3.

    PCA of the virus nucleotides is associated with HCV subtypes.

  4. 4.

    QQplot for genome-to-genome analysis.

  5. 5.

    Scatter plot of -log10(P) of association tests performed in the White ancestry patient infected with genotype 3a virus against the whole cohort.

  6. 6.

    Association between viral position 1444 and HLA-A alleles.

  7. 7.

    Sequence logo representations of the virus nucleotide and the amino acid profiles around position 1444.

  8. 8.

    Association analysis across the MHC region for presence and absence of F amino acid at site 1444, whilst conditioning (including as a covariate) on genotypes at rs3095267 (top imputed SNP) and HLA-A*01:01.

  9. 9.

    Linkage disequilibrium between the HLA alleles.

  10. 10.

    Bi-directionality of escape and reversion for viral amino acid sites associated with HLA alleles at 20% FDR.

  11. 11.

    Interaction between IFNL4 genotypes and HLA allele escape mutations.

  12. 12.

    Association between dN/dS and IFNL4 genotypes at the viral gene level.

  13. 13.

    Sliding window analysis of dN and dS along viral genome.

  14. 14.

    RNA replication of S52 ΔN genotype 3a HCV replicon including amino acid changes at a subset of sites associated with IFNL4 and nominally associated with viral load.

  15. 15.

    Viral amino acids affect on viral load vs. IFNL4 odds ratio of escape from consensus for viral sites associated with IFNL4 genotypes at a 20% FDR.

  16. 16.

    Viral amino acids affect on viral load vs. IFNL4 odds ratio of escape from consensus for viral sites associated with IFNL4 genotypes for all sites.

Supplementary information

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–16, Supplementary Tables 1–6 and Supplementary Note

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DOI

https://doi.org/10.1038/ng.3835

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