Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B

  1. Ben Krause-Kyora  Is a corresponding author
  2. Julian Susat
  3. Felix M Key
  4. Denise Kühnert
  5. Esther Bosse
  6. Alexander Immel
  7. Christoph Rinne
  8. Sabin-Christin Kornell
  9. Diego Yepes
  10. Sören Franzenburg
  11. Henrike O Heyne
  12. Thomas Meier
  13. Sandra Lösch
  14. Harald Meller
  15. Susanne Friederich
  16. Nicole Nicklisch
  17. Kurt W Alt
  18. Stefan Schreiber
  19. Andreas Tholey
  20. Alexander Herbig
  21. Almut Nebel
  22. Johannes Krause  Is a corresponding author
  1. Kiel University, Germany
  2. Max Planck Institute for the Science of Human History, Germany
  3. University Hospital Zurich, Switzerland
  4. Broad Institute, United States
  5. Heidelberg University, Germany
  6. University of Bern, Switzerland
  7. State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Germany

Abstract

The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genomes by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results show that HBV circulates in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. These ancient virus forms appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses.

Data availability

Raw sequence read files have been deposited at the European Nucleotide Archive under accession no. PRJEB24921

The following data sets were generated

Article and author information

Author details

  1. Ben Krause-Kyora

    Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
    For correspondence
    b.krause-kyora@ikmb.uni-kiel.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9435-2872
  2. Julian Susat

    Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Felix M Key

    Department of Archeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2812-6636
  4. Denise Kühnert

    Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  5. Esther Bosse

    Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Alexander Immel

    Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Christoph Rinne

    Institute of Pre- and Protohistoric Archaeology, Kiel University, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Sabin-Christin Kornell

    Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. Diego Yepes

    Systematic Proteomics and Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Sören Franzenburg

    Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.
  11. Henrike O Heyne

    Stanley Center for Psychiatric Research, Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Thomas Meier

    Institute for Pre- and Protohistory and Near Eastern Archaeology, Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  13. Sandra Lösch

    Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  14. Harald Meller

    State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
    Competing interests
    The authors declare that no competing interests exist.
  15. Susanne Friederich

    State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
    Competing interests
    The authors declare that no competing interests exist.
  16. Nicole Nicklisch

    State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
    Competing interests
    The authors declare that no competing interests exist.
  17. Kurt W Alt

    State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
    Competing interests
    The authors declare that no competing interests exist.
  18. Stefan Schreiber

    Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.
  19. Andreas Tholey

    Systematic Proteomics and Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.
  20. Alexander Herbig

    Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
    Competing interests
    The authors declare that no competing interests exist.
  21. Almut Nebel

    Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
    Competing interests
    The authors declare that no competing interests exist.
  22. Johannes Krause

    Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
    For correspondence
    krause@shh.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9144-3920

Funding

European Research Council (APGREID)

  • Johannes Krause

Deutsche Forschungsgemeinschaft (Al 287-7-1)

  • Kurt W Alt

Deutsche Forschungsgemeinschaft (Me 3245/1-1)

  • Harald Meller

Collaborative Research Center (1266)

  • Ben Krause-Kyora

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: Our human remains used are prehistoric European specimens. No consent from them can be required. No decedent groups claim responsibility or ancestry to those people.

Reviewing Editor

  1. Stephen Locarnini, Doherty Institute, Australia

Publication history

  1. Received: March 14, 2018
  2. Accepted: May 9, 2018
  3. Accepted Manuscript published: May 10, 2018 (version 1)
  4. Version of Record published: June 19, 2018 (version 2)

Copyright

© 2018, Krause-Kyora et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Ben Krause-Kyora
  2. Julian Susat
  3. Felix M Key
  4. Denise Kühnert
  5. Esther Bosse
  6. Alexander Immel
  7. Christoph Rinne
  8. Sabin-Christin Kornell
  9. Diego Yepes
  10. Sören Franzenburg
  11. Henrike O Heyne
  12. Thomas Meier
  13. Sandra Lösch
  14. Harald Meller
  15. Susanne Friederich
  16. Nicole Nicklisch
  17. Kurt W Alt
  18. Stefan Schreiber
  19. Andreas Tholey
  20. Alexander Herbig
  21. Almut Nebel
  22. Johannes Krause
(2018)
Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B
eLife 7:e36666.
https://doi.org/10.7554/eLife.36666

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