Short Report

Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B

Kiel University, Germany
Max Planck Institute for the Science of Human History, Germany
University Hospital Zurich, Switzerland
Broad Institute, United States
Heidelberg University, Germany
University of Bern, Switzerland
State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Germany

May 10, 2018

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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

1. Krause J et al
(2018) High-throughput sequence data for Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B
PRJEB24921.

https://www.ebi.ac.uk/ena

Article and author information

Author details

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.

"This ORCID iD identifies the author of this article:" 0000-0001-9435-2872
Julian Susat

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany

Competing interests
The authors declare that no competing interests exist.
Felix M Key

Department of Archeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany

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The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2812-6636
Denise Kühnert

Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zürich, Switzerland

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The authors declare that no competing interests exist.
Esther Bosse

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany

Competing interests
The authors declare that no competing interests exist.
Alexander Immel

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany

Competing interests
The authors declare that no competing interests exist.
Christoph Rinne

Institute of Pre- and Protohistoric Archaeology, Kiel University, Kiel, Germany

Competing interests
The authors declare that no competing interests exist.
Sabin-Christin Kornell

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany

Competing interests
The authors declare that no competing interests exist.
Diego Yepes

Systematic Proteomics and Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany

Competing interests
The authors declare that no competing interests exist.
Sören Franzenburg

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany

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The authors declare that no competing interests exist.
Henrike O Heyne

Stanley Center for Psychiatric Research, Broad Institute, Cambridge, United States

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The authors declare that no competing interests exist.
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.
Sandra Lösch

Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland

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The authors declare that no competing interests exist.
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.
Susanne Friederich

State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany

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The authors declare that no competing interests exist.
Nicole Nicklisch

State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany

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The authors declare that no competing interests exist.
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.
Stefan Schreiber

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany

Competing interests
The authors declare that no competing interests exist.
Andreas Tholey

Systematic Proteomics and Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany

Competing interests
The authors declare that no competing interests exist.
Alexander Herbig

Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany

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The authors declare that no competing interests exist.
Almut Nebel

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany

Competing interests
The authors declare that no competing interests exist.
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.

"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.

Copyright

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.