Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B
Ben Krause-Kyora,Julian Susat,Felix M. Key,Denise Kühnert,Esther Bosse,Alexander Immel,Christoph Rinne,Sabin-Christin Kornell,Diego Yepes,Soeren Franzenburg,Henrike O. Heyne,Thomas Meier,Sandra Lösch,Harald Meller,Susanne Friederich,Nicole Nicklisch,Kurt W. Alt,Stefan Schreiber,Andreas Tholey,Alexander Herbig,Almut Nebel,Johannes Krause +21 more
TL;DR: This work reconstructed two Neolithic and one medieval HBV genomes by de novo assembly from shotgun DNA sequencing data and observed HBV-specific peptides using paleo-proteomics, showing that HBV circulates in the European population for at least 7000 years.
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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 went possibly 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.
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Citations
SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
Glenn Tesler
- 01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
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Ancient pathogen genomics as an emerging tool for infectious disease research
TL;DR: Focusing on the evolutionary history of the plague pathogen Yersinia pestis, the authors present unique insights afforded by the study of ancient pathogen genomes.
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The evolution and clinical impact of hepatitis B virus genome diversity
Peter Revill,Peter Revill,Thomas Tu,Thomas Tu,Hans J Netter,Lilly Yuen,Stephen Locarnini,Margaret Littlejohn,Margaret Littlejohn +8 more
TL;DR: HBV seems to undergo very little long-term mutational variation despite multiple host–virus factors driving short-term viral variations, which must be considered in the development of new therapeutic regimens.
140
A 5700 year-old human genome and oral microbiome from chewed birch pitch.
Theis Zetner Trolle Jensen,Theis Zetner Trolle Jensen,Jonas Niemann,Jonas Niemann,Katrine Højholt Iversen,Katrine Højholt Iversen,Anna K. Fotakis,Shyam Gopalakrishnan,Åshild J. Vågene,Mikkel Winther Pedersen,Mikkel-Holger S. Sinding,Martin R. Ellegaard,Morten E. Allentoft,Liam T. Lanigan,Alberto J. Taurozzi,Sofie Holtsmark Nielsen,Michael W. Dee,Martin Mortensen,Mads C. Christensen,Søren A. Sørensen,Matthew J. Collins,Matthew J. Collins,M. Thomas P. Gilbert,M. Thomas P. Gilbert,Martin Sikora,Simon Rasmussen,Hannes Schroeder +26 more
TL;DR: A 5,700 year-old piece of chewed birch pitch from Denmark is reported from which a complete ancient human genome and oral microbiome DNA is sequenced and it is found that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe thanhunter-gathererrs from central Scandinavia.
Evolutionary biology of human hepatitis viruses.
TL;DR: Both surprising conservation and striking differences are described of the unique biological properties and infection patterns of human hepatitis viruses and their animal homologues, including transmission routes, liver tropism, oncogenesis, chronicity, pathogenesis and envelopment.
66
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