Ancient hepatitis B viruses from the Bronze Age to the Medieval period

Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient seque...

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Published in:Nature (London) Vol. 557; no. 7705; pp. 418 - 423
Main Authors: Mühlemann, Barbara, Jones, Terry C., Damgaard, Peter de Barros, Allentoft, Morten E., Shevnina, Irina, Logvin, Andrey, Usmanova, Emma, Panyushkina, Irina P., Boldgiv, Bazartseren, Bazartseren, Tsevel, Tashbaeva, Kadicha, Merz, Victor, Lau, Nina, Smrčka, Václav, Voyakin, Dmitry, Kitov, Egor, Epimakhov, Andrey, Pokutta, Dalia, Vicze, Magdolna, Price, T. Douglas, Moiseyev, Vyacheslav, Hansen, Anders J., Orlando, Ludovic, Rasmussen, Simon, Sikora, Martin, Vinner, Lasse, Osterhaus, Albert D. M. E., Smith, Derek J., Glebe, Dieter, Fouchier, Ron A. M., Drosten, Christian, Sjögren, Karl-Göran, Kristiansen, Kristian, Willerslev, Eske
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 01.05.2018
Nature Publishing Group
Subjects:
631/250/254
631/250/255/234/2513/1549
706/689/19/2472
Africa
alignment
Analysis
Animals
Archaeological Science
Asia
Bioinformatics
Biological evolution
Deoxyribonucleic acid
DNA
Europe
Evolution
Evolution, Molecular
Genetic aspects
Genetics and Genomics
Genetik och genomik
Genomes
Genomics
Genotype
Genotypes
Hepatitis
Hepatitis B
Hepatitis B - virology
Hepatitis B virus
Hepatitis B virus - classification
Hepatitis B virus - genetics
Hepatitis B virus - isolation & purification
Historia
Historical metallurgy
History
History, Ancient
History, Medieval
Hominidae - virology
Human genome
Human migration
Human Migration - history
Humanities and Social Sciences
Humans
India
Iron
laborativ arkeologi
Letter
Medieval period
Migration
Monkeys & apes
mosaic structure
multidisciplinary
origin
Phylogenetics
Phylogeny
recombinant sequences
Recombination
Recombination, Genetic
reveals
Science
Science (multidisciplinary)
Software
Viruses
United States > US
Africa
ISSN:0028-0836, 1476-4687, 1476-4687
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Abstract Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10 −6 –1.51 × 10 −5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages 1 , 2 . We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone. Phylogenies reconstructed using 12 hepatitis B virus genomes, which were recovered from ancient human genome data, reveal a complex history of hepatitis B evolution that is not evident when using only modern samples.
AbstractList Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10 −6 –1.51 × 10 −5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages 1 , 2 . We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone. Phylogenies reconstructed using 12 hepatitis B virus genomes, which were recovered from ancient human genome data, reveal a complex history of hepatitis B evolution that is not evident when using only modern samples.
Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10 -1.51 × 10 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages . We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10.sup.-6-1.51 × 10.sup.-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages.sup.1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 x 10(-6-)1.51 x 10(-5) nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages(1,2). We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10.sup.-6-1.51 × 10.sup.-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages.sup.1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.Phylogenies reconstructed using 12 hepatitis B virus genomes, which were recovered from ancient human genome data, reveal a complex history of hepatitis B evolution that is not evident when using only modern samples.
Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-6-1.51 × 10-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-6-1.51 × 10-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-6-1.51 × 10-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
Audience Academic
Author Moiseyev, Vyacheslav
Pokutta, Dalia
Smrčka, Václav
Price, T. Douglas
Tashbaeva, Kadicha
Epimakhov, Andrey
Boldgiv, Bazartseren
Sikora, Martin
Usmanova, Emma
Damgaard, Peter de Barros
Osterhaus, Albert D. M. E.
Fouchier, Ron A. M.
Jones, Terry C.
Logvin, Andrey
Panyushkina, Irina P.
Bazartseren, Tsevel
Kristiansen, Kristian
Sjögren, Karl-Göran
Orlando, Ludovic
Vinner, Lasse
Lau, Nina
Drosten, Christian
Glebe, Dieter
Hansen, Anders J.
Willerslev, Eske
Vicze, Magdolna
Kitov, Egor
Rasmussen, Simon
Voyakin, Dmitry
Mühlemann, Barbara
Merz, Victor
Smith, Derek J.
Allentoft, Morten E.
Shevnina, Irina
Author_xml – sequence: 1
  givenname: Barbara
  surname: Mühlemann
  fullname: Mühlemann, Barbara
  organization: Center for Pathogen Evolution, Department of Zoology, University of Cambridge
– sequence: 2
  givenname: Terry C.
  surname: Jones
  fullname: Jones, Terry C.
  organization: Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Institute of Virology, Charité, Universitätsmedizin Berlin
– sequence: 3
  givenname: Peter de Barros
  surname: Damgaard
  fullname: Damgaard, Peter de Barros
  organization: Centre for GeoGenetics, Natural History Museum, University of Copenhagen
– sequence: 4
  givenname: Morten E.
  surname: Allentoft
  fullname: Allentoft, Morten E.
  organization: Centre for GeoGenetics, Natural History Museum, University of Copenhagen
– sequence: 5
  givenname: Irina
  surname: Shevnina
  fullname: Shevnina, Irina
  organization: Archaeological Laboratory, Faculty of History and Law, A. A. Baitursynov Kostanay State University
– sequence: 6
  givenname: Andrey
  surname: Logvin
  fullname: Logvin, Andrey
  organization: Archaeological Laboratory, Faculty of History and Law, A. A. Baitursynov Kostanay State University
– sequence: 7
  givenname: Emma
  surname: Usmanova
  fullname: Usmanova, Emma
  organization: Saryarka Archaeological Institute, Karaganda State University
– sequence: 8
  givenname: Irina P.
  surname: Panyushkina
  fullname: Panyushkina, Irina P.
  organization: Laboratory of Tree-Ring Research, University of Arizona
– sequence: 9
  givenname: Bazartseren
  surname: Boldgiv
  fullname: Boldgiv, Bazartseren
  organization: Department of Biology, School of Arts and Sciences, National University of Mongolia
– sequence: 10
  givenname: Tsevel
  surname: Bazartseren
  fullname: Bazartseren, Tsevel
  organization: Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences
– sequence: 11
  givenname: Kadicha
  surname: Tashbaeva
  fullname: Tashbaeva, Kadicha
  organization: National Academy of Sciences
– sequence: 12
  givenname: Victor
  surname: Merz
  fullname: Merz, Victor
  organization: Pavlodar State University
– sequence: 13
  givenname: Nina
  surname: Lau
  fullname: Lau, Nina
  organization: Centre for Baltic and Scandinavian Archaeology
– sequence: 14
  givenname: Václav
  surname: Smrčka
  fullname: Smrčka, Václav
  organization: Institute for History of Medicine and Foreign Languages of the First Faculty of Medicine, Charles University
– sequence: 15
  givenname: Dmitry
  surname: Voyakin
  fullname: Voyakin, Dmitry
  organization: Margulan Institute of Archaeology
– sequence: 16
  givenname: Egor
  surname: Kitov
  fullname: Kitov, Egor
  organization: N. N. Miklouho-Maklay Institute of Ethnology and Anthropology, Russian Academy of Sciences
– sequence: 17
  givenname: Andrey
  surname: Epimakhov
  fullname: Epimakhov, Andrey
  organization: South Ural Department, Institute of History and Archaeology UBRAS, South Ural State University
– sequence: 18
  givenname: Dalia
  surname: Pokutta
  fullname: Pokutta, Dalia
  organization: Department of Archaeology and Classical Studies, Stockholm University
– sequence: 19
  givenname: Magdolna
  surname: Vicze
  fullname: Vicze, Magdolna
  organization: Matrica Museum
– sequence: 20
  givenname: T. Douglas
  surname: Price
  fullname: Price, T. Douglas
  organization: Department of Historical Studies, University of Gothenburg
– sequence: 21
  givenname: Vyacheslav
  surname: Moiseyev
  fullname: Moiseyev, Vyacheslav
  organization: Department of Physical Anthropology, Peter the Great Museum of Anthropology and Ethnography
– sequence: 22
  givenname: Anders J.
  surname: Hansen
  fullname: Hansen, Anders J.
  organization: Centre for GeoGenetics, Natural History Museum, University of Copenhagen
– sequence: 23
  givenname: Ludovic
  surname: Orlando
  fullname: Orlando, Ludovic
  organization: Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier
– sequence: 24
  givenname: Simon
  surname: Rasmussen
  fullname: Rasmussen, Simon
  organization: Department of Bio and Health Informatics, Technical University of Denmark
– sequence: 25
  givenname: Martin
  surname: Sikora
  fullname: Sikora, Martin
  organization: Centre for GeoGenetics, Natural History Museum, University of Copenhagen
– sequence: 26
  givenname: Lasse
  surname: Vinner
  fullname: Vinner, Lasse
  organization: Centre for GeoGenetics, Natural History Museum, University of Copenhagen
– sequence: 27
  givenname: Albert D. M. E.
  surname: Osterhaus
  fullname: Osterhaus, Albert D. M. E.
  organization: Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover
– sequence: 28
  givenname: Derek J.
  surname: Smith
  fullname: Smith, Derek J.
  organization: Center for Pathogen Evolution, Department of Zoology, University of Cambridge
– sequence: 29
  givenname: Dieter
  surname: Glebe
  fullname: Glebe, Dieter
  organization: Institute of Medical Virology, Justus Liebig University of Giessen, National Reference Centre for Hepatitis B and D Viruses, German Center for Infection Research (DZIF)
– sequence: 30
  givenname: Ron A. M.
  surname: Fouchier
  fullname: Fouchier, Ron A. M.
  organization: Department of Viroscience, Erasmus Medical Centre
– sequence: 31
  givenname: Christian
  surname: Drosten
  fullname: Drosten, Christian
  organization: Institute of Virology, Charité, Universitätsmedizin Berlin, German Center for Infection Research (DZIF)
– sequence: 32
  givenname: Karl-Göran
  surname: Sjögren
  fullname: Sjögren, Karl-Göran
  organization: Department of Historical Studies, University of Gothenburg
– sequence: 33
  givenname: Kristian
  surname: Kristiansen
  fullname: Kristiansen, Kristian
  organization: Department of Historical Studies, University of Gothenburg
– sequence: 34
  givenname: Eske
  surname: Willerslev
  fullname: Willerslev, Eske
  email: ewillerslev@snm.ku.dk
  organization: Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Cambridge GeoGenetics Group, Department of Zoology, University of Cambridge, Wellcome Trust Sanger Institute
BackLink https://www.ncbi.nlm.nih.gov/pubmed/29743673$$D View this record in MEDLINE/PubMed
https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-157746$$DView record from Swedish Publication Index (Stockholms universitet)
https://gup.ub.gu.se/publication/268388$$DView record from Swedish Publication Index (Göteborgs universitet)
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Snippet Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with...
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SubjectTerms 631/250/254
631/250/255/234/2513/1549
706/689/19/2472
Africa
alignment
Analysis
Animals
Archaeological Science
Asia
Bioinformatics
Biological evolution
Deoxyribonucleic acid
DNA
Europe
Evolution
Evolution, Molecular
Genetic aspects
Genetics and Genomics
Genetik och genomik
Genomes
Genomics
Genotype
Genotypes
Hepatitis
Hepatitis B
Hepatitis B - virology
Hepatitis B virus
Hepatitis B virus - classification
Hepatitis B virus - genetics
Hepatitis B virus - isolation & purification
Historia
Historical metallurgy
History
History, Ancient
History, Medieval
Hominidae - virology
Human genome
Human migration
Human Migration - history
Humanities and Social Sciences
Humans
India
Iron
laborativ arkeologi
Letter
Medieval period
Migration
Monkeys & apes
mosaic structure
multidisciplinary
origin
Phylogenetics
Phylogeny
recombinant sequences
Recombination
Recombination, Genetic
reveals
Science
Science (multidisciplinary)
Software
Viruses
Title Ancient hepatitis B viruses from the Bronze Age to the Medieval period
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Volume 557
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