1. Genetics and Genomics
  2. Microbiology and Infectious Disease
Download icon

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. Massachusetts General Hospital, United States
  6. Broad Institute of MIT & Harvard, United States
  7. Heidelberg University, Germany
  8. University of Bern, Switzerland
  9. State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Germany
  10. Danube Private University, Austria
  11. University Hospital Basel, University of Basel, Switzerland
  12. University of Basel, Switzerland
  13. University Hospital Schleswig-Holstein, Germany
Short Report
Cite this article as: eLife 2018;7:e36666 doi: 10.7554/eLife.36666
2 figures, 1 table, 1 data set and 7 additional files

Figures

Figure 1 with 9 supplements
Origin of samples.

Geographic location of the samples from which ancient HBV genomes were isolated. Radiocarbon dates of the specimens is given in two sigma range. Icons indicate the sample material (tooth or mummy). HBV genomes obtained in this study are indicated by black frame.

https://doi.org/10.7554/eLife.36666.002
Figure 1—figure supplement 1
Skull of the investigated Karsdorf individual 537 is from a male with an age at death of around 25–30 years.
https://doi.org/10.7554/eLife.36666.003
Figure 1—figure supplement 2
Mandible fragment of the Sorsum individual XLVII 11 analyzed in this study is from a male.
https://doi.org/10.7554/eLife.36666.004
Figure 1—figure supplement 3
Skull of the analyzed Petersberg individual from grave 820 is from a male with an age at death of around 65–70 years.
https://doi.org/10.7554/eLife.36666.005
Figure 1—figure supplement 4
Principal Component Analysis (PCA) of the human Karsdorf and Sorsum samples together with previously published ancient populations projected on 27 modern day West Eurasian populations (not shown) based on a set of 1.23 million SNPs (Mathieson et al., 2015).
https://doi.org/10.7554/eLife.36666.006
Figure 1—figure supplement 5
Damage plots showing deamination patterns of hg19-specific reads for the HalfUDG-treated libraries of (a) Karsdorf, (b) Sorsum, (c) Petersberg.
https://doi.org/10.7554/eLife.36666.007
Figure 1—figure supplement 6
Damage plots showing deamination patterns of HBV-specific reads for the HalfUDG-treated libraries of (a) Karsdorf, (b) Sorsum, (c) Petersberg.

References shown in Supplementary file 1 were used to carry out the alignment.

https://doi.org/10.7554/eLife.36666.008
Figure 1—figure supplement 7
MS/MS spectrum of the proteotypic HBV-peptide DLLDTASALYR from the HBV-protein external core antigen (residues 58–68).

([M + 2 hr]2+): m/z = 1237.6429 Da. Mass accuracy of the precursor peptide = 0.56 ppm.

https://doi.org/10.7554/eLife.36666.009
Figure 1—figure supplement 8
Principal Component Analysis (PCA) of the human Karsdorf and Sorsum samples together with previously published ancient populations projected on 27 modern day West Eurasian populations (shown in gray) based on a set of 1.23 million SNPs (Mathieson et al., 2015).
https://doi.org/10.7554/eLife.36666.010
Figure 1—figure supplement 9
Principal Component Analysis (PCA) of the human Petersberg sample projected on 27 modern day West Eurasian populations based on a set of 1.23 million SNPs (Mathieson et al., 2015).
https://doi.org/10.7554/eLife.36666.011
Figure 2 with 9 supplements
Network.

Network of 493 modern, two published ancient genomes (light yellow box), and three ancient hepatitis B virus (HBV) obtained in this study (grey box). Colors indicate the eight human HBV genotypes (A–H), two monkey genotypes (Monkeys I, African apes and Monkeys II, Asian monkeys) and ancient genomes (red).

https://doi.org/10.7554/eLife.36666.013
Figure 2—source data 1

Results of the recombination analysis using the methods RDP, GENECOV, Chimera, MaxChi, BootScan, SiScan, 3Seq within the RDP v4 software package with all modern full reference genomes (n = 493) and five ancient genomes.

https://doi.org/10.7554/eLife.36666.023
Figure 2—source data 2

Multiple sequence alignment of the 493 representative and five ancient HBV genomes.

The multiple sequence alignment was stripped of any sites that had gaps in more than 95%.

https://doi.org/10.7554/eLife.36666.024
Figure 2—source data 3

Maximum-likelihood tree based on the multiple sequence alignment of the 493 representative and five ancient HBV genomes with 2000 replicates.

https://doi.org/10.7554/eLife.36666.025
Figure 2—source data 4

Neighbour-Joining tree based on the multiple sequence alignment of the 493 representative modern and five ancient HBV genomes with 10000 replicates.

https://doi.org/10.7554/eLife.36666.026
Figure 2—figure supplement 1
Consensus sequence of the Karsdorf HBV genome.

Organization of overlapping open reading frames and approximate location of single-stranded portion of plus strand are indicated. Gaps in the sequence are marked in red. The green plot depicts the coverage of the re-mapping of raw reads against the consensus. Circular plots were generated using circos-0.69-6 and coverage information from the re-mapping. 

https://doi.org/10.7554/eLife.36666.014
Figure 2—figure supplement 2
Consensus sequence of the Sorsum HBV genome.

Organization of overlapping open reading frames and approximate location of single-stranded portion of plus strand are indicated. Gaps in the sequence are marked in red. The green plot depicts the coverage of the re-mapping of raw reads against the consensus. Circular plots were generated using circos-0.69-6 and coverage information from the re-mapping. 

https://doi.org/10.7554/eLife.36666.015
Figure 2—figure supplement 3
Consensus sequence of the Petersberg HBV genome. 

Organization of overlapping open reading frames and approximate location of single-stranded portion of plus strand are indicated. Gaps in the sequence are marked in red. The green plot depicts the coverage of the re-mapping of raw reads against the consensus. Circular plots were generated using circos-0.69-6 and coverage information from the re-mapping. 

https://doi.org/10.7554/eLife.36666.016
Figure 2—figure supplement 4
Genetic (hamming) distance of our three ancient HBV genomes compared to all 493 reference genomes.

Gaps or non-called sites (’N') were ignored.

https://doi.org/10.7554/eLife.36666.017
Figure 2—figure supplement 5
BootScan analysis of the sequence Karsdorf.

In each case, sequence fragments of 200 bases incrementing by 20 bases, 100 bootstrap replicates, were compared with sequence groups of (a) the eight human genotypes, two primate genotypes, and four ancient genomes and (b) the eight human genotypes, two primate genotypes (color coded as described in the legend).

https://doi.org/10.7554/eLife.36666.018
Figure 2—figure supplement 6
BootScan analysis of the sequence Sorsum.

In each case, sequence fragments of 200 bases incrementing by 20 bases, 100 bootstrap replicates, were compared with sequence groups or 50% consensus sequences of (a) the eight human genotypes, two primate genotypes, and four ancient genomes and (b) the eight human genotypes, two primate genotypes (color coded as described in the legend).

https://doi.org/10.7554/eLife.36666.019
Figure 2—figure supplement 7
BootScan analysis of the sequence Petersberg.

In each case, sequence fragments of 200 bases incrementing by 20 bases, 100 bootstrap replicates, were compared with sequence groups or 50% consensus sequences of (a) the eight human genotypes, two primate genotypes, and four ancient genomes and (b) the eight human genotypes, two primate genotypes (color coded as described in the legend).

https://doi.org/10.7554/eLife.36666.020
Figure 2—figure supplement 8
SimPlot analysis of (a) Karsdorf, (b) Sorsum and (c) Petersberg.

In each case, sequence fragments of 200 bases incrementing by 20 bases, 100 bootstrap replicates, were compared with sequence groups of the eight human genotypes, four primate genotypes and four ancient genomes (color coded as described in the legend).

https://doi.org/10.7554/eLife.36666.021
Figure 2—figure supplement 9
Plot of phylogenetic root-to-tip distance relative to sampling time (TempEst).

Each dot represents one sample.

https://doi.org/10.7554/eLife.36666.022

Tables

Table 1
Results of the genome reconstruction
https://doi.org/10.7554/eLife.36666.012
*Merged readsLength of HBV consensus sequenceMean HBV coverageGaps in the consensus sequence at nt position*Mapped reads HBV*Mapped reads humanMean human coverageHuman genomes/HBVgenomes
Karsdorf386,780,8923183104X2157–2175; 3107–3128; 3133–318310,718122,568,3102.96X1: 35.1
Sorsum367,574,767318247X-32499,856,0011.17X1: 40.2
Petersberg419,413,082316146X880–1000; 1232–1329; 1331–1415; 1420–1581; 1585–15982125105,476,6772.88X1: 16
  1. *number.

    nt, nucleotide.

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. 1
    High-throughput sequence data for Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B
    1. Krause J
    (2018)
    Publicly available at the European Nucleotide Archive (accession no. PRJEB24921).

Additional files

Supplementary file 1

Accession numbers for the reference genomes used in the first alignment step to catch HBV diversity in the sample.

Since monkey HBV strains are not classified into genotypes the column is left blank.

https://doi.org/10.7554/eLife.36666.027
Supplementary file 2

Number of reads mapping against the references shown in Supplementary file 1 before and after duplicate removal.

https://doi.org/10.7554/eLife.36666.028
Supplementary file 3

Number of contigs and combined contig length of the de novo assembly for chosen K-values.

https://doi.org/10.7554/eLife.36666.029
Supplementary file 4

Final consensus length after retrieving gap information from the multiple sequence alignment with Geneious.

https://doi.org/10.7554/eLife.36666.030
Supplementary file 5

Number of reads mapping against hg19 before and after duplicate removal and percentage of the genome where coverage is at least one.

https://doi.org/10.7554/eLife.36666.031
Supplementary file 6

Basic statistics for the mapping against the references shown in table S1.

Shown are mean coverage, mean coverage for the covered region, genome length, number of missing bases and covered bases

https://doi.org/10.7554/eLife.36666.032
Transparent reporting form
https://doi.org/10.7554/eLife.36666.033

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)