22.04.2021

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

  • 1.

    Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015).

  • 2.

    Damgaard, P. d. B. et al. 137 ancient human genomes from across the Eurasian steppes. Nature https://doi.org/10.1038/s41586-018-0094-2 (2018).

  • 3.

    Lai, C. L., Ratziu, V., Yuen, M.-F. & Poynard, T. Viral hepatitis B. Lancet 362, 2089–2094 (2003).

  • 4.

    Schweitzer, A., Horn, J., Mikolajczyk, R. T., Krause, G. & Ott, J. J. Estimations of worldwide prevalence of chronic hepatitis B virus infection: a systematic review of data published between 1965 and 2013. Lancet 386, 1546–1555 (2015).

  • 5.

    Murhekar, M. V., Murhekar, K. M. & Sehgal, S. C. Epidemiology of hepatitis B virus infection among the tribes of Andaman and Nicobar Islands, India. Trans. R. Soc. Trop. Med. Hyg. 102, 729–734 (2008).

  • 6.

    Locarnini, S., Littlejohn, M., Aziz, M. N. & Yuen, L. Possible origins and evolution of the hepatitis B virus (HBV). Semin. Cancer Biol. 23, 561–575 (2013).

  • 7.

    Littlejohn, M., Locarnini, S. & Yuen, L. Origins and evolution of hepatitis B virus and hepatitis D virus. Cold Spring Harb. Perspect. Med. 6, a021360 (2016).

  • 8.

    Kramvis, A. Genotypes and genetic variability of hepatitis B virus. Intervirology 57, 141–150 (2014).

  • 9.

    Hannoun, C., Horal, P. & Lindh, M. Long-term mutation rates in the hepatitis B virus genome. J. Gen. Virol. 81, 75–83 (2000).

  • 10.

    Zhou, Y. & Holmes, E. C. Bayesian estimates of the evolutionary rate and age of hepatitis B virus. J. Mol. Evol. 65, 197–205 (2007).

  • 11.

    Paraskevis, D. et al. Dating the origin of hepatitis B virus reveals higher substitution rate and adaptation on the branch leading to F/H genotypes. Mol. Phylogenet. Evol. 93, 44–54 (2015).

  • 12.

    Zehender, G. et al. Enigmatic origin of hepatitis B virus: an ancient travelling companion or a recent encounter? World J. Gastroenterol. 20, 7622–7634 (2014).

  • 13.

    Kramvis, A. et al. Relationship of serological subtype, basic core promoter and precore mutations to genotypes/subgenotypes of hepatitis B virus. J. Med. Virol. 80, 27–46 (2008).

  • 14.

    MacDonald, D. M., Holmes, E. C., Lewis, J. C. & Simmonds, P. Detection of hepatitis B virus infection in wild-born chimpanzees (Pan troglodytes verus): phylogenetic relationships with human and other primate genotypes. J. Virol. 74, 4253–4257 (2000).

  • 15.

    Nielsen, R. et al. Tracing the peopling of the world through genomics. Nature 541, 302–310 (2017).

  • 16.

    Rasmussen, S. et al. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 163, 571–582 (2015).

  • 17.

    Feldman, M. et al. A high-coverage Yersinia pestis genome from a sixth-century Justinianic plague victim. Mol. Biol. Evol. 33, 2911–2923 (2016).

  • 18.

    Reid, A. H., Fanning, T. G., Hultin, J. V. & Taubenberger, J. K. Origin and evolution of the 1918 “Spanish” influenza virus hemagglutinin gene. Proc. Natl Acad. Sci. USA 96, 1651–1656 (1999).

  • 19.

    Duggan, A. T. et al. 17th century variola virus reveals the recent history of smallpox. Curr. Biol. 26, 3407–3412 (2016).

  • 20.

    Kahila Bar-Gal, G. et al. Tracing hepatitis B virus to the 16th century in a Korean mummy. Hepatology 56, 1671–1680 (2012).

  • 21.

    Patterson Ross, Z. et al. The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathog. 14, e1006750 (2018).

  • 22.

    Bond, W. W. et al. Survival of hepatitis B virus after drying and storage for one week. Lancet 317, 550–551 (1981).

  • 23.

    Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).

  • 24.

    Simmonds, P. & Midgley, S. Recombination in the genesis and evolution of hepatitis B virus genotypes. J. Virol. 79, 15467–15476 (2005).

  • 25.

    Bouckaert, R. et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLOS Comput. Biol. 10, e1003537 (2014).

  • 26.

    Simmonds, P. Reconstructing the origins of human hepatitis viruses. Phil. Trans. R. Soc. Lond. B 356, 1013–1026 (2001).

  • 27.

    Tedder, R. S., Bissett, S. L., Myers, R. & Ijaz, S. The ‘Red Queen’ dilemma – running to stay in the same place: reflections on the evolutionary vector of HBV in humans. Antivir. Ther. 18, 489–496 (2013).

  • 28.

    Duchêne, S., Holmes, E. C. & Ho, S. Y. W. Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proc. R. Soc. Lond. B 281, 20140732 (2014).

  • 29.

    Zehender, G. et al. Reliable timescale inference of HBV genotype A origin and phylodynamics. Infect. Genet. Evol. 32, 361–369 (2015).

  • 30.

    Hannoun, C., Söderström, A., Norkrans, G. & Lindh, M. Phylogeny of African complete genomes reveals a West African genotype A subtype of hepatitis B virus and relatedness between Somali and Asian A1 sequences. J. Gen. Virol. 86, 2163–2167 (2005).

  • 31.

    Pickrell, J. K. et al. Ancient west Eurasian ancestry in southern and eastern Africa. Proc. Natl Acad. Sci. USA 111, 2632–2637 (2014).

  • 32.

    Ghosh, S. et al. Unique hepatitis B virus subgenotype in a primitive tribal community in eastern India. J. Clin. Microbiol. 48, 4063–4071 (2010).

  • 33.

    Basu, A., Sarkar-Roy, N. & Majumder, P. P. Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure. Proc. Natl Acad. Sci. USA 113, 1594–1599 (2016).

  • 34.

    Drexler, J. F. et al. Bats carry pathogenic hepadnaviruses antigenically related to hepatitis B virus and capable of infecting human hepatocytes. Proc. Natl Acad. Sci. USA 110, 16151–16156 (2013).

  • 35.

    Geer, L. Y. et al. The NCBI BioSystems database. Nucleic Acids Res. 38, D492–D496 (2010).

  • 36.

    Bell, T. G., Yousif, M. & Kramvis, A. Bioinformatic curation and alignment of genotyped hepatitis B virus (HBV) sequence data from the GenBank public database. Springerplus 5, 1896 (2016).

  • 37.

    Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).

  • 38.

    Reimer, P. J. et al. IntCal13 and Marine13 radiocarbon age calibration curves 0–50,000 years cal bp. Radiocarbon 55, 1869–1887 (2013).

  • 39.

    Lindgreen, S. AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes 5, 337 (2012).

  • 40.

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

  • 41.

    Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).

  • 42.

    Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).

  • 43.

    Drosten, C., Weber, M., Seifried, E. & Roth, W. K. Evaluation of a new PCR assay with competitive internal control sequence for blood donor screening. Transfusion 40, 718–724 (2000).

  • 44.

    Willerslev, E. & Cooper, A. Review Paper. Ancient DNA. Proc. R. Soc. Lond. B 272, 3–16 (2005).

  • 45.

    Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).

  • 46.

    Orlando, L., Gilbert, M. T. P. & Willerslev, E. Reconstructing ancient genomes and epigenomes. Nat. Rev. Genet. 16, 395–408 (2015).

  • 47.

    Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).

  • 48.

    Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).

  • 49.

    Needleman, S. B. & Wunsch, C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970).

  • 50.

    Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276–277 (2000).

  • 51.

    Martin, D. P., Murrell, B., Golden, M., Khoosal, A. & Muhire, B. RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol. 1, vev003 (2015).

  • 52.

    Martin, D. & Rybicki, E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 16, 562–563 (2000).

  • 53.

    Padidam, M., Sawyer, S. & Fauquet, C. M. Possible emergence of new geminiviruses by frequent recombination. Virology 265, 218–225 (1999).

  • 54.

    Martin, D. P., Posada, D., Crandall, K. A. & Williamson, C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res. Hum. Retroviruses 21, 98–102 (2005).

  • 55.

    Smith, J. M. Analyzing the mosaic structure of genes. J. Mol. Evol. 34, 126–129 (1992).

  • 56.

    Posada, D. & Crandall, K. A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl Acad. Sci. USA 98, 13757–13762 (2001).

  • 57.

    Gibbs, M. J., Armstrong, J. S. & Gibbs, A. J. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16, 573–582 (2000).

  • 58.

    Boni, M. F., Posada, D. & Feldman, M. W. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176, 1035–1047 (2007).

  • 59.

    Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

  • 60.

    Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).

  • 61.

    Ronquist, F. & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574 (2003).

  • 62.

    Rambaut, A., Lam, T. T., Max Carvalho, L. & Pybus, O. G. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2, vew007 (2016).

  • 63.

    Bouckaert, R. R. & Drummond, A. J. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evol. Biol. 17, 42 (2017).

  • 64.

    Duchêne, S., Duchêne, D., Holmes, E. C. & Ho, S. Y. W. The performance of the date-randomization test in phylogenetic analyses of time-structured virus data. Mol. Biol. Evol. 32, 1895–1906 (2015).

  • 65.

    Kass, R. E. & Raftery, A. E. Bayes Factors. J. Am. Stat. Assoc. 90, 773–795 (1995).

  • 66.

    Rambaut, A., Suchard, M. A., Xie, D. & Drummond, A. J. Tracer v1.6. (2017).

  • 67.

    Sanchez, G. et al. Human (Clovis)–gomphothere (Cuvieronius sp.) association 13,390 calibrated yBP in Sonora, Mexico. Proc. Natl Acad. Sci. USA 111, 10972–10977 (2014).

  • 68.

    Bourgeon, L., Burke, A. & Higham, T. Earliest human presence in North America dated to the Last Glacial Maximum: new radiocarbon dates from Bluefish Caves, Canada. PLoS ONE 12, e0169486 (2017).

  • 69.

    Andernach, I. E., Nolte, C., Pape, J. W. & Muller, C. P. Slave trade and hepatitis B virus genotypes and subgenotypes in Haiti and Africa. Emerg. Infect. Dis. 15, 1222–1228 (2009).

  • 70.

    Kayser, M. et al. Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific. Mol. Biol. Evol. 23, 2234–2244 (2006).

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