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Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

View ORCID ProfileMeriam Guellil, Lucy van Dorp, View ORCID ProfileSarah A. Inskip, View ORCID ProfileJenna M. Dittmar, Lehti Saag, Kristiina Tambets, Ruoyun Hui, Alice Rose, Eugenia D’Atanasio, Aivar Kriiska, Liivi Varul, A.M.H.C. Koekkelkoren, Rimma D. Goldina, View ORCID ProfileCraig Cessford, Anu Solnik, View ORCID ProfileMait Metspalu, Johannes Krause, View ORCID ProfileAlexander Herbig, View ORCID ProfileJohn E. Robb, Charlotte J. Houldcroft, View ORCID ProfileChristiana L. Scheib
doi: https://doi.org/10.1101/2022.01.19.476912
Meriam Guellil
1Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu, 51010, Estonia
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  • ORCID record for Meriam Guellil
Lucy van Dorp
2UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, London, WC1E 6BT, United Kingdom
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Sarah A. Inskip
3McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
4Department of Archaeology and Ancient History, University of Leicester, University Road, Leicester, LE1 7RH, United Kingdom
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Jenna M. Dittmar
3McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
5Department of Archaeology, University of Aberdeen, United Kingdom
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Lehti Saag
1Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu, 51010, Estonia
2UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, London, WC1E 6BT, United Kingdom
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Kristiina Tambets
1Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu, 51010, Estonia
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Ruoyun Hui
3McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
6Alan Turing Institute, United Kingdom
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Alice Rose
3McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
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Eugenia D’Atanasio
7Institute of Molecular Biology and Pathology, CNR, Rome, Italy
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Aivar Kriiska
8Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
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Liivi Varul
9Archaeological Research Collection, School of Humanities, Tallinn University, Tallinn 10130, Estonia
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A.M.H.C. Koekkelkoren
10IDDS Groep bv, ’s Gravendijckseweg 37, 2201 CZ Noordwijk, Netherlands
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Rimma D. Goldina
11Department History of Udmurtia, Archaeology and Ethnology, Udmurt State University, 1, Universitetskaya St. 1, 426034 Izhevsk, Russia
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Craig Cessford
12Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
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Anu Solnik
13Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu, 51010 Estonia
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Mait Metspalu
1Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu, 51010, Estonia
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Johannes Krause
14Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
15Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Alexander Herbig
13Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu, 51010 Estonia
14Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
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John E. Robb
16Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
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Charlotte J. Houldcroft
17Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
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  • For correspondence: cls83@ut.ee ch504@cam.ac.uk
Christiana L. Scheib
1Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu, 51010, Estonia
18St John’s College, University of Cambridge, Cambridge, CB2 1TP, United Kingdom
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  • For correspondence: cls83@ut.ee ch504@cam.ac.uk
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Summary

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1’s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 × 10-7 - 1.13 × 10-6 for non-African diversity leading to an estimated age of sampled modern Eurasian diversity to 4.68 (3.87 - 5.65) kya. Extrapolation of these rates indicate the age of sampled HSV-1 to 5.29 (4.60-6.12 kya, suggesting lineage replacement coinciding with late Neolithisation and implicating Bronze Age migrations6 in the distribution of HSV-1 through Eurasia.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 21, 2022.
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Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia
Meriam Guellil, Lucy van Dorp, Sarah A. Inskip, Jenna M. Dittmar, Lehti Saag, Kristiina Tambets, Ruoyun Hui, Alice Rose, Eugenia D’Atanasio, Aivar Kriiska, Liivi Varul, A.M.H.C. Koekkelkoren, Rimma D. Goldina, Craig Cessford, Anu Solnik, Mait Metspalu, Johannes Krause, Alexander Herbig, John E. Robb, Charlotte J. Houldcroft, Christiana L. Scheib
bioRxiv 2022.01.19.476912; doi: https://doi.org/10.1101/2022.01.19.476912
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Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia
Meriam Guellil, Lucy van Dorp, Sarah A. Inskip, Jenna M. Dittmar, Lehti Saag, Kristiina Tambets, Ruoyun Hui, Alice Rose, Eugenia D’Atanasio, Aivar Kriiska, Liivi Varul, A.M.H.C. Koekkelkoren, Rimma D. Goldina, Craig Cessford, Anu Solnik, Mait Metspalu, Johannes Krause, Alexander Herbig, John E. Robb, Charlotte J. Houldcroft, Christiana L. Scheib
bioRxiv 2022.01.19.476912; doi: https://doi.org/10.1101/2022.01.19.476912

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