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

doi:10.1126/sciadv.abo4435

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

Department of Evolutionary Anthropology

Publications: Contribution to journal › Article › Peer Reviewed

Abstract

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.

Original language	English
Article number	eabo4435
Number of pages	13
Journal	Science Advances
Volume	8
Issue number	30
DOIs	https://doi.org/10.1126/sciadv.abo4435
Publication status	Published - 29 Jul 2022

Funding

This work is supported by the Wellcome Trust (award no. 2000368/Z/15/Z) and St. John's College, Cambridge (J.E.R., S.A.I., C.C., A.R., and C.L.S.); The Max Planck Society (J.K. and A.H.); the Estonian Research Council grant PUT (PRG243) (L.S., A.S., M.M., and C.L.S) and PUT (PRG1027) (K.T., L.S., M.G., and A. K.); the European Union through the European Regional Development Fund (project no. 2014-2020.4.01.16-0030) (C.L.S., M.G., and M.M.); the European Regional Development Fund (project no. 2014-2020.4.01.15-0012) (M.M.); and the ERC Synergy Grant HistoGenes (no. 856453) (A.H.). L.v.D is supported by a UCL Excellence Fellowship. C.J.H. acknowledges support from the NIHR Cambridge Biomedical Research Centre Antimicrobial Resistance theme. A.R. acknowledges support from the British Archaeological Association.

Austrian Fields of Science 2012

106014 Genomics

Keywords

OF-AFRICA MIGRATION
VIRUS TYPE-1
BONE-COLLAGEN
ISOTOPE RATIOS
BRONZE-AGE
NITROGEN ISOTOPES
TROPHIC LEVEL
CARBON
ENRICHMENT
INFECTION

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10.1126/sciadv.abo4435

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Guellil, M., van Dorp, L., Inskip, S. A., Dittmar, J. M., Saag, L., Tambets, K., Hui, R., Rose, A., D'Atanasio, E., Kriiska, A., Varul, L., Koekkelkoren, A. M. H. C., Goldina, R. D., Cessford, C., Solnik, A., Metspalu, M., Krause, J., Herbig, A., Robb, J. E., ... Scheib, C. L. (2022). Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. Science Advances, 8(30), Article eabo4435. https://doi.org/10.1126/sciadv.abo4435

@article{f6b3cd174e764b8d9a7ee963fc75f9b7,

title = "Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia",

abstract = "Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5{\texttimes} with paired human genomes up to 10.16{\texttimes}. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.",

keywords = "OF-AFRICA MIGRATION, VIRUS TYPE-1, BONE-COLLAGEN, ISOTOPE RATIOS, BRONZE-AGE, NITROGEN ISOTOPES, TROPHIC LEVEL, CARBON, ENRICHMENT, INFECTION",

author = "Meriam Guellil and \{van Dorp\}, Lucy and Inskip, \{Sarah A.\} and Dittmar, \{Jenna M.\} and Lehti Saag and Kristiina Tambets and Ruoyun Hui and Alice Rose and Eugenia D'Atanasio and Aivar Kriiska and Liivi Varul and Koekkelkoren, \{A. M. H. C.\} and Goldina, \{Rimma D.\} and Craig Cessford and Anu Solnik and Mait Metspalu and Johannes Krause and Alexander Herbig and Robb, \{John E.\} and Houldcroft, \{Charlotte J.\} and Scheib, \{Christiana L.\}",

note = "Publisher Copyright: Copyright {\textcopyright} 2022 The Authors.",

year = "2022",

month = jul,

day = "29",

doi = "10.1126/sciadv.abo4435",

language = "English",

volume = "8",

journal = "Science Advances",

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Guellil, M, van Dorp, L, Inskip, SA, Dittmar, JM, Saag, L, Tambets, K, Hui, R, Rose, A, D'Atanasio, E, Kriiska, A, Varul, L, Koekkelkoren, AMHC, Goldina, RD, Cessford, C, Solnik, A, Metspalu, M, Krause, J, Herbig, A, Robb, JE, Houldcroft, CJ & Scheib, CL 2022, 'Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia', Science Advances, vol. 8, no. 30, eabo4435. https://doi.org/10.1126/sciadv.abo4435

TY - JOUR

T1 - Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

AU - Guellil, Meriam

AU - van Dorp, Lucy

AU - Inskip, Sarah A.

AU - Dittmar, Jenna M.

AU - Saag, Lehti

AU - Tambets, Kristiina

AU - Hui, Ruoyun

AU - Rose, Alice

AU - D'Atanasio, Eugenia

AU - Kriiska, Aivar

AU - Varul, Liivi

AU - Koekkelkoren, A. M. H. C.

AU - Goldina, Rimma D.

AU - Cessford, Craig

AU - Solnik, Anu

AU - Metspalu, Mait

AU - Krause, Johannes

AU - Herbig, Alexander

AU - Robb, John E.

AU - Houldcroft, Charlotte J.

AU - Scheib, Christiana L.

PY - 2022/7/29

Y1 - 2022/7/29

N2 - Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.

AB - Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.

KW - OF-AFRICA MIGRATION

KW - VIRUS TYPE-1

KW - BONE-COLLAGEN

KW - ISOTOPE RATIOS

KW - BRONZE-AGE

KW - NITROGEN ISOTOPES

KW - TROPHIC LEVEL

KW - CARBON

KW - ENRICHMENT

KW - INFECTION

UR - https://www.scopus.com/pages/publications/85135379988

U2 - 10.1126/sciadv.abo4435

DO - 10.1126/sciadv.abo4435

M3 - Article

SN - 2375-2548

VL - 8

JO - Science Advances

JF - Science Advances

IS - 30

M1 - eabo4435

ER -

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Abstract

Funding

Austrian Fields of Science 2012

Keywords

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