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^*

^*Corresponding author for this work

Archaeology

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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 - 27 Jul 2022

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Ancient herpes simplex 1 genomes reveal recent viral structure in EurasiaFinal published version, 3.56 MBLicence: CC BY

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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

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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× 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.",

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{\textquoteright}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.}",

year = "2022",

month = jul,

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doi = "10.1126/sciadv.abo4435",

language = "English",

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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

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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 - 2022/7/27

Y1 - 2022/7/27

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.

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DO - 10.1126/sciadv.abo4435

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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

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