posted on 2023-01-12, 16:30authored byM Guellil, L van Dorp, SA Inskip, JM Dittmar, L Saag, K Tambets, R Hui, A Rose, E D’Atanasio, A Kriiska, L Varul, AMHC Koekkelkoren, RD Goldina, C Cessford, A Solnik, M Metspalu, J Krause, A Herbig, JE Robb, CJ Houldcroft, CL Scheib
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.
Funding
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.
History
Citation
Guellil, M., van Dorp, L., Inskip, S. A., Dittmar, J. M., Saag, L., Tambets, K., ... & Scheib, C. L. (2022). Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. Science Advances, 8(30), eabo4435.