Guellil Meriam, van Dorp Lucy, Inskip Sarah A, Dittmar Jenna M, Saag Lehti, Tambets Kristiina, Hui Ruoyun, Rose Alice, D'Atanasio Eugenia, Kriiska Aivar, Varul Liivi, Koekkelkoren A M H C, Goldina Rimma D, Cessford Craig, Solnik Anu, Metspalu Mait, Krause Johannes, Herbig Alexander, Robb John E, Houldcroft Charlotte J, Scheib Christiana L
Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia.
UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK.
Sci Adv. 2022 Jul 29;8(30):eabo4435. doi: 10.1126/sciadv.abo4435. Epub 2022 Jul 27.
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.
人类单纯疱疹病毒1型（HSV - 1）是一种通过口腔接触传播的终身感染病毒，全球大多数成年人都受到感染。将采样多样性按系统发育地理聚类为欧洲、泛欧亚和非洲群体，这表明该病毒与人类走出非洲的迁徙共同进化，不过也有人提出其起源要晚得多。我们展示了三个完整的古代欧洲HSV - 1基因组和一个部分基因组，年代可追溯到公元3世纪至17世纪，测序深度高达9.5倍，与之配对的人类基因组测序深度高达10.16倍。考虑到现代和古代基因组数据集，我们应用系统发育方法将采样的现代欧亚HSV - 1多样性的年代估计为4680（3870至5650）年前。将估计速率外推到全球数据集表明现存采样HSV - 1的年代为5290（4600至6120）年前，这表明HSV - 1谱系替换与新石器时代晚期以及青铜时代的迁徙相吻合。
