Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

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Scheib, Christiana L  ORCID logo
Houldcroft, Charlotte J  ORCID logo
Robb, John 

Human herpes simplex virus 1 (HSV-1), a lifelong 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 to the 3rd-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 - 5.65) kya. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60-6.12) kya, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.


Funder: Wellcome Trust

31 Biological Sciences, 3105 Genetics, 43 History, Heritage and Archaeology, 44 Human Society, 4301 Archaeology, 4303 Historical Studies, 4401 Anthropology, Sexually Transmitted Infections, Infectious Diseases, 2.2 Factors relating to the physical environment, 2 Aetiology, Infection
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Science Advances
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American Association for the Advancement of Science
Wellcome Trust (200368/Z/15/Z)