Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia
journal contributionposted on 2023-01-12, 16:30 authored by M 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.