% pubman genre = article @article{item_3401707, title = {{Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia}}, author = {Guellil, Meriam and van Dorp, Lucy and Inskip, Sarah A. and Dittmar, Jenna M. and Saag, Lehti and Tambets, Kristiina and Hui, Ruoyun and Rose, Alice and D{\textquoteright}Atanasio, Eugenia and Kriiska, Aivar and Varul, Liivi and Koekkelkoren, A.M.H.C. and Goldina, Rimma D. and Cessford, Craig and Solnik, Anu and Metspalu, Mait and Krause, Johannes and Herbig, Alexander and Robb, John E. and Houldcroft, Charlotte J. and Scheib, Christiana L.}, language = {eng}, issn = {2375-2548}, doi = {10.1126/sciadv.abo443}, publisher = {American Association for the Advancement of Science (AAAS)}, year = {2022}, abstract = {{Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1{\textquoteright}s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5$\times$ with paired human genomes up to 10.16$\times$. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 $\times$ 10-7}}, contents = {Introduction Results - Retrieved genomes are likely from typical infections - Demographic history of HSV-1 in a global context Discussion Material and Methods - Ethics statement - Sampling - Generation of aDNA libraries - Sequencing - aDNA authentication - Metagenomic screening - Targeted capture of HSV-1 - Alignment of viral data to the reference sequence - Genotyping - HSV-1 linkage disequilibrium and population genetic analysis - Compilation of comparative HSV data - Preparation of genome sequences - HSV-1 phylogenetic analysis and recombination filtering - Phylogenetic dating - Alignment of human data to the reference sequence and quality control - Genetic sex estimation, mtDNA, and Y haplotyping - Human variant calling and imputation of genotypes}, journal = {{Science Advances}}, volume = {8}, number = {30}, }