Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

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.

Abstract

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.

Citation

Guellil, M., van Dorp, L., Inskip, S. A., Dittmar, J. M., Saag, L., Tambets, K., Hui, R., Rose, A., D’Atanasio, E., Kriiska, A., Varul, L., Koekkelkoren, A., Goldina, R. D., Cessford, C., Solnik, A., Metspalu, M., Krause, J., Herbig, A., Robb, J. E., Houldcroft, C. J., & Scheib, C. L. (2022). Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. Science Advances, 8(30), https://doi.org/10.1126/sciadv.abo4435

• Journal Article Type: Article
• Acceptance Date: Jun 10, 2022
• Online Publication Date: Jul 27, 2022
• Publication Date: 2022
• Deposit Date: Sep 26, 2022
• Publicly Available Date: Sep 26, 2022
• Journal: Science Advances
• Electronic ISSN: 2375-2548
• Publisher: American Association for the Advancement of Science
• Peer Reviewed: Peer Reviewed
• Volume: 8
• Issue: 30
• DOI: https://doi.org/10.1126/sciadv.abo4435
• Public URL: https://durham-repository.worktribe.com/output/1191053