Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Guellil, M.; van Dorp, L.; Inksip, S. A.; Dittmar, J. M.; Saag, L.; Tambets, K.; Hui, R.; Rose, A.; D'Atanasio, E.; Kriiska, A.; Varul, L.; Koekkelkoren, A. M. H. C.; Goldina, R. D.; Cessford, C.; Solnik, A.; Metspalu, M.; Krause, J.; Herbig, A.; Robb, J. E.; Houldcroft, C.; Scheib, C. L.

doi:10.1101/2022.01.19.476912

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bioRxiv · 10.1101/2022.01.19.476912

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

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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-1s 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 9.5x with paired human genomes up to 10.16x. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 x 10-7 - 1.13 x 10-6 for non-African diversity leading to an estimated age of sampled modern Eurasian diversity to 4.68 (3.87 - 5.65) kya. Extrapolation of these rates indicate the age of sampled HSV-1 to 5.29 (4.60-6.12 kya, suggesting lineage replacement coinciding with late Neolithisation and implicating Bronze Age migrations6 in the distribution of HSV-1 through Eurasia.

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Guellil, M., van Dorp, L., Inksip, S. A., Dittmar, J. M., Saag, L., Tambets, K., Hui, R., Rose, A., D'Atanasio, E., Kriiska, A., Varul, L., Koekkelkoren, A. M. H. C., Goldina, R. D., Cessford, C., Solnik, A., Metspalu, M., Krause, J., Herbig, A., Robb, J. E., Houldcroft, C., Scheib, C. L.. 2022-01-21. Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. https://doi.org/10.1101/2022.01.19.476912

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