Louis L'Hôte, Luisa Sacristán, Róisín Ferguson, Alex Siekmann, Leland Rogers, Barbara Richter, Herbert Weissenböck, Jenny Lorke, Lara Artemis, Élodie Lévêque, Richard Hark, Patricia Engel, Mary Teresa Josephine Webber, Madison Bennett, Kristine Rose-Beers, Emma Nichols, Marta Munoz Alegre, Max Ramsøe, Sarah Fiddyment, Laura C Viñas-Caron, Dimitry V Papin, Ian C Light-Maka, Felix M Key, Jonas Albarnaz, Tim Downing, Jonathan Pekar, Philippe Lemey, Daniel G Bradley, Jiří Vnouček, Cheryl A Makarewicz, Joanna Story, Matthew Collins, Matthew D Teasdale, Annelise Binois-Roman, Sébastien Calvignac-Spencer, Kevin G Daly
Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded since antiquity. We report 21 novel ancient SPPV genomes spanning the Eurasian steppe Bronze Age (∼1700 BCE) to the Early Modern period in Western Europe, including multiple genomes obtained from medieval parchment. We estimate that major capripoxvirus lineages diverged ∼11,500 to 3700 years ago, overlapping known translocations and bio-cultural developments in sheep. Our dataset supports SPPV diverging first within the lineage leading to goatpox virus and lumpy skin disease virus, and that known gene inactivation events within SPPV and goatpox virus occur in our earliest SPPV genomes. These findings reveal that the food security of Eurasian communities has been threatened by sheeppox for more than 3700 years and provide insights into the genomic evolution and potential host adaptation of SPPV.