3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes | bioRxiv

biorxiv.org/content/10.64898/2…

Sheeppox virus (SPPV; Capripoxvirus sheeppox) is a major livestock pathogen which causes economic hardship in the Global South through reduced production and death of vulnerable sheep. The disease is thought to have affected Eurasian societies for millennia, with descriptions of sheeppox-like disease recorded since Roman antiquity. Here we report the recovery of 21 novel ancient SPPV genomes spanning the Bronze Age period in the Eurasian steppes (~1,700 BCE) to the Early Modern period in Western Europe. Our dataset includes multiple genomes obtained from medieval parchment manuscripts, demonstrating that skin-based documents represent an under-recognized source of pathogen genomes from the past. Using this temporal genomic dataset, we estimate that major capripoxvirus lineages diverged ~11,500-3,700 years ago, depending on tree topology and mutation model, and overlapping known major translocations and bio-cultural developments in sheep. Our dataset supports SPPV representing the earliest split from the lineage leading to goatpox virus and lumpy skin disease virus (Capripoxvirus goatpox and Capripoxvirus lumpyskinpox). We determine that known gene inactivation events within SPPV and goatpox virus are also found in our earliest SPPV genomes and therefore occurred rapidly following its divergence. Together, these findings reveal that the food security of Eurasian communities have been threatened by sheeppox for over 3,700 years, and provide new temporal insights to the genomic evolution and potential host adaptation of sheeppox virus. ### Competing Interest Statement The authors have declared no competing interest. Taighde Éireann - Research Ireland, ror.org/010t7sr36, 21/PATH-S/9515(T) European Research Council, ror.org/0472cxd90