Medieval manuscripts are “biological time capsules” for deadly sheeppox virus

中世纪手稿：致命羊痘病毒的“生物时间胶囊”

Sheeppox is a highly contagious, often fatal viral disease that was largely eradicated from much of European livestock in the 20th century. But there is still the occasional regional outbreak, such as the one that afflicted many flocks of sheep in Greece last year. 羊痘是一种高度传染性且通常致命的病毒性疾病，在20世纪已在欧洲大部分地区的牲畜中基本被根除。但偶尔仍会出现区域性爆发，例如去年希腊许多羊群所遭受的疫情。

In order to reconstruct how the virus has evolved over the last 3,500 years, scientists extracted and sequenced sheeppox DNA preserved in the animal skins used for the parchment of numerous medieval manuscripts. They reported their findings in a new paper published in the journal Science Advances. 为了重建该病毒在过去3500年间的演变过程，科学家们提取并测序了保存在中世纪手稿羊皮纸中的羊痘病毒DNA。他们将研究结果发表在《科学进展》（Science Advances）杂志上。

“The recording of ancient DNA of pathogens has completely changed our understanding of infectious disease in the past, and here we show that parchment can also preserve animal pathogen DNA. It is possible that archives and libraries around the world also contain the genetic traces of disease outbreaks in animals in the past,” said co-author Louis L’Hôte, a graduate student at University College Dublin. “These genomes help us understand how these pathogens evolved and how they impacted past societies—such as sheeppox virus, which we show has been affecting Eurasian sheep herds for at least three and a half millennia.” “病原体古DNA的记录彻底改变了我们对过去传染病的理解，而在这里我们证明了羊皮纸也能保存动物病原体的DNA。世界各地的档案馆和图书馆可能也包含着过去动物疾病爆发的遗传痕迹，”合著者、都柏林大学研究生路易斯·洛特（Louis L’Hôte）表示。“这些基因组帮助我们了解这些病原体是如何进化的，以及它们如何影响了过去的社会——例如羊痘病毒，我们证明它至少在三千五百年来一直影响着欧亚大陆的羊群。”

Per the authors, the earliest known written evidence of sheeppox infection dates to the first century CE, when Roman accounts described outbreaks of skin lesions (“pustules”) in the animals. There are more frequent mentions of deadly outbreaks of “pockes” or “variola” in sheep by the Middle Ages, recorded in various agricultural texts and accounting documents in France, Spain, and England. 据作者所述，已知最早的羊痘感染书面证据可追溯到公元一世纪，当时罗马的记录描述了动物身上出现的皮肤病变（“脓疱”）。到了中世纪，法国、西班牙和英国的各种农业文本和会计文件中，关于羊群中致命的“痘疮”（pockes）或“天花”（variola）爆发的记载更为频繁。

There seemed to be a decline in outbreaks in 17th-century France, although frequent outbreaks re-emerged in the 18th and 19th centuries, often with high mortality rates in the flocks. Great Britain did not experience a sheeppox resurgence until 1847. However, very little was known about the genetic history of the sheeppox virus. That’s why L’Hôte et al. turned to analyzing DNA in medieval manuscripts—the parchments were often made from sheep leather. 17世纪的法国疫情似乎有所减少，尽管在18和19世纪频繁爆发，且羊群的死亡率往往很高。英国直到1847年才再次出现羊痘疫情。然而，人们对羊痘病毒的遗传史知之甚少。这就是为什么洛特等人转向分析中世纪手稿中的DNA——因为这些羊皮纸通常是由羊皮制成的。

A number of analytical techniques have emerged in recent decades to help create these kinds of historical molecular records. For instance, last year we reported on research that used microbial DNA analysis of human remains to identify the likely pathogens that killed many soldiers in Napoleon’s army in 1812. Two pathogens in particular stood out: Salmonella enterica, which causes paratyphoid fever, and Borrelia recurrentis, which is transmitted by body lice and causes relapsing fever. Both are consistent with written contemporary accounts. 近几十年来，许多分析技术应运而生，帮助建立这类历史分子记录。例如，去年我们报道了一项研究，该研究利用人类遗骸的微生物DNA分析，确定了1812年拿破仑军队中导致许多士兵死亡的潜在病原体。其中两种病原体尤为突出：导致副伤寒的肠道沙门氏菌（Salmonella enterica），以及通过体虱传播并导致回归热的回归热螺旋体（Borrelia recurrentis）。这两者都与当时的文字记录相吻合。

The team collected samples from medieval manuscripts housed in collections at Yale University, Cambridge University, Corpus Christi College, University College Dublin, the Lambeth Palace Library, and Trinity College, among others. Those works included pages from a 15th-century Speculum Historiale; the 15th-century Clairvaux manuscripts; several 9th-century gospel text fragments; the 9th-century Achadeus Psalter; the early 11th-century Trinity Gospels; the Lambeth Bible; and the 1,000-year-old York Gospels. 研究团队从耶鲁大学、剑桥大学、基督圣体学院、都柏林大学、兰贝斯宫图书馆和三一学院等机构收藏的中世纪手稿中采集了样本。这些作品包括15世纪的《历史之镜》（Speculum Historiale）书页；15世纪的克莱沃（Clairvaux）手稿；几份9世纪的福音书残片；9世纪的《阿卡迪乌斯诗篇》（Achadeus Psalter）；11世纪早期的《三一福音书》（Trinity Gospels）；《兰贝斯圣经》（Lambeth Bible）以及拥有1000年历史的《约克福音书》（York Gospels）。

Multiple pages, often from the same manuscript, were found to contain DNA from the sheeppox pathogen, which means infected animals were likely used to make the parchment—and thus, that medieval flocks experienced frequent outbreaks of sheeppox. The authors were surprised when they also found evidence of the sheeppox virus on parchment made from calfskin and goatskin, suggesting either cross-species infection or contamination when the parchment was being made. 研究发现，通常来自同一手稿的多页纸张中都含有羊痘病原体的DNA，这意味着受感染的动物很可能被用于制作羊皮纸——因此，中世纪的羊群经历了频繁的羊痘爆发。令作者惊讶的是，他们还在由小牛皮和山羊皮制成的羊皮纸上发现了羊痘病毒的证据，这表明可能存在跨物种感染，或者是在制作羊皮纸时发生了污染。

The team also extracted DNA from Bronze Age sheep teeth collected at settlement sites in Russia and Central Kazakhstan, since teeth can preserve DNA evidence of infection over thousands of years. After comparing those ancient sequences with the medieval ones, the authors concluded that the sheeppox virus diverged from the goatpox and lumpy skin disease viruses (all members of the Capripoxvirus family) between 11,500 and 3,700 years ago. That coincides roughly with the domestication of animals in Europe. 研究团队还从俄罗斯和哈萨克斯坦中部定居点采集的青铜时代羊牙中提取了DNA，因为牙齿可以保存数千年的感染DNA证据。在将这些古老的序列与中世纪的序列进行比较后，作者得出结论：羊痘病毒是在11500年至3700年前从山羊痘病毒和结节性皮肤病病毒（均为山羊痘病毒属成员）中分化出来的。这大致与欧洲动物的驯化时间相吻合。

All told, the team recovered 21 ancient genomes from 1700 BCE to early modern Europe. “Parchment making has been considered a vanishing craft, but we are beginning to understand just how much of the past it has retained,” said co-author Kevin G. Daly, also of UCD. “This project shows that parchments not only preserve our cultural history for hundreds of years, but also the landscape of disease in our livestock in the medieval period. This kind of exciting, surprising discovery is only possible when researchers from a range of disciplines come together to share their expertise and data.” 总而言之，研究团队恢复了从公元前1700年到近代欧洲的21个古基因组。“羊皮纸制作一直被认为是一门正在消失的工艺，但我们开始意识到它保留了多少过去的信息，”同样来自都柏林大学的合著者凯文·G·戴利（Kevin G. Daly）说。“这个项目表明，羊皮纸不仅为我们保存了数百年的文化历史，还记录了中世纪时期牲畜的疾病状况。这种令人兴奋、出人意料的发现，只有当来自不同学科的研究人员齐聚一堂，分享他们的专业知识和数据时才有可能实现。”