Ancient virus hunters: how we discovered sheeppox DNA hidden in medieval gospels

Humans and domesticated animals have lived together for millennia, and this relationship has shaped their destinies in countless ways. Animals offered people food, companionship, traction (pulling ploughs), clothing and transport.

They also provided something less obvious but extraordinarily important: parchment to write on. This robust, plentiful and portable material enabled many people to record and store their histories in the days before mass-produced paper.

Parchment was made with the skins of a range of animals. From first-hand experience in a workshop in Malta , one of us (Kevin) saw how quickly these skins can be transformed into parchment suitable for writing.

After soaking them in vats of water containing quicklime, the flesh and hair tissue is removed using hefty blades and elbow grease. The skins are then stretched on frames overnight or longer – leaving a taut membrane that just needs smoothing and light treatment to be ready for use. Within a matter of days, a biological tissue is processed into a remarkably durable historical material.

Parchment has another fascinating quality. It preserves DNA from the animal killed in its making. From our latest study , it is clear that DNA can survive in parchment (even if fragmented) for well over a thousand years – although the precise time depends on how well the parchment has been archived and stored.

As researchers of how livestock was used in early societies, this raised other intriguing questions. Could biological traces of infection also survive the skin’s transformation into parchment, if the animal was infected with a disease when it died?

And if a pathogen (disease-causing organism) was present at a sufficiently high level, might some of its biological signatures remain preserved in the finished material many hundreds of years later?

Sheeppox in parchment

Two projects based at the University of York and the Bodleian Library in Oxford kindly allowed us to peer through their genetic data from parchment primarily originating in central and western Europe. These were skins from cattle, sheep and goats dating back to roughly AD700-1400, which had mostly been used in religious documents.

To our surprise, we discovered strong evidence of the ovine relative of the deadly smallpox virus, known as sheeppox virus , in this ancient parchment.

While today, sheeppox is considered eliminated in Europe, it is still endemic in other parts of the world, including large regions of Africa and Asia. Sheeppox is highly infectious and very lethal, particularly in young sheep (there are also a few cases of the virus infecting goats). Infected animals are left covered in characteristic pox scars.

We discovered sheeppox virus DNA in a surprising proportion of the European parchments: 32 parchment folia gave at least a hint of the pathogen.

Inside the famous York Gospels – one of the few pre-Normal Conquest gospels to have survived the 16th-century Reformation – we found three pages with the virus DNA, including a legal document appended hundreds of years after the bible’s production around AD990. Sampling of this priceless document required careful use of erasers , to remove a minimal amount of the parchment surface for biomolecular analysis.

We also found sheeppox virus DNA in the Corpus Glossary – a combined Latin and Old English dictionary, probably made around AD800. Traces were also present in 15th-century ancient paper samples from Clairvaux in north-west France, which may have been strengthened (or “sized”) with collagen obtained from animal parts or parchment scraps.

All this has added to our understanding of how disease affected livestock and farming during the middle ages and earlier. Our work is not limited to parchment: we have also screened DNA data from the teeth, bone and diseased skin of animals dating back thousands of years .

Even older viral DNA

Sheeppox affected European sheep herds for centuries in the medieval period – but they weren’t the oldest viral genomes we discovered. These came from two sheep teeth from the Eurasian steppe, roughly 3,700 and 3,200 years old, which had already been sampled for their animal DNA but were also hiding pathogen DNA.

In his treatise On Agriculture (De Re Rustica, 60-65BC), the Roman writer Columella described a “pusula” disease that was affecting sheep – which we now assume to be sheeppox. Which means farmers have been battling it for thousands of years.

Using the viral DNA from those ancient teeth, we could estimate when the sheeppox virus split from its closest relatives: other Capripoxviruses which infect goats or cattle. While our different models gave a range between 11,500 and 3,500 years ago, the consistent median estimate was around 5,000 years ago.

By bringing together livestock species including cattle, sheep and goats through domestication and pastoralism, early Eurasian farmers may have created the circumstances for these pathogens to evolve and adapt to new hosts – and we’re still living with them today.

Since 2024, there have been several sheeppox virus outbreaks in southern Europe , and the disease is an ongoing issue for farmers all over the world. It’s therefore important to fully understand the biology of this virus, both for the development of improved interventions against the pathogen, and to understand how future pathogens may evolve to infect new hosts – potentially causing the next viral pandemic.

Ancient genomes from other Capripoxviruses – such as the goat-infecting goatpox virus and cattle-infecting lumpy skin disease virus – could help answer this.

While we did not discover any cases in our research, investigation of parchments from other regions, such as parts of southern Europe where goatskin was more commonly used, may prove informative.

There is also one outstanding mystery from our study. We found the sheeppox virus in many cattle and goat skin parchments. While cross-contamination during parchment preparation was possible in some cases, others potentially pointed to the sheeppox virus having infected animals it no longer does today.

So, our research suggests these early societies may have faced a quite different array of infectious diseases threatening their livelihoods, food security, and the welfare of their herds. As the sheeppox virus subsequently adapted to infect sheep more efficiently, it may also have become less effective at infecting other species.