Ancient Human DNA Reveals Earliest Zoonotic Diseases Appeared 6,500 Years Ago

The COVID-19 pandemic was, at its heart, a serious reminder that our health can be significantly impacted by diseases from other animals. Obviously, this is not a new story; we’ve known for decades that emerging diseases often jump to humans from other species, but how long has this been going on for? According to the largest study to date on the history of infectious diseases, our ancestors’ early interactions with domesticated animals, alongside large-scale migration, likely began a new era of disease for our species.

Pathogens are an enduring and old problem for human health. They have literally been plaguing us throughout our evolutionary history, but many people take for granted their current resistance to many historical threats. Until around 1850, at least a quarter of all children died before the age of one, and another quarter died before turning 15. Although the causes of death were diverse at this time, it is estimated that at least half of all those deaths were due to infections, many of which we have vaccines for today.

Our interaction with diseases across our collective history has left lasting impressions on our genomes, as pressure from bacteria or viruses has consistently shaped our genetic variation. But despite their significance in the story of our species, we are still not clear when different pathogens first emerged and how or why they spread.

In order to address this gap, researchers at the University of Copenhagen and the University of Cambridge analyzed DNA from 1,300 prehistoric individuals found in archaeological sites across Eurasia, using samples extracted from the specimens’ teeth and bones. Some of the human remains were up to 37,000 years old.

The team recovered DNA from 214 known human pathogens, and used this to develop a kind of map of disease emergence across this time, including when zoonotic diseases – infections that are transmitted to humans from animals – first occurred.

The results indicate that a pivotal point in our relationship with disease occurred around 6,500 years ago. This was the point when humans became closer to domestic animals, while also seeing larger-scale migrations of pastoralists from the Pontic Steppe – a vast grassland region that extends from Eastern Europe to Western Asia – to northwestern Europe.

“We’ve long suspected that the transition to farming and animal husbandry opened the door to a new era of disease – now DNA shows us that it happened at least 6,500 years ago,” Professor Eske Willerslev, the study lead from the University of Copenhagen, explained in a statement.

“These infections didn’t just cause illness – they may have contributed to population collapse, migration, and genetic adaptation.”

The study also identified the earliest known genetic trace of the plague bacterium, Yersinia pestis, in a 5,500-year-old sample. This is the same bacterium that wreaked havoc on medieval populations across Europe and is thought to have killed between one-quarter and one-half of the population of that time.

The team also found traces of other diseases we know today, including: malaria (caused by Plasmodium species), which appeared around 4,200 years ago; leprosy (Mycobacterium leprae) from 1,400 years ago; hepatitis B virus, appearing 9,800 years ago; and diphtheria (Corynebacterium diphtheriae), emerging around 11,100 years ago.

Aside from giving us a better understanding of when diseases first emerged, the results may also help us understand how they do so and how they mutate, while also aiding in the development of future vaccines.

“If we understand what happened in the past, it can help us prepare for the future, where many of the newly emerging infectious diseases are predicted to originate from animals,” said Associate Professor Martin Sikora, the study’s first author.

“Mutations that were successful in the past are likely to reappear. This knowledge is important for future vaccines, as it allows us to test whether current vaccines provide sufficient coverage or whether new ones need to be developed due to mutations,” added Willerslev.

The study is published in Nature.