Mapping the Virological Consequences of 5500 years of Domestication and Shifting Breeding Practices in Horses and Donkeys

The emergence of animal domestication and farming practices during the last 10,000-years is thought to have enhanced humans' exposure to infectious diseases, but the consequences of these developments for the health of domesticated animals themselves have been largely overlooked.

Understanding the long-term effects of domestication and breeding practices on the epidemiology and evolution of animal pathogens is yet of foremost importance given current concerns regarding modern farming practices and their impact on animal and public health.

Recent major advances in sequencing and biomolecular techniques have allowed the recovery of rare and degraded DNA molecules from ancient biological samples, including those of pathogens which can persist in the remains of their hosts for millennia.

Here, we will leverage a massive collection of ancient equine DNA (aDNA) libraries spanning more than 50,000-years to investigate the past epidemiological and evolutionary dynamics of DNA viruses in horses and donkeys from the earliest stages of domestication to modern days.

An innovative approach will be implemented for the systematic enrichment of viral DNA in aDNA libraries prior to sequencing, to maximize viral detection sensitivity.

Metagenomic analyses of resulting datasets will allow characterizing ancient equine viromes and their variations through time.

Ancient viral sequences will be used for genomic and phylodynamic analyses to reconstruct past viral genomic changes, geographical spread and transmission dynamics.

Inferred patterns will be interpreted in the light of detailed knowledge about horse and donkey's domestication and management history which has been generated in recent years.

VIRODOM will provide major insights into the evolutionary history of important equine pathogens which remain understudied and contribute to the development of an integrative, One Health vision of infectious disease's history and evolution.