An Ancient Coronavirus from Individuals in France, Circa 16th Century

Background: At a time when COVID-19 pandemic was responsible for more than six million deaths worldwide, the antiquity of coronaviruses remained undefined. We investigated individuals buried in 16th century in France, for the direct and paleo serological diagnosis of Coronavirus.Methods: The 2011-2012-excavation of the former abbey Saint-Pierre in Baume-les-Messieurs, northeastern France uncovered 12 skeletons ranging from the 13th-18th centuries and identified as men between 30-60 years old at the time of death. Dental pulps were recovered from the teeth of the 10 individuals and pooled by individuals. Total proteins extracted from dental pulps were incorporated for microbial paleoserology targeting the Coronavirus SARS-CoV-2, HCoV-229E and OC43 antigens and for Coronavirus peptide research using metaproteomics; in the presence of negative controls.Results: Three peptide sequences totaling 36 amino acids indicative of a Coronavirus were retrieved from dental pulp remains collected from two individuals buried circa 16th century, in whom paleoserology confirmed a specific immunological response against modern-day severe acute respiratory syndrome Coronavirus-2 and human Coronavirus 229E.Conclusions: These data most likely identified a betacoronavirus with no modern correspondent as infecting two individuals in the 16th century France; extending the antiquity of coronaviruses by more than three centuries. Historical, archaeozoological and paleoproteomic data suggested close contacts between these two individuals and domestic swine, cattle, and poultry, suggesting an ancient zoonotic coronavirus. Coronaviruses have been undesirable companions of populations long before the ongoing coronavirus disease 2019 outbreak emerged.