Periodic Reporting for period 4 - CoDisEASe (Communicable Disease in the Age of Seafaring)
Período documentado: 2023-06-01 hasta 2024-11-30
The CoDisEASe (Communicable Disease Exchange in the Age of Seafaring) project aimed to explore various aspects of infectious disease transmission in historical populations through the study of ancient DNA. Molecular signatures of some pathogens can preserve in archaeological tissues, and scientific techniques have now matured to the point where these ancient pathogens can be studied at the genomic level. CoDisEASe aimed to draw upon novel developments in the retrieval of ancient molecules to study genetic changes in infectious diseases on a broad geographic and temporal scale that ventured thousands of years into our evolutionary past. This granted us an opportunity to investigate which diseases were endemic in different periods of human history, how they have changed over time, and how they have moved around the globe. Archaeological human remains from the American pre-colonial period featured prominently in the project, and yielded previously unknown details about population health in this broad period of human history. Infectious disease in Europe was also investigated in the Medieval and post-Medieval periods to reveal an unprecedented detail of disease experience, transmission, and ecology. Infectious diseases such as plague, syphilis, Hansen’s Disease (leprosy), malaria, and tuberculosis were explored throughout the project. This work was complemented by an analysis of human genes involved in immune function to better understand how disease burdens have influenced our genetic makeup over several millennia.
Archaeological human remains were obtained from many countries from the Americas (including Antigua and Barbuda, Argentina, Chile, Mexico, Peru) and Europe (including Belgium, Germany, Lithuania, Poland, Spain). The remains were processed by researchers employed by the grant. Through scientific diligence and ingenuity, the PI and her team determined that syphilis and the related diseases bejel and yaws had their roots in the Americas, and were introduced to Europe following trans-Atlantic sea voyages in the late 15th century (doi.org/10.1038/s41586-024-08515-5). We also demonstrated that yaws was circulating in northern Europe shortly after the first Columbian voyage, through its discovery in a genetic female from Lithuania in what may be the earliest European epidemic attributed to this type of disease (doi.org/10.1038/s41598-020-66012-x). These findings constitute the most substantial step to date toward resolving an intense and longstanding debate on the origin of these diseases, and establishing a timeframe for their global dispersal. Similar results were obtained for Hansen’s Disease, or leprosy. Prior to this research, many infectious disease experts agreed that Hansen’s Disease was introduced to the Americas in the colonial period. While this is true for the globally dominant form, research made possible through CoDisEASe identified what is currently a rare type that circulated in South America for thousands of years before any contacts with European populations (doi.org/10.1038/s41559-025-02771-y). Through further exploration of infectious disease in Medieval and post-Medieval Europe, this research also revealed important details about local transmission of plague (doi.org/10.1371/journal.ppat.1011404) and the movement of malaria within a unique context of military deployment in Europe (doi.org/10.1038/s41586-024-07546-2).
Research in pursuit of the goals of this grant were made possible through use of cutting-edge techniques for both the retrieval of degraded ancient molecules and computational methods for their identification. Ancient DNA work poses many challenges: over the years, DNA molecules degrade into small fragments that are chemically damaged, and the remaining trace amounts can be obscured when bacteria from the soil or the environment dominate in archaeological tissues. These factors make it difficult to distinguish environmental microbes from those that were present in the individual at the time of death. CoDisEASe made use of updated laboratory methods to access bacterial DNA that had preserved for hundreds or thousands of years in archaeological tissues, and aimed to identify the ancient pathogens represented amidst a complex microbial background through use of the most robust and up to date methods of detection. With this approach we were able to find and track infectious diseases on a scale never before possible: this culminated in research outputs that have redefined the evolutionary history of syphilis and Hansen’s disease (leprosy), as we succeeded in identifying pathogens that were not known to be present in a given time period or location. We also investigated evolution of human immune function with similar rigour using powerful laboratory techniques catered to the recovery of immune genes from archaeological human remains. Concurrent investigation of both hosts and pathogens in our past offers incredible potential for understanding how evolutionary forces have shaped us over a prolonged time period.