Ancient pathogen genomics as an emerging tool for infectious disease research

Abstract

| Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA , enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review , we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.

Ancient RNA virus epidemics through the lens of recent adaptation in human genomes

“…When viruses impose a selective pressure on a host, adaptation happens in response at of knowledge of ancient viruses can be explained by the difficulty to recover ancient viral DNA 70 (Spyrou et al, 2019), and by the fact that many viruses have their genomes coded by RNA that 71 is known to degrade much faster than DNA. In light of the scarcity of molecular remains, how 72 can we identify the viruses that drove ancient epidemics during human evolution?…”

A 2,000-year-old specimen with intraerythrocyticBartonella quintana

“…This report introduces paleocytology as an innovative approach for the analysis of ancient dental pulp to study both host- and host-associated pathogens, complementing the study of ancient biomolecules 2,3,27,54 .…”

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

“…Over the coming years it is likely that high-resolution paleogenomics will shed light on human-mediated selection and the phenotypic changes in livestock that underpinned the "Secondary Products Revolution" in early agricultural societies [252]. Another major area of growth during the coming decade will be identifying and analyzing microbial pathogen genomes using archaeological material from domestic animals and wild congeners [253,254]. This approach will provide new information for infectious disease research in livestock and companion animals, particularly for diseases such as bovine tuberculosis caused by Mycobacterium bovis, which may have emerged as livestock population densities increased during the Neolithic period [255].…”