Real-time characterisation of pathogen evolution and the effect of post-contact epidemics on the native population of Mexico through ancient DNA

Understanding the molecular processes behind the initial contact between pathogens and immunologically-naive populations in major pandemics is crucial when developing strategies to face the potential devastating effects of reintroduction of a pathogen. Ancient DNA (aDNA) studies have revealed the causes of major historical epidemics and the genetic makeup of some ancient pathogens. aDNA can jointly characterise the genetic makeup of pathogens and hosts at the time of first contact. This is of particular interest in places such as Mexico, where a large fraction of the genetic variation in the native population was lost as a consequence of major outbreaks caused by pathogens introduced during colonisation by Europeans.

We will use aDNA to investigate the genetic interactions between host and pathogen in the native population and the pathogens zintroduced during the Spanish colonisation of Mexico. We will generate more than 20 ancient genomes from a pre-Hispanic skeleton collection in Mexico City and a collection of skeletons of people who died from the epidemic after Spanish colonisation. Pathogen DNA will also be retrieved and sequenced.

We will use the collections to identify variants that influence susceptibility to infection and the pathogenicity of ancient pathogens to determine the amount of genetic variation lost as a consequence of epidemics cause by pathogens introduced during colonisation.