The impact of infectious diseases on the immunogenetics of Indigenous South Americans after the arrival of Europeans
Epidemic and pandemic events can leave their footprint on the genomes of affected populations, as the frequency of genetic variants linked to susceptibility or resistance to the disease can shift in the surviving individuals. Such variants are often located within genes relevant for the immune system. Previous studies have shown such an effect in northern North American and Mesoamerican native populations, where significant changes in the frequency of alleles in the Major Histocompatibility Complex have been reported after the arrival of Europeans to the Americas. Here, we analyse Human Leukocyte Antigen (HLA) data from 24 ancient individuals (1420 to 1532 CE) buried within the Incan site of Machu Picchu, Peru. When compared with present-day populations from the Andean region, we detect shifts in both HLA class I and class II alleles, with class II alleles HLA-DRB1*08:02 and DRB1*09:01 significantly increasing in frequency in all present-day populations compared to Machu Picchu individuals. Using an in-silico tool, we tested the HLA diversity found in Machu Picchu against the full proteomes of two viruses known to have caused epidemics after the arrival of Europeans to the Americas. Our data are in line with these pathogens being involved in shaping the immunogenetic diversity of the survivors of post-contact epidemic events.