Investigating the genetic and ancestral diversity of an immune response locus

Abstract

Neanderthal introgression is known to affect a variety of traits of modern humans, including immune response. Specifically, genes involved in defense against RNA viruses have been shown to be enriched in Neanderthal ancestry. However, less is known about the impact of archaic admixture on response to DNA viruses. In this study we investigate the genetic and ancestral diversity of a locus linked to increased measurements of viral load in blood of Epstein-Barr virus. To do this we utilized genomic data from present-day populations, an archaic introgression map and genome-wide association summary statistics for EBV load in blood. We identified a Neanderthal-like haplotype which carried the highest number of increase-associated alleles. However, several haplotypes of predominantly African ancestry also carried a small proportion of increase-associated alleles. We found that the local lead SNP segregates in both the Neanderthal haplotype and in one African haplotype. These findings suggest that Neanderthal introgression is likely not the sole contributor to the virus association signal and that there is notable genetic diversity possibly linked to the GWAS signature at this locus in African populations as well.