Human leukocyte antigen susceptibility map for SARS-CoV-2

Austin Nguyen; Julianne K David; Sean K Maden; Mary A Wood; Benjamin R Weeder; Abhinav Nellore; Reid F Thompson

Global HLA allele and haplotype frequencies HLA-A, -B, and -C allele and haplotype frequency data were obtained from the Allele Frequency Net Database (52) for 805 distinct populations pertaining to 101 different countries and 2628 distinct major/minor (4-digit) alleles, corresponding to 20,478 distinct haplotypes (https://github.com/pdxgx/covid19). We also identified full HLA genotype data for 3,382 individuals whose HLA types were confined to the 145 HLA alleles studied herein. Population allele and haplotype frequency data were aggregated by country as a mean of all constituent population allele or haplotype frequencies weighted by sample size of the population, but not accounting for representative ethnic demographic size of the population. Global allele frequency maps were generated using the rworldmap v1.3-6 package (78) , with total global allele and haplotype frequency estimates calculated as the mean of per-country allele and haplotype frequencies, weighted by each country's population in 2005.