For EBV infection, we and others have previously confirmed the presence of variants in the HLA Class II region driving associations for EBV EBNA-1 antibody response in different populations11–14; here we replicated these findings in HLA-DQA1 (rs9272371, p = 3.63 × 10−44) (Fig. 5a) and identified an additional distinct variant (rs3129867, pcond = 2.78 × 10−11) in HLA-DRA (Fig. 5b) contributing to IgG levels in Uganda that was not identified as distinct in our initial pilot study11. Here, HLA-DQA1 is linked to Epstein-Barr virus infection.