Fig. 3: Fine-mapping the likely causal variants associated with day 28 post-prime anti-RBD antibody levels (normalized within immunoassay performed at MSD and PPD laboratories) in COV001 and COV002.

a,b, Stepwise conditional analyses using linear regression were performed in 1,023 individuals restricted by self-reported White ethnicity and PCA axes and with IBD values less than or equal to 0.185. The primary unconditional association analysis across the class II MHC region (a) and HLA-DQB1 locus (b) is shown in the top rows, with points shaped by variant type (AA, HLA allele (HLA), insertion–deletion (INDEL) or SNP) and colored by linkage disequilibrium (r²) with the index variant (rs9273817). The key variants of interest (rs9273817, rs1130456 and HLA-DQB1*06) are highlighted. The middle and bottom rows of a and b represent the same points after adjustment for rs9273817 (middle row) and also DRB1-71E/R (bottom row) using the same shape and color definitions as the first row. c, 1,076 individuals from COV001/COV002 grouped by carriage of either DQB1*06 or DRB1-71E/R in absence of the other demonstrate the most significant differences between groups tested using the two-sided Student’s t-test as shown by violin plots overlain by box plots. The box plot center line represents the median; the box limits represent the upper and lower quartiles; and the whiskers are the 1.5× IQR. ***P < 0.001. EUR, European.