Plasmablast Ig repertoire dynamics through repeat Plasmodium falciparum challenges reveal signatures of negative selection

Abstract To understand the development of immunity against malaria, a controlled human malaria challenge (CHMI) model was used to expose malaria-naïve individuals to the same P. falciparum (Pf) strain (NF54) four times over two years. Consistent with the gradual immunity observed naturally, the time to parasite detection increased significantly (delayed patency (DP)) by the 3rd CHMI. Plasmablast Ig repertoire maturation was tracked 7 days after peak parasitemia at each CHMI. Clone copy numbers and CDR3 counts for the major clones (CDR3 >200 or clone copy >20 000) increased significantly after exposure to Pf in all participants with DP and peaked at CHMI-2 in most DP. In contrast, the participants without DP had no significant increase in clone copy number or CDR3 count until CHMI-4. In these major clones, the ratio of replacement to silent mutations (R/S) declined from baseline through the 4 CHMIs and there was a significant decrease in R/S for the 12 Ig heavy chain variable genes associated with anti-Pf immunity in DP only. Phylogenetic analysis indicated that clones with longer tree lengths (more divergence) correlated with increasing negative selection (omega). These patterns suggest that a certain level of B cell activation is needed to reduce parasite replication and DP. However, there is a limit to the maturation of specific clones, possibly because most additional replacement mutations do not improve affinity and are selected against.