BCR Sequence Analyses

2,393 sequences were assigned Ig genes, out of 2,397 input sequences (99.83%). Gene assignment and other downstream analysis were performed with the Immcantation suite container version 4.1.0, which includes IMGT reference germlines downloaded on 2020-08-12, IgBLAST version 1.16.0, Change-O 1.0.0, Alakazam 1.0.2 and SHazaM 1.0.2. After gene assignment with IgBLAST, 126 unproductive sequences were removed. Data were processed to retain one heavy chain sequence and at most two light chain sequences per well. In wells with multiple heavy chain sequences, we retained the one with the highest cdr3_read_count, and required it to account for more than 50% of the total heavy chain cdr3_read_count in the well. In wells with more than two light chain sequences, we retained the two sequences with the highest cdr3_read_count, each accounting for more than 25% of the total light chain cdr3_read_count in the well, and together for more that 75% of the total light chain cdr3_read_count in the well. Sequences from wells presenting light chain only were removed from the analysis. One well was excluded for possible contamination (subject 2, well A07, Pfs230 Alhydrogel). A total of 1,345 sequences passed these filters (733 heavy, 612 light), and constitute the final set of sequences analyzed, with an average of 57 sequences per subject for the Alhydrogel group, and 60 sequences for the AS01 group. Most of the sequences (79.26%) from the heavy chain sequences correspond to VH:VL pairs (Supplementary Figure 4).