Fig. 1: CSP-reactive lineages from blood PBs following the third dose of RTS,S.

a,b, IgG lineages for each vaccinee (bars, n = 45) that are clonally expanded (that is, have two or more distinct nucleotide clones; green), that consist of two or more identical nucleotide clones (gray) or that contain only one observed PB (blue) are shown by either number of lineages (a) or number of PBs per vaccinee (b). c, By vaccinee (n = 45), the size of each expanded lineage was calculated by dividing the number of PBs in that lineage (2–84 PBs per lineage) by the number in each vaccinee’s P3D-expanded lineage repertoire (37–492 PBs per vaccinee) and then assigning a rank-size. Boxes indicate interquartile ranges, lines within boxes are medians and whiskers represent minimum and maximum across vaccinees for each rank-size (44–1,246 PBs per rank, 22–301 lineages per rank). Dotted line indicates that the top four rank-size lineages contain 33% of PBs in all P3D-expanded lineages (n = 11,478 PBs, 2,662 lineages). d–e, ELISA reactivity, SHM levels and vaccinee protection status of mAbs from expanded lineages (n = 349). d, Number of nucleotide mutations from germline (SHM) for mAbs that are not reactive (dark blue, n = 185), show an indeterminant, weak signal (orange, n = 29) or are reactive (light green, n = 135) in a CSP ELISA. Domain specificity for CSP-reactive mAbs is shown in the box with a dashed green outline. Monoclonal antibodies reactive by ELISA to the NANP6 repeat-region peptide (dark green, n = 98), to the C-terminal region peptide (Pfs16, royal blue, n = 20) or not reactive in either peptide ELISA (gray, n = 9). Lines represent median values, ***P < 0.0001, **P < 0.001, unpaired two-tailed Mann–Whitney test. CSP-reactive mAbs that were not tested in peptide ELISAs (n = 8) are not shown. e, Percentage of tested antibodies from expanded lineages that originated from protected (green, n = 36) and unprotected (blue, n = 9) vaccinees that are CSP-reactive (82 out of 249, and 53 out of 100 mAbs, respectively), repeat-region NANP6 peptide-reactive (59 out of 244, and 39 out of 97 mAbs, respectively) and the subset from only dominant rank-size one to four lineages that are CSP-reactive (52 out of 142, and 31 out of 46 mAbs, respectively); **P < 0.001, *P < 0.01, two-tailed Fisher’s exact test. f, For each vaccinee (x axis), each symbol indicates a single lineage. The lineages (n = 369) from which a clone was selected for testing are indicated by CSP reactivity: CSP-reactive (green dots, n = 139), indeterminant (orange dots, n = 29) or not reactive (royal blue triangles, n = 201). All lineages that were not tested are shown (gray circles, n = 13,134; 2,313 expanded and 10,821 single-PB lineages). Protected vaccinees have a lower ratio of CSP-reactive versus nonreactive lineages than unprotected vaccinees (bootstrap analysis, P = 0.0011). Red circles indicate the two lineages containing the amino acid sequence of AB-000317.