Extended Data Fig. 4: Longitudinal P. falciparum genotype analysis of participants who were infected at baseline and remained 18S qRT-PCR positive by study day 21.

Panels a-l show allelic diversity for 6 P. falciparum gene fragments determined via amplicon sequencing (AmpSeq) of DBS from 12 participants who had P. falciparum infection detected by 18S qRT-PCR at enrollment (when AL was administered) and who remained infected through at least study day 21 after CIS43LS/placebo administration (study day 0). Clearance of infection was defined as two consecutive negative 18S qRT-PCR results after enrollment. Associated 18S qRT-PCR and thick blood smear (TBS) records are presented at the top of each participant plot. Timepoints ascend left to right from enrollment (8–13 days before study day 0) through 24 weeks for most participants. Circles represent alleles detected by AmpSeq and are grouped according to the analyzed locus (boxes). Circles are ordered vertically within boxes according to timepoint of first detection (earliest at bottom). Matching circle colors represent repeated observations of the same allele, either longitudinally (that is, left to right, see also colored edges) or between participants. The simultaneous detection of multiple alleles within a single locus indicates a polyclonal infection state. A total of 147 unique alleles were observed across all loci for the 12-participant dataset.