Fig. 4: Presence, distribution, and impact of genetic variation within diagnostic qPCR targets of Ascaris lumbricoides.

a Shown are the genomic coordinates of three repeats - repeat 1, 2, and 3 - highlighting primer and probe binding sites (solid rectangles) used in the qPCR diagnostic test, the position of genetic variants (x-axis) - either individual samples (black points) or mean across samples (pink points) - and their frequency within each country (y-axis). Putative qPCR-disruptive variants found at the 3’ end of the primer binding sites are depicted by dashed rectangles. b qPCR efficiencies were determined by generating standard curves of five serial dilutions (100 pg/μl to 10 fg/μl) on each of the repeats in the absence (wildtype; wt) or presence of the SNP (mutant; mut). The mean value of three replicates per concentration is shown. The 90-110% dashed lines show acceptable qPCR efficiency cutoffs. c The mean fold-loss was calculated to assess the effect of the SNP in qPCR quantitation and product loss due to late amplification. The mean fold loss of the mutant is relative to the wildtype repeat, within each assay. The mean normalised C_q difference was estimated from all serial dilutions. Country codes are as follows: BEN = Benin; ETH = Ethiopia; KEN = Kenya; MMR = Myanmar; MOZ = Mozambique; MYS = Malaysia; ZAF = South Africa. Source data are provided as a Source Data file.