Fig. 1: Illustrative sampling schemes for individuals in the incident and chronic cohorts.

Tick marks represent days and weeks, and sampling/screening time points are shown as circles. Positive (+) and negative (–) symbols inside circles indicate parasite status, as determined by the indicated assays. A In the incident infection cohort individuals were screened to confirm parasite negativity by microscopy, presumptively treated for sub-patent infection (light pink circle), and screened 3 weeks later with qualitative nested polymerase chain reaction-based on detection of Plasmodium specific 18s ribosomal DNA (nPCR) (black circle) to confirm the absence of sub-patent infection. They were then screened weekly with nPCR (white circles) until the onset of an infection. Intensive follow-up (grey circles) proceeded every day for 1 week, and weekly until day 35 after parasite detection. Study participants were closely monitored for the development of malaria symptoms. Participants were treated with artemether-lumefantrine upon the detection of symptoms or 35 days after initial detection of infection: whichever came first. B Individuals in the chronic infection cohort were screened monthly with nPCR to confirm chronic infection (blue circles), defined as two sequential visits with confirmed parasitaemia without any symptoms of malaria disease. Intensive follow-up proceeding from confirmation of chronic infection (grey circles) was as for incident infections. Participants were treated with artemether-lumefantrine upon the detection of symptoms or at day 35 of follow-up: whichever came first. Mosquito feeding (indicated with mosquito symbols) was conducted in both cohorts at the onset of intensive sampling (day 0) and at day 14 and 35 in the absence of symptoms. Mosquito feeding assays were additionally conducted on the day of symptom detection.