Study design and analysis pipeline.

(A) Blood samples from all participants from 4 villages of the Upper River Region of The Gambia were collected up to 16 times over 2.5 years. The peak of clinical malaria cases occurs at the end and right after the rainy season. Made with Natural Earth. (B) Overall, 522 blood samples (307 fingerprick and 215 venous blood) were genotyped and/or whole genome sequenced, resulting in 425 high-quality barcodes and 199 high-quality genomes Additionally, 6 drug resistance markers were successfully genotyped and/or called from whole genomes, in a total of 438 isolates. (C) High-quality barcodes and genomes were sampled over 16 time points between December 2014 to May 2017.

High parasite recombinatorial diversity in 4 villages in The Gambia inferred from inter-individual genetic relatedness.

The genetic diversity of parasites was assessed from barcodes sampled between December 2014 and December 2016, keeping just one barcode per continuous infection, which resulted in 284 remaining barcodes. (A) Distribution of IBD values between barcodes (left panel), and with a cap at 500 pairs to highlight related barcodes at lower frequency (right panel). (B) Relatedness network of 284 isolates with barcodes represented as nodes and IBD values represented as edges. Barcodes are grouped into clusters using the compound spring embedder layout algorithm from Cytoscape (version 3.10.1).

Combined effects of spatial and temporal distances on parasite relatedness.

The proportions of related barcodes (IBD ≥ 0.5) between each pair of households are binned into time intervals of various lengths such that the number of observations in each bin is similar. Each box shows the 25-75% interquartile range of the percentage of related barcodes, with horizontal bar as the median. Groups of related barcodes were compared with Welch t-tests (*: p value < 0.05, ****: p value < 0.00005, ns: non-significant). (A) All pairs of isolates grouped together in the same time interval. (B) Pairs of isolates were grouped by their relative spatial distance.

Effect of seasonality on parasite recombinatorial genetic diversity.

(A) Proportion of related barcodes (IBD ≥ 0.5) between all sample collections from December 2014 to December 2016. (B) Proportion of similar barcodes between pairs of sample collections within the same season (‘within high’ and ‘within low’) and one season apart when the high transmission season precedes the low transmission season and conversely (respectively ‘transition high to low’ and ‘transition low to high’). Genetic similarities were compared between the ‘transition low to high’ group and all other groups with Welch t-tests (*: p value < 0.05, **: p value < 0.005).

Continuous P. falciparum infections with the same dominant genotype.

A total of 34 individuals were infected with highly related barcodes (IBD ≥ 0.9) at two or more time points. Individuals are ranked by their duration of continuous infection from the longest to the shortest, with a black line linking identical genotypes. For three individuals (ranked 25th, 26th and 28th), two different parasite strains were present concurrently, represented by curved lines. Unlinked P. falciparum positive tick marks indicate a different barcode (IBD < 0.9) or barcode not available.