Plasmodium falciparum population structure in southwestern Africa: Initial genome wide sequence data from Angola

Angola, seventh in Africa both in area and in estimated number of malaria deaths in 2020,encompasses the southwestern-most edge of the distribution of Plasmodium falciparum in the continent. It is surrounded by distinct P. falciparum subpopulations, one in central Africa(Cameroon/Gabon) to the north, and another in south-central Africa (Democratic Republic of the Congo) to the northeast. Due to the lack of P. falciparum population genomics studies in Angola, it is unknown how genetically distinct its parasite population is from those of its neighbours, or whether molecular markers specific to the Angolan P. falciparum population(s) can be identified, to inform on parasite migration within and between countries. To address these knowledge gaps, we will generate and analyze whole-genome sequence (WGS) data for ~150 P. falciparum samples from children ≤ 5 years old, obtained from several Angolan provinces. Blood samples collected between 2006-2009, by fingerprick on filter paper, will be used. For each sample, DNA was extracted within one year ofcollection and stored at -20ºC. Initially, to determine if the DNA was still viable for genome-wide analysis, we used P. falciparum selective whole genome amplification on four samples. Genomic libraries were sequenced in an Illumina NovaSeq sequencer, to generate paired-end 150 bp-long reads, and average genome coverage >35X. The sequencing data was mapped against the canonical P. falciparum 3D7 reference genome, single nucleotide polymorphisms (SNPs) identified according tobest practices, and a principal component analysis was done using the recovered high confidence SNPcalls, together with SNP calls from ~400 publicly available P. falciparum samples from East, West and Central Africa. Preliminary results show that Angolan samples group with others from Central Africa,indicating that these decade-old samples have adequate quality for WGS studies. WGS data currently being generated for the remaining >100 samples will be used to identify Angola-specific molecular markers and to initiate a study of P. falciparum demography in southwestern Africa, with a focus in Angola.