A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains

Abstract

Malaria is a major public health problem that is actively being addressed in a global eradication campaign. Increased population mobility through international air travel has elevated the risk of re-introducing parasites to elimination areas and dispersing drug-resistant parasites to new regions. A simple genetic marker that quickly and accurately identifies the geographic origin of infections would be a valuable public health tool for locating the source of imported outbreaks. Here we analyse the mitochondrion and apicoplast genomes of 711 Plasmodium falciparum isolates from 14 countries, and find evidence that they are non-recombining and co-inherited. The high degree of linkage produces a panel of relatively few single-nucleotide polymorphisms (SNPs) that is geographically informative. We design a 23-SNP barcode that is highly predictive (~92%) and easily adapted to aid case management in the field and survey parasite migration worldwide.

Figure 1. Plasmodium falciparum mitochondrion and apicoplast genomes.

The nucleotide sequence landscape of the densely packed P. falciparum mitochondrion (mt) and apicoplast (apico) genomes. Protein-coding (green) and non-translated RNA (blue) regions in the ‘annotation’ ring are transcribed from either strand (inner, negative strand; outer, positive strand). The 20-fold difference in coverage between the genomes is visible (see also Supplementary Fig. 1). All mutations within mt (151 SNPs, 5,967-bp linear) and apico core (488 SNPs, 29,430-bp circular, excluding an inverted repeat) are shown relative to the P. falciparum 3D7 (version 3.0) reference genome coordinates. SNPs are densely packed throughout, with more non-synonymous (NS) protein-coding changes (red) in apico than in mt. Synonymous, intronic, intra-genic (green) and RNA changes (blue) are also marked. The minor allele frequency (MAF), Fst and barcode SNPs are marked in the outer three rings and are colour coded in the same way (the full catalogue is available online). The 23 barcoding SNPs (5 mt, 4 NS; 18 apico, 9 NS) are marked in the outer ring.

Figure 2. SNP barcode across P. falciparum mitochondrion and apicoplast genomes.

The 23 SNP loci form 34 distinct haplotypes that help identify a parasite’s geographical origin: South America, SAM; West Africa, WAF; East Africa, EAF; Southeast Asia, SEA; and Oceania, OCE. Most (76.5%, 26/34) haplotypes are unique to a single region. Haplotype 10 corresponds to the 3D7 reference strain, and its mitochondrion (mt) core haplotype is observed in all five regions. Two haplotypes (14 and 30) are seen in three regions. The overall accuracy is 92.1% (655/711; SAM 100%, WAF 94.5%, EAF 68.4%, SEA 98.8% and OCE 96.0%).