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Table 2 Molecular methods to identify and map the geographic origin of malaria infections

From: Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia–Pacific region

Markers Species Platforma Assays Comments Publications
Variable surface antigens: pvcsp and pvmsp1 P. vivax Capillary sequencing Primers available to amplify the gene regions Diversity may reflect selection from the host immune system, rather than geographic ancestry. Lower resolution than genome-wide SNP barcodes [105,106,107]
Microsatellites P. vivax Capillary sequencing Primers available to amplify the gene regions of a 9-marker set used by the APMEN vivax Working Group Microsatellites are often neutral but have high mutation rates constraining geographic ancestry. A single marker (MS20) appears to discriminate temperate from tropical P. vivax infections. Lower resolution than genome-wide SNP barcodes [108, 109]
Mitochondrial genes P. falciparum and P. vivax Capillary sequencing Primers available to amplify the gene regions Mitochondrial genome is historically conserved and robust to recombination. Extensive reference datasets available from across the globe in GenBank. Lower resolution than genome-wide SNP barcodes [110,111,112,113]
23-SNP mitochondrial and apicoplast barcode P. falciparum Targeted SNP genotyping In silico only (no assays developed to date) Mitochondrial and apicoplast genomes are historically conserved and robust to recombination. Addition of the apicoplast genome provides more variants, increasing resolution. Robust regional-level resolution [114]
42-SNP genome-wide barcode P. vivax Targeted SNP genotyping Real-time PCR high-resolution melt (HRM) assays. Amplicon sequencing Illumina assays Less robust to effects of recombination over time than mitochondria and apicoplast. Robust regional-level resolution [115]
28-SNP, 50-SNP and 51-SNP genome-wide barcodes P. vivax Targeted SNP genotyping In silico at present but Illumina amplicon sequencing and minION assays in development Less robust to effects of recombination over time than mitochondria and apicoplast. Robust country-level resolution in many areas. Online data analysis tool available, amenable to missing data and polyclonal infections: vivaxGEN-GEO (https://geo.vivaxgen.org/) [68]
  1. aSee Table 3 for comparative assessments of different genotyping approaches