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 | |
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 | |
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 | |
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] |