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Table 4 Overview of several SNP panels for barcoding P. falciparum and P. vivax infections

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

Marker panel Species Description Applications Genotyping platforms Countries implementing the panel Publication
1SpotMalaria 101 SNPs P. falciparum 101 SNPs including neutral variants, species-specific variants and drug-resistance markers in K13, pfcrt, pfdhfr, pfdhps, pfmdr1 and pfpm2/pfpm3 SNPs and copy number, Drug resistance prevalence, species confirmation, infection complexity, genetic relatedness Illumina amplicon sequencing Bangladesh, Cambodia, Ghana, Benin, Brazil, Cameroon, Colombia, Congo, Ethiopia, The Gambia, Guinea, India, Indonesia, Kenya, Laos, Malaysia, Mali, Myanmar, Peru, Senegal, Sudan, Tanzania, Thailand, Vietnam Unpublished
2WEHI 155 SNPs P. falciparum 155 SNPs all neutral variants, a subset are geographic markers Infection complexity, genetic relatedness, geographic region Fluidigm SNPType™
Assay
Papua New Guinea, Solomon Islands, Mali Unpublished
Broad Institute 24 SNPs P. falciparum 24 polymorphic, neutral variants Infection complexity, genetic relatedness High-resolution melt Ethiopia, Malawi, Nigeria, Panama, Senegal, Zambia, Zimbabwe [116]
3Swiss TPH 5 genes P. falciparum 5 gene regions: cpmp, cpp, ama1-D3, csp, msp7 High sensitivity assessment of infection complexity, longitudinal tracking Illumina amplicon sequencing Papua New Guinea, Cambodia [42]
4UCSF 100 microhaplotypes P. falciparum 100 globally diverse multi-allelic amplicons Infection complexity, genetic relatedness Illumina amplicon sequencing Mozambique [117]
Broad Institute 42 SNPs P. vivax 542 polymorphic, neutral variants, including region-specific variants for geographic assessment Infection complexity, genetic relatedness, geographic region High-resolution melt Brazil, French Guiana, Ethiopia, Sri Lanka (and countries below) [116]
1SpotMalaria 113 SNPs P. vivax 538 of 42 Broad SNPs, plus species-specific variants, drug-resistance markers in pvmdr1, pvdhfr, pvdhps Drug resistance prevalence, species confirmation, infection complexity, genetic relatedness, geographic region Illumina amplicon sequencing Afghanistan, Bangladesh, Bhutan, Cambodia, Colombia, Ethiopia, Indonesia, Iran, Mauritania, Malaysia, Myanmar, Republic of Korea, Sudan, Thailand, Vietnam Unpublished
2WEHI 148 SNPs P. vivax 148 SNPs, all neutral variants Infection complexity, genetic relatedness Illumina amplicon sequencing Papua New Guinea, Cambodia Unpublished
Menzies-Sanger 100 microhaplotypes P. vivax 100 globally diverse multi-allelic amplicons Infection complexity, genetic relatedness Illumina amplicon sequencing (Under development) Unpublished
  1. 1https://www.malariagen.net/projects/spotmalaria. 2Walter and Eliza Hall Institute of Medical Research. 3Swiss Tropical and Public Health Institute. 4University of California, San Francisco. 5Barcodes designed with intentional overlap to support data sharing between partners