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

Noviyanti, Rintis; Miotto, Olivo; Barry, Alyssa; Marfurt, Jutta; Siegel, Sasha; Thuy-Nhien, Nguyen; Quang, Huynh Hong; Anggraeni, Nancy Dian; Laihad, Ferdinand; Liu, Yaobao; Sumiwi, Maria Endang; Trimarsanto, Hidayat; Coutrier, Farah; Fadila, Nadia; Ghanchi, Najia; Johora, Fatema Tuj; Puspitasari, Agatha Mia; Tavul, Livingstone; Trianty, Leily; Utami, Retno Ayu Setya; Wang, Duoquan; Wangchuck, Kesang; Price, Ric N.; Auburn, Sarah

doi:10.1186/s12936-020-03330-5

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Guinea, India, Indonesia, Kenya, Laos, Malaysia, Mali, Myanmar, Peru, Senegal, Sudan, Tanzania, Thailand, Vietnam	Unpublished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complexity, genetic relatedness, geographic region	Fluidigm SNPType™ Assay	Papua New Guinea, Solomon Islands, Mali	Unpublished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

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

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