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SpotMalaria

Started 2015

Parasite
 

Introduction

SpotMalaria harnesses genomic technologies to monitor the global evolution of malaria parasites, delivering knowledge that will increase the efficiency of malaria elimination and eradication efforts.

Objectives & Coordination

Malaria control and elimination programmes often face practical obstacles that can be tackled more effectively with information about the parasite population.

Novel laboratory methods and analytical tools make it possible to rapidly sequence and genotype Plasmodium genomes from dried blood spots (DBS) collected from malaria patients – allowing for more comprehensive coverage in malaria endemic areas.

SpotMalaria connects local and national partners creating a sampling and reporting network for collecting large numbers of dried blood spots and uses a simple standardised operating procedure (SOP) that is easy to implement in the field.

Our main goal is to provide partners with actionable information to support malaria control interventions. We use state-of-the-art genetic and genomic technologies to rapidly genotype Plasmodium falciparum samples isolated from the finger-prick blood samples.

Our SpotMalaria partners receive a Genetic Report Card for each sample that they contribute, showing whether the parasites carry mutations that make them resistant to antimalarial drugs such as artemisinin or its ACT partner drugs. This allows our partners to rapidly detect changes in drug efficacy and to respond to these changes.

Currently, we report on genetic variations that are relevant to resistance to several antimalarial drugs:

  • artemisinin (kelch13, arps10, mdr2, fd, crt genes)
  • piperaquine (plasmepsin2-3, exo)
  • chloroquine, amodiaquine, mefloquine (crt, mdr1)
  • sulfadoxine, pyrimethamine (dhfr, dhps)

In addition, we report on other genetic variations relevant to parasite epidemiology:

  • Detection of additional species of Plasmodium in a P. falciparum infection, such as P. vivax, P. knowlesi, P. malariae, P. ovale
  • Genetic barcodes (101 high-diversity SNPs across the genomes), used to estimate complexity of infection (COI), identify expanding strains and the geographic origins of samples.

We use a set of highly informative single nucleotide polymorphisms (SNPs) to “barcode” parasites, from which we can estimate complexity of infection. We are also able to determine if an infection comprises additional species of Plasmodium, such as P. vivax, P. malariae, P. ovale, and P. knowlesi.

The next project phase will focus on developing easy to use tools that incorporate genetic report card data in the context of the ever-growing database of genotyped malaria parasites. We are also working on methods that allow expansion of genotyping to global partner sites to speed up genotyping time. Additionally, we are working on genotyping methods for typing a similar set of informative loci in P. vivax dried blood spot samples.

Our partners

In the early phases two networks of scientists, clinicians and public health teams have helped refine SpotMalaria. We have expanded our scope and while still working closely with these networks, we now have partners and collaborations from 24 different countries in Asia, Africa, and South America.

GenRe-Mekong

GenRe Mekong logoGenRe-Mekong is funded by the Bill & Melinda Gates Foundation to support malaria elimination efforts in the Greater Mekong Subregion, which straddles regions of Cambodia, Vietnam, Laos, Thailand, and South China. The GenRe-Mekong project aims to supply strategically important information from genetic data to national control programmes and other elimination projects, in the most easily implementable, timely, comprehensive and cost-effective manner possible.

Pathogens genomic Diversity Network Africa (PDNA)

The prospect of malaria elimination in Africa presents unique challenges. Malaria is more common and acquired immunity can mean that drug pressure is lower, in addition to the non-biological factors, for example social and political factors, that can affect transmission dynamics. While drug resistance is a large problem, there is also a need to determine how parasite genetics both influence and are influenced by these differences across African populations. To answer these questions, we’re partnering with researchers from the PDNA to establish important baseline genetic data across as many populations as possible.

Ghansah et al. Monitoring parasite diversity for malaria elimination in sub-Saharan Africa. Science, 2014; 345(6202): 1297-8. DOI: 10.1126/science.1259423.

Read more about the PDNA.

Sampling locations

Bangladesh, Benin, Brazil, Cambodia, Cameroon, Colombia, Congo, Ethiopia, The Gambia, Ghana, Guinea, India, Indonesia, Kenya, Laos, Malaysia, Mali, Myanmar, Peru, Senegal, Sudan, Tanzania, Thailand, Vietnam.

For partners

Resources for partners working on parasites

Acknowledgements

For partners that have publications using data produced by the project we ask that the following statement is included in the acknowledgements.

This publication uses data from the MalariaGEN SpotMalaria project as described in ‘Jacob CG et al.; Genetic surveillance in the Greater Mekong Subregion and South Asia to support malaria control and elimination; eLife 2021;10:e62997 DOI: 10.7554/eLife.62997‘. The project is coordinated by the MalariaGEN Resource Centre with funding from Wellcome (206194, 090770). The authors would like to thank the staff of Wellcome Sanger Institute Sample Management, Genotyping, Sequencing and Informatics teams for their contribution.

Partner studies

23 Feb 2022 1132 Using whole genome sequence data to analyse the spatio-temporal genetic diversity of malaria parasites in Kilifi, Kenya

Partner study description Effective control and final elimination of malaria in the face of declining transmission and increasing spatial heterogeneity of disease and infection will require the identification and targeting of hotspots or…

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8 Jan 2020 1141 Genomic characterization of Plasmodium falciparum from asymptomatic infections in The Gambia

Partner study description The dry season in The Gambia presents a bottleneck for the total parasite population as there is little or no malaria transmission. Some individuals maintain a malaria infection through this…

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22 Jun 2021 1162 Genomic variation and antimalarial resistance evolution in The Gambia

In terms of malaria prevalence, The Gambia can be divided into two strata: low prevalence in the western part and relatively high prevalence in the eastern part. Nevertheless, within these two strata, prevalence…

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22 Jun 2021 1164 Plasmodium falciparum clearance times in Malian villages following artesunate monotherapy

A multicentre study to evaluate the in vivo, in vitro and molecular efficacy of artesunate in monotherapy for the uncomplicated malaria treatment is currently running in two study sites in Mali; Bougoula-hameau, at…

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22 Jun 2021 1168 Genomic surveillance of Plasmodium falciparum in the Kassena-Nankana Districts, Ghana

In the Kassena-Nankana Districts (KNDs) malaria is highly endemic with marked seasonal variation in transmission intensity. The high transmission season coincides with the rainy season, which is from July to October and low…

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25 May 2021 1180 Tracking Artemisinin Resistance Collaboration (TRAC II) with SpotMalaria

A multi-centre, open-label randomized trial to assess the efficacy, safety and tolerability of Triple Artemisinin-based Combination Therapies (TACTs) compared to Artemisinin-based Combination Therapies (ACTs) in uncomplicated falciparum malaria and to map the geographical…

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22 Jun 2021 1182 Understanding the determinants of malaria heterogeneity and the spatial and temporal spread of malaria in The Gambia

In terms of malaria prevalence, The Gambia can be divided into two strata: low prevalence in the western part and relatively high prevalence in the eastern part. Nevertheless, within these two strata, prevalence…

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23 Feb 2022 1183 Alternative mechanisms for erythrocyte invasion by Plasmodium falciparum

Partner study description This study looks at samples collected from two sites in Ghana. The first is Lekma Hospital, Teshie, Accra; near the coast, an eastern suburb of Accra. Malaria transmission in Teshie…

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23 Feb 2022 1195 Tracking Artemisinin Resistance Collaboration (TRAC II)

Partner study description A multi-centre, open-label randomized trial to assess the efficacy, safety and tolerability of Triple Artemisinin-based Combination Therapies (TACTs) compared to Artemisinin-based Combination Therapies (ACTs) in uncomplicated falciparum malaria and to…

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23 Feb 2022 1197 Multidisciplinary research for malaria control and prevention in Mali

Partner study description This study looked at different field sites in Mali representing three different major eco-zones across West Africa that are different with regard to endemicity and current implementation of control strategies:…

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22 Jun 2021 1198 Malaria Elimination Task Force

The objectives of this programme were to scale-up the targeted mass drug administration strategy regionally, and measure its effect on the incidence of clinical malaria in eastern Karen/Kayin state, Myanmar, a difficult-to-access hilly…

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23 Feb 2022 1200 Genomic surveillance of Plasmodium falciparum in the Ashanti region of Ghana

Partner study description This study collected Plasmodium falciparum samples in the Ashanti region of Ghana for genomic sequencing.

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26 May 2021 1208 Genetic epidemiology of Plasmodium falciparum malaria and associated antimalarial drug resistance in Lao PDR

Genetic surveillance project conducted by the National Malaria Control Programme in partnership with GenRe-Mekong in endemic region of the Lao PDR. This is part of a large project of genetic surveillance of malaria…

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26 May 2021 1209 Genetic epidemiology of Plasmodium falciparum malaria and associated antimalarial drug resistance in Central Vietnam

Genetic surveillance project conducted by the National Malaria Control Programme in partnership with GenRe-Mekong in endemic region of Vietnam. This is part of a large project of genetic surveillance of malaria in the…

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25 May 2021 1210 Epidemiology of malaria in northeast Thailand: a case-control study

This study aimed to determine risk factors for catching malaria in northeast Thailand, including travel, to identify where people were likely being infected and determine how much antimalarial drug resistance there is.

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22 Jun 2021 1224 Identification of molecular mechanisms of ACT treatment failure in Vietnam

This study is a country-wide retrospective analysis of molecular markers with potential impact on resistance before and after ACT introduction (18-year period).

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1 Jun 2023 1226 Molecular characterization of drug resistance in Plasmodium falciparum

Partner study description A prospective study designed to identify molecular markers of antimalarial drug resistance in Plasmodium falciparum in Yola, Nigeria. Objectives of the study are: To detect clinically significant genes associated with…

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28 Nov 2022 1227 Plasmodium falciparum surveillance in Peru, Colombia and Honduras

This study and the adjoined Plasmodium vivax study 1250 collectively form a project aimed towards providing genetic and clinical data of circulating P. falciparum and P. vivax populations in different endemic regions in…

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25 May 2021 1238 Research on malaria molecular and genomic epidemiology in all drug-resistance regions of Vietnam: case-control research on the risk factors

Genetic surveillance project conducted by the National Malaria Control Programme in partnership with GenRe-Mekong in endemic regions of Vietnam. The study aimed to determine risk factors for catching malaria in high endemic areas…

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25 May 2021 1239 Targeted Malaria Elimination in Chey Saen District, Preah Vihear Province, Cambodia

Given the emergence of Plasmodium falciparum (Pf) artemisinin resistance Médecins sans Frontières launched in May 2014 a research programme in Chey Saen district (Cambodia), aimed at preventing its spread. The activities of passive…

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22 Jun 2021 1241 Viability and pathogenicity of Plasmodium spp in infected blood donor units and immunological and genetic markers associated with malaria infections

The main aim of the study shall be to determine the viability and the pathogenicity of Plasmodium falciparum in donor blood units during storage under standard conditions (2-8ᵒC). Specifically, the study has been…

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20 Apr 2022 1247 Surveillance of antimalarial drug resistance related genes in Plasmodium falciparum in Sudan

Partner study description This is a cross sectional and screening study to determine the prevalence of drug resistant alleles in Sudanese Plasmodium falciparum field isolates which has been collected from different areas in…

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28 Nov 2022 1250 Plasmodium vivax surveillance in Peru, Colombia and Honduras

This study and the adjoined Plasmodium falciparum study 1227 collectively form a project aimed towards providing genetic and clinical data of circulating P. falciparum and P. vivax populations in different endemic regions in…

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8 Sep 2022 1262 Randomized trial to assess the safety, tolerability and efficacy of arterolane-piperaquine, arterolane-piperaquine+mefloquine and artemether-lumefantrine

Partner study description Randomized trial to assess the safety, tolerability and efficacy of arterolane-piperaquine, arterolane-piperaquine+mefloquine and artemether-lumefantrine. Number of subjects 219. We obtain parasite clearance half lives and travel surveys.

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18 Aug 2022 1263 Genotyping of Antimalarial Resistance Markers from Dried Blood Spot

Resistance of Plasmodium species to previous generations of medicines, such as chloroquine and sulfadoxine-pyrimethamine (SP), influenced the replacement of chloroquine (CQ) with sulfadoxine-pyrimethamine (SP) then artemisinin-based combination therapy (ACT) for treatment of malaria…

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31 May 2023 1268 Pan-African Malaria Genetic Epidemiology Network (PAMGEN) Plasmodium falciparum samples

Partner study description The Plasmodium falciparum samples due to be collected from seven countries (The Gambia, Ghana, Mali, Cameroon, Ethiopia, Tanzania and Madagascar) will contribute to the Pan-African Malaria Genetic Epidemiology Network (PAMGEN)…

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31 May 2023 1269 Pan-African Malaria Genetic Epidemiology Network (PAMGEN) Plasmodium vivax samples

Partner study description The Plasmodium vivax samples due to be collected from Ethiopia and Madagascar will contribute to the Pan-African Malaria Genetic Epidemiology Network (PAMGEN) project. The aim of PAMGEN is to create…

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21 Jun 2022 1283 Malaria Drug Resistance Molecular Markers of Plasmodium falciparum in Sudan

Malaria remains a major public health problem in Sudan and worldwide. One of the major problems hindering the efforts to combat malaria is the emergence of drug resistant parasites and the subsequent treatment…

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28 Nov 2022 1291 MIRANDA study

The main objective of this study is to demonstrate that pregnant women attending Antenatal Care (ANC) clinics in the DRC are a suitable, pragmatic sentinel population for the genetic surveillance of antimalarial drug…

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21 Sep 2022 1294 Investigation of Host and Parasite Genetic Factors Mediating asymptomatic Plasmodium falciparum infections

Partner study description As part of his PhD project, Collins Morang’a collected asymptomatic and symptomatic individuals during the dry and wet season from Navrongo, respectively. Navrongo is a region of high malaria transmission…

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16 May 2023 1306 Genetic diversity of Malaria parasites in Nigeria

Partner study description This proposal has been developed in response to recently published pilot data showing mutations in genes associated with resistance to artemisinins. The overall objective is to characterise genomic variation inPlasmodium…

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Publications

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