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GenRe-Mekong

Started 2016

Parasite
 

Introduction

GenRe-Mekong (Genetic Reconnaissance of Malaria in the Greater Mekong Subregion) is a genetic surveillance project, aiming to provide National Malaria Control Programmes (NMCPs) in the Greater Mekong Subregion and other public health stakeholders with timely and actionable knowledge to support their decision-making in activities relevant to malaria elimination efforts.

Objectives & Coordination

In the Greater Mekong Subregion (GMS, comprising Cambodia, Vietnam, Laos, Thailand, Myanmar and parts of China), National Malaria Control Programs (NMCPs) are called upon to take difficult policy decisions in the face of a rapidly changing epidemiological landscape. These decisions include: assessing treatment efficacy, reviewing frontline drug policies, assessing the effectiveness of targeted interventions, identifying transmission hubs to target, and monitoring imported cases. To support their decision-making, NMCPs make use of clinical and epidemiological data, as well as results of therapeutic efficacy studies. GenRe-Mekong adds to this evidence base by providing comprehensive genetic information about the parasite populations.

GenRe-Mekong analyzes small dried blood spots samples, collected using a simple standardised operating procedure that is easy to implement at public health sites, even in resource-constrained endemic regions. Samples are processed by the SpotMalaria genotyping platform, which leverages on leading-edge high-throughput technologies to extract large amounts of parasite genetic information from each sample. The results are captured in Genetic Report Cards (GRCs), datasets regularly delivered to NMCPs to keep them abreast of rapid epidemiological changes. The underlying technological platform is designed to keep sample processing costs low, enabling large-scale genetic epidemiology survey with dense geographical coverage and large sample sizes.

The most urgent problem faced by NMCPs in the GMS is the rapid emergence and spread of strains resistance to antimalarial drugs. Accordingly, GenRe-Mekong has focussed in its first phase on use cases relevant to drug resistance, by genotyping variants known to be associated with resistance to several antimalarials. To facilitate integration into NMCP decision-making workflows, our analysis pipelines translate genotypes associated with drug resistance into phenotype predictions, producing maps which can be more easily interpreted by public health officials.

GenRe-Mekong protects individual patient privacy, but encourages aggregation and sharing of standardized data across national borders, to answer regional questions about epidemiology, gene flow and parasite evolution. To maximize benefits to the research community, GenRe-Mekong also conducts whole-genome sequencing of selected high-quality samples, which are contributed to the MalariaGEN Plasmodium falciparum Community Project to support high-resolution genetic epidemiology analyses of population structure, gene flow and association with phenotypes.

For in-depth details of the project, please refer to the preprint of the first GenRe-Mekong publication.

Genetic Report Cards

We use ‘Genetic Report Cards‘ to provide information on genetic variation relevant to drug resistance for each sample. 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 genome), used to estimate complexity of infection (COI), identify expanding strains and reconstruct the geographic origins of samples.

GenRe-Mekong is funded by the Bill & Melinda Gates Foundation.

Sampling locations

Bangladesh, Cambodia, India, Laos, Myanmar, Thailand, Vietnam.

Data

We routinely release genotype data to our partner studies; in addition, we periodically release public access datasets. This is the first public release of the GenRe-Mekong v1.0 data set and samples from this collection contribute to the P. falciparum community project data release

Current

26 Jan 2021 GenRe-Mekong v1.0
Species: P. falciparum

Genotype data for 9,623 samples from 8 countries

Open access

For partners

The DBS collection protocol for GenRe-Mekong is available in parasite partner study resources.

Additionally, video guides specific to GenRe-Mekong sample collection are available with subtitles in English.

Partner studies

To date, GenRe-Mekong has worked with NMCPs in seven countries (Lao PDR, Vietnam, Cambodia, Myanmar, Thailand India and Bangladesh), and supported large-scale multisite research and elimination projects across the region.

21 Nov 2015 1125 Investigating artemisinin resistance emergence on Thai-Burmese border

Partner study description Plasmodium falciparum resistance to artemisinin derivatives emerged on the Thai Myanmar border between 2000 and 2010. The Shoklo Malaria Research Unit (SMRU) has collected phenotypic data on more than 3,000…

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26 May 2021 1148 Assessing the contribution of migration to the emergence and spread of antimalarial drug resistance in Southeast Bangladesh

This study measured population movement by travel surveys and mobile phone call record data and combined these with parasite genotype data and malaria incidence to examine the role of population movement on the…

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26 May 2021 1172 Resistance to artemisinin and ACT partner drugs in Cambodia

Investigating clinical and molecular aspects of resistance to artemisinin and ACT partner drugs, in particular piperaquine.

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25 May 2021 1179 Targeted Chemo-elimination (TCE) of Malaria (TME)

Targeted Malaria Elimination (TME) studies took place in western Myanmar, Vietnam, Cambodia, and Laos during 2013-17, led by the Mahidol-Oxford Tropical Medicine Research Unit. This project consisted of 2 stages. Firstly, multiple malaria…

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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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26 May 2021 1181 Monitoring the susceptibility of Plasmodium falciparum to antimalarial drugs in malaria endemic areas in southern Vietnam

Routine monitoring of the efficacy of anti-malarial drugs used is necessary for effective case management, early detection of drug resistance and to provide background information for the development and evaluation of drug policies.…

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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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26 May 2021 1207 Integrating genetic epidemiology as an intensified surveillance tool into the National Center for Parasitology Entomology and Malaria Control of Cambodia

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

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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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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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Publications