GenRe-Mekong

 

 

 

Started 2016

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), NCMPs 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

Distribution of GenRe-Mekong sampling sites

  • Bangladesh (BD)
  • Cambodia (KH)
  • Laos (LA)
  • Myanmar (MM)
  • Thailand (TH)
  • Vietnam (VN)
  • India (IN)

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

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.

People

We are working with partners to ensure that the list of people associated with a partner study is up-to-date. People involved in this project include:

Aung Myint Thu

Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand

Borimas Hanboonkunupakarn

Mahidol Oxford Tropical Medicine Research Unit (MORU), Thailand
Faculty of Tropical Medicine, Mahidol University, Thailand

Prof Francois Nosten

Professor in Tropical Medicine, Group Head / PI, Consultant Physician and Fellow
Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford Old Road campus, Oxford, UK
Director
Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand

Huynh Hong Quang

Institute of Malariology, Parasitology, and Entomology (IMPE) Quy Nhon, Ministry of Health, Vietnam

Keobouphaphone Chindavongsa

Center of Malariology, Parasitology and Entomology (CMPE), Lao PDR

Lorenz von Seidlein

Mahidol Oxford Tropical Medicine Research Unit (MORU), Thailand

Mallika Imwong

Mahidol University, Thailand

Assoc Prof Mayfong Mayxay

Head of Field Research
Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao PDR
Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao PDR

Ngo Viet Thanh

Oxford University Clinical Research Unit (OUCRU), Vietnam

Prof Nicholas J White

Professor of Tropical Medicine and Chair of Wellcome Trust SE Asian Tropical Medicine Research Programmes
Mahidol-Oxford Tropical Medicine Research Unit (MORU), Thailand

Rapeephan Maude

Mahidol-Oxford Tropical Medicine Research Unit (MORU), Thailand
Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Thailand

Rob van der Pluijm

Mahidol Oxford Tropical Medicine Research Unit (MORU), Thailand

Rupam Tripura

Mahidol Oxford Tropical Medicine Research Unit (MORU)

Dr Thomas E Wellems

Chief, Laboratory of Malaria and Vector Research and Chief, Malaria Genetics Section
National Institute of Allergy and Infectious Diseases (NIAID), NIH, USA

Tom Peto

Mahidol-Oxford Tropical Medicine Research Unit (MORU), Thailand