MalariaGEN (Malaria Genomic Epidemiology Network)

To stop malaria — a disease which kills over half a million people every year — we must understand it better.

MalariaGEN is a data-sharing network of partners in over 40 countries who build and share large-scale human, malaria parasite, and mosquito data resources. We study malaria epidemiology and evolution to create accessible resources for malaria control.

These datasets facilitate the search for new drugs, insecticides, and vaccines, as well as genomic surveillance tools to help control and eliminate malaria.

The problem

There are an estimated quarter of a billion malaria cases each year, over half a million of which are fatal. Three quarters of malaria deaths are children under 5 years old, while over 95% of deaths are on the African continent. The disease, which is caused by mosquito-borne Plasmodium parasites that invade human red blood cells, causes considerable human suffering and creates a massive socioeconomic burden for people in many of the poorest countries in the world.

One of the main obstacles to controlling malaria is an evolutionary arms race between parasite, mosquito, and human populations. Parasites and mosquitoes are continually adapting in response to the genetic pressure exerted by antimalarial drugs, insecticides, and other public health interventions.

The network

The Malaria Genomic Epidemiology Network (MalariaGEN) is a community of researchers who are working together to understand how genetic variation in human, parasite, and mosquito populations affects the biology and epidemiology of malaria. MalariaGEN aims to use this knowledge to develop better tools for malaria control.

MalariaGEN brings together the work of many scientific partner studies in malaria-endemic regions around the world, each of which is led by an independent investigator — “MalariaGEN partners” — and has its own scientific objectives. 

MalariaGEN adds value to partners’ studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data. 

This model supports a series of large-scale collaborative consortial and community projects that are conducted across multiple populations, bringing together detailed clinical and epidemiological data with state-of-the-art technologies for genome sequencing and web tools for data analysis.

The MalariaGEN community is global, with more than 300 scientists, public health professionals, clinicians, parasitologists, entomologists, communicators, and community-builders contributing from more than 40 countries. The team based in the Genomic Surveillance Unit at the Wellcome Sanger Institute supports the MalariaGEN community, communicates findings, builds data pipelines, and receives and processes samples.

Human

The origins of the MalariaGEN project were in human genetics. In 2005, clinical and epidemiological researchers from malaria-endemic countries, and others with expertise and technological resources in high-throughput analysis of genetic variation, came together to form the MalariaGEN Consortium. The Consortium developed an international scientific programme to investigate why, in regions where people are repeatedly exposed to malaria parasites, some people die from the infection while others survive. More recent efforts have focused on parasite and vector genetics.

Find out more on the MalariaGEN website.

Parasite

The Plasmodium parasites that cause malaria have a remarkable talent for survival. Through small genetic changes, they can evade the human immune system, develop resistance to antimalarial drugs, and adapt to changes in the mosquitoes that transmit the parasites.

Genomic surveillance of Plasmodium is a powerful tool in tracking the evolution of the drug resistant variants that challenge malaria control programmes. Identifying genetic variations is helping scientists and health professionals answer crucial questions about the mechanisms of drug resistance, whether it is newly emerged, or spreading from other areas, and which locations are at risk from drug-resistant strains.

Datasets:

Plasmodium falciparum (Pf7, with 20k+ whole genome sequences, was released in 2023)

Plasmodium vivax (Pv4, with 1.8k+ whole genome sequences, was released in 2022)

GenRe-Mekong (v1.0, with 9.6k+ Genetic Report Cards, was released in 2021)

Find out more on the MalariaGEN website.

Mosquito

Vector control (i.e. stopping or killing mosquitoes) has played a major role in reducing the burden of malaria, through the use of long-lasting insecticidal nets and indoor residual spraying of insecticides. But since 2015, progress towards malaria elimination has stalled in many regions.

We must improve our ability to identify and survey the full range of mosquito species responsible for malaria transmission. We also need to improve our understanding of how transmission is varying over time and space. Combining data on mosquito populations, vector control strategies, and malaria transmission will give us the evidence we need to tailor vector control strategies to different settings.

Datasets:

Ag1000G (now Anopheles gambiae genomic surveillance, with 3,000+ whole genome sequences)

Anopheles funestus genomic surveillance (ongoing)

Vector Observatory – Asia (e.g. Amin1, 302 whole genome sequences from wild-caught An. minimus in Cambodia)

Find out more on the MalariaGEN website.

History, ethics, governance and funding 

The foundations for a data-sharing network in the genomic epidemiology of malaria were developed in 2003-5 with grants from the Medical Research Council and the Gates Foundation. MalariaGEN was formally established in 2005 as part of the Grand Challenges in Global Health initiative, with joint funding from the Wellcome Trust and the Gates Foundation through the Foundation for the National Institutes of Health. The administration of MalariaGEN is primarily funded by the Wellcome Trust, however MalariaGEN brings investigators together from around the world that are funded from a range of sources.

There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies for data sharing and data access.