Malaria Parasite Genomic Surveillance

Genomic Surveillance Unit

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We were a team within the Genomic Surveillance Unit, we generated and curated genomic public health data on the Plasmodium parasites that cause malaria. We also developed new scientific and bioinformatic techniques that expanded our ability to track genetic changes in these dangerous parasites. Following a strategic review the Wellcome Sanger Institute decided to disband its Genomic Surveillance Unit in 2026 as part of a broader institutional shift to focus exclusively on fundamental discovery science.

About us

Greg Moss / Wellcome Sanger Institute

Selective Whole Genome Amplification (sWGA) allows whole parasite genomes to be extracted from dried blood spots.

We were biologists, bioinformaticians, technicians, and data scientists working at the intersection of computation, biology, lab methods, and public health. With a strong emphasis on creating useful data for our public health partners, we sought to understand the malaria parasite and its evolution. We worked collaboratively with other teams in the Genomic Surveillance Unit and around the world to scale the extraction of useful, high-quality genomic data from malaria parasites.

Our work

The Pf7 data resource, published in 2023, is the largest Plasmodium falciparum whole-genome dataset in the world.

Building on nearly twenty years of experience integrating with the MalariaGEN network, we created data resources that track genetic changes in Plasmodium parasites, mostly of the two species responsible for most malaria deaths: P. falciparum and P. vivax. The largest of these resources is Pf7, a dataset containing more than 20,000 whole genome sequences of P. falciparum parasites from 33 countries. The P. vivax version of that dataset, Pv4, contains nearly 2,000 whole genome sequences.

We helped build up surveillance capacity in malaria-endemic areas through projects like the NIHR-funded Genomic Surveillance Hubs in West Africa Global Health Research Group and by supporting partners across the world in their genomic surveillance efforts. 

Building on successes with amplicon sequencing for tracking antimalarial drug resistance, we built an Amplicon Toolkit with other teams in the Genomic Surveillance Unit. This suite of tools and services allowed partners to implement amplicon sequencing for genomic surveillance of malaria parasites. It was an end-to-end product that included metadata curation, training, sequence upload, bioinformatic analysis, data return, and genetic report cards.

Our team’s lab experience helped create new ways to make sequencing the parasites easier. For example, we looked at how to enhance Plasmodium vivax DNA within samples to be able to look at this parasite in more detail and how to extract DNA from malaria rapid diagnostic tests, essentially a waste product from malaria diagnosis. We also researched and developed also techniques to access complex parts of the parasite genome using long read sequencing technologies.