Malaria Parasite Genomic Surveillance

Genomic Surveillance Unit

We are a team within the Genomic Surveillance Unit, we generate and curate genomic public health data on the Plasmodium parasites that cause malaria. We also develop new scientific and bioinformatic techniques that expand our ability to track genetic changes in these dangerous parasites.

About us

Greg Moss / Wellcome Sanger Institute
A gloved hand reaches into a clear plastic bag to remove filter paper with dried blood spots. These blood spots contain malaria parasites that will be sequenced.
Selective Whole Genome Amplification (sWGA) allows whole parasite genomes to be extracted from dried blood spots.

We are 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 seek to understand the malaria parasite and its evolution. We work 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

A screenshot from Pf7 shows summary statistics for the dataset: 16k samples passed Quality Control, from 97 locations in 37 countries.
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 create 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 help 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 are building an Amplicon Toolkit with other teams in the Genomic Surveillance Unit. This suite of tools and services will allow partners to implement amplicon sequencing for genomic surveillance of malaria parasites. It will be an end-to-end product that includes metadata curation, training, sequence upload, bioinformatic analysis, data return, and genetic report cards.

Our team’s lab experience helps create new ways to make sequencing the parasites easier. For example, we are looking 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. Ongoing research and development also includes how to access complex parts of the parasite genome using long read sequencing technologies.

Core team

Photo of Dr Jacob Almagro-Garcia

Dr Jacob Almagro-Garcia

Translational Research Lead

Photo of Dr William Hamilton

Dr William Hamilton

Senior Staff Scientist

Photo of Alexandria Harrott

Alexandria Harrott

Technical Specialist

Photo of Chiyun Lee

Chiyun Lee

Senior Data Scientist

Photo of Kate Rowlands

Kate Rowlands

Team Coordinator

Photo of Dr Eyyub Unlu

Dr Eyyub Unlu

Data Scientist

Photo of Dr Nina White

Dr Nina White

Senior Data Scientist

Previous team members

Photo of Dr Kim Judge

Dr Kim Judge


Photo of Georgia Elizabeth Whitton

Georgia Elizabeth Whitton

Senior Data Scientist