NOMADS 2: Expanding nanopore sequencing of malaria

Tools to prevent and treat malaria are growing more advanced and easier to access—but just as our tools evolve, so, too does the malaria parasite. As countries push to reduce and ultimately eliminate malaria, parasite surveillance will be essential to provide early warning signals for emerging biological threats to the fight against malaria and determine appropriate responses to a changing parasite.

Nanopore–based sequencing platforms offer the potential for affordable malaria molecular surveillance in resource–limited settings to track and ultimately counteract emerging threats, such as drug resistance and diagnostic escape.

With support from the Bill and Melinda Gates Foundation, NOMADS developed a cost–effective, scalable assay to detect antimalarial drug resistance in P. falciparum using nanopore sequencing, and demonstrated its feasibility in a pilot conducted in collaboration with the Zambia National Malaria Elimination Centre.

Building on that success, NOMADS 2 is continuing to strengthen and expand the use of nanopore sequencing for malaria genomic surveillance by:

• Integrating the NOMADS assay into routine malaria surveillance in Zambia
• Expanding nanopore sequencing to new geographies through collaboration and capacity building
• Optimizing existing and developing novel nanopore sequencing assays for malaria molecular surveillance

Integrate nanopore sequencing into routine surveillance in Zambia

NOMADS worked with the Zambia National Malaria Elimination Centre (NMEC) to establish a genomic surveillance unit that will deploy the NOMADS assay on samples from across Zambia to routinely assess levels of drug resistance and diagnostic escape.

In collaboration with the NMEC, we will combine existing epidemiological and entomological data streams into sampling strategies. By regularly connecting researchers with decision–makers and other specialists, NOMADS 2 will provide data needed by malaria programs to make decisions on control efforts, for example on identifying effective drugs.

Expand nanopore sequencing to new geographies through collaboration and capacity building

NOMADS 2 aims to create a malaria nanopore sequencing community by building sequencing capacity across several countries. Through equipment provision, training, and remote support, we will equip in–country collaborators in at least three new target geographies, to establish in–country malaria genomic surveillance. We will also develop training materials that will enable even more geographies to adopt the assay in their setting.

Optimize existing and develop novel nanopore sequencing assays for malaria molecular surveillance

We will continue to optimize the existing NOMADS assay focused on drug resistance and diagnostic escape to reduce cost and increase performance. Simultaneously, we will develop new approaches in response to our collaborators' needs, such as mosquito genomic surveillance.