SIMPLEGEN: A modeling approach to inform malaria genetic surveillance

This project aims to develop a simulation pipeline (SIMPLEGEN) to systematically explore the utility of genetic data in malaria surveillance across different epidemiological settings. Plasmodium genetic data are increasingly recognized for their potential to provide valuable epidemiological insights, yet the lack of a well-defined framework for evaluating their utility before sample collection remains a significant barrier. This project seeks to address this gap by creating an open, community-driven framework that can benchmark various genetic data analysis methods and sampling designs. 

The SIMPLEGEN pipeline will incorporate an in-built transmission model, calibrated against publicly available epidemiological and genetic datasets, to simulate genetic data in diverse transmission scenarios. This will enable national malaria control programs (NMCPs) to explore specific sampling designs in silico before committing resources and allow for quantitative comparisons of different analysis methods.

The project will actively engage two key communities: developers of software and analysis tools, and practitioners, including local researchers and NMCPs. This engagement aims to foster a collaborative environment where the practical application of genomic surveillance can be advanced. By bringing together these communities, the project aims to ensure that the tools and methods developed are both scientifically robust and practically useful for controlling and eliminating malaria.

Gates Foundation grant information

Enabling Technologies & Assays
Modelling
Parasite Genetic Diversity
Surveillance

Jul 2021 — Jun 2024

$584,633

United Kingdom

Malaria Molecular Surveillance (MMS)