NIHR Global Health Research Group on Establishing Regional Hubs for Genomic Surveillance in West Africa, at the Wellcome Sanger Institute

Our goal is to expand capacity for genomic surveillance of malaria parasites and mosquito vectors in West Africa, and to generate essential information required for National Malaria Control Programmes (NMCPs) to plan sustainable interventions. Leveraging previous achievements in capacity building in The Gambia and Ghana, we aim to establish regional sequencing hubs that will provide NMCPs with timely, actionable genomic surveillance data. Objective 1 is to establish targeted amplicon sequencing pipelines that will generate surveillance data needed to address threats to sustainable malaria control identified by the World Health Organisation. These include: • the threat of parasite resistance to first line antimalarials and treatment failure • increasing vector resistance to pyrethroids causing a reduction in the efficacy of bednets • vector species diversity and residual transmission • parasite gene deletions that cause rapid diagnostic tests to fail • reintroduction of parasites as an obstacle to local control and elimination. Objective 2 is for the sequencing hubs in Ghana and The Gambia to achieve reliable production of genomic surveillance data and, through continual improvement of underlying technologies and operational processes, to progressively increase the scale of production and reduce turnaround time. Objective 3 is to establish a sampling framework for genomic surveillance of parasites and vectors in partnership with research groups and NMCPs in Ghana, The Gambia, Senegal, Nigeria, Burkina Faso, Guinea and Sierra Leone. Objective 4 is to integrate genomic surveillance into national and regional malaria control initiatives, building on existing links with NMCPs and with the PDNA network. We also aim to form a strong working relationship with the new African Pathogen Genomics Initiative. Thanks to previous NIHR funding, the Ghana and Gambia sequencing hubs will be generating surveillance data on parasite drug resistance from the outset of this project. We will progressively enlarge our sampling framework and expand the range of surveillance data products to address the wider set of use cases outlined above. PATHWAY TO IMPACT Reducing the burden of malaria in West Africa would result in a substantial reduction in child mortality and have a massively beneficial impact on socioeconomic progress and human wellbeing in this region of the world. The impact of genomic surveillance on infectious disease control has been brought to the public’s attention by the Covid-19 pandemic. This project is a small but strategically important step on the pathway to achieving the same for malaria. By developing logistical processes, strengthening cross-border partnerships and starting to deliver actionable data, we aim to provide proof of concept of public health impact and an operational model that will lead to multilateral investment in a more comprehensive regional sampling framework. Technical reports prepared from project data will be used as a discussion tool to monitor project progress and to engage on how to optimise for integration into existing epidemiological practice. In the final stage, the data generated across all sites will be aggregated and reviewed with a wide range of stakeholders to derive key lessons for malaria control across the region.