Title: NIHR Global Health Research Group on Establishing Regional Hubs for Genomic Surveillance in West Africa, at the Wellcome Sanger Institute
Funder: Department of Health and Social Care

Abstract: 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. _x000D_ _x000D_ 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:_x000D_ _x000D_ • the threat of parasite resistance to first line antimalarials and treatment failure_x000D_ • increasing vector resistance to pyrethroids causing a reduction in the efficacy of bednets_x000D_ • vector species diversity and residual transmission_x000D_ • parasite gene deletions that cause rapid diagnostic tests to fail_x000D_ • reintroduction of parasites as an obstacle to local control and elimination._x000D_ _x000D_ 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. _x000D_ _x000D_ 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. _x000D_ _x000D_ 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._x000D_ _x000D_ 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._x000D_ _x000D_ PATHWAY TO IMPACT_x000D_ _x000D_ 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. _x000D_ _x000D_ 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. _x000D_ _x000D_ 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.

Lay abstract: GENOMIC SURVEILLANCE SYSTEMS ARE ESSENTIAL FOR SUSTAINABLE MALARIA CONTROL IN AFRICA_x000D_ National malaria control programmes (NMCPs) need effective tools to monitor resistance to control measures and to provide early warning if their interventions are causing resistance to rise to unacceptable levels so they can change strategy. Advances in genomic surveillance revolutionised the UK response to the COVID pandemic and demonstrated the power of this tool across the world. Proof-of-concept of malaria genetic surveillance in West Africa led by the University of Ghana (UG) and the MRC Unit in The Gambia (MRCG) has shown that data is better integrated into decision making if the genetic data is generated in-country and the NMCP is involved and engaged in the process._x000D_ _x000D_ REGIONAL GENOMIC SURVEILLANCE HUBS INCREASE UPTAKE AND BUILD CAPACITY_x000D_ Knowledge of genetics, genetic markers and genetic epidemiology is outside the domain of expertise of most NMCPs. Therefore, subject matter experts need to work with NMCPs to bridge the gap and support implementation. Discrete but connected hubs can support NMCP-managed activities in different countries and integrate data generated into regional analyses. Hub leaders also serve as advocates to connect these data to a global data sharing network by forging strong relationships in both directions and acting as stakeholder representatives._x000D_ _x000D_ Bringing malaria genetic surveillance data across the world benefits public health. If a new form of parasite drug resistance or mosquito insecticide resistance emerges elsewhere in the world, it will greatly help an NMCP to monitor and manage the problem if the genomic analysis software is continually updated to incorporate the most useful genetic markers, which are likely to have been discovered elsewhere. However, those new to sharing data openly benefit from working closely with subject matter experts who are knowledgeable and sensitive to cultural, operational and technical challenges in achieving this._x000D_ _x000D_ INVESTMENT IN GENOMIC SURVEILLANCE IN AFRICA HAS POTENTIAL BEYOND MALARIA_x000D_ Genomic surveillance of COVID has been world-headline news, demonstrating the power of genetics for public health particularly in the UK. Rapid advances building on malaria genomic surveillance in West Africa have the potential to catalyse relationships and advancement in malaria. For example, building on capacity for malaria genetic surveillance in our current programme of research, scientists at UG applied these tools to sequence genomes of the SARS-CoV-2 virus from confirmed cases in Ghana. Combined with local leadership, genomic surveillance tools can be applied to pathogens and viruses for both endemic and pandemic infectious disease. _x000D_ _x000D_ WHAT WE AIM TO ACHIEVE_x000D_ Having established end-to-end implementation of genomic surveillance of malaria using Amplicon sequencing at UG and MRCG, we will work with leaders to instigate their own discrete but complementary regional networks including developing capacity for managing multi-partner collaborations. Hub leaders will work with their collaborators to provide training from sample collection through to the translation of genomic data into actionable knowledge. By the end of this project, we aim to be integrating these systems into the routine working practices of NMCPs in countries that are part of the regional networks of Ghana and The Gambia, and to provide a working example of how such systems could be deployed at other locations in Africa.

Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION;2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY)
Health categories: INFECTION