SARS-CoV-2 sequencing training in West and Central Africa

Introduction

The SARS-CoV-2 pandemic has highlighted a huge discrepancy in access to a range of public health interventions, from diagnostics and surveillance, to prevention and treatment. While the UK alone had produced over 2,000,000 sequences by February 2022, West and Central Africa had sequenced less than 25,000 genomes, despite accounting for a population 10 times the size. With low sequencing capacity, real-time data become limited leading to a weakened national response and the facilitates the circulation of Variants of Concern (VoCs).

Therefore, in August 2021, the Wellcome Trust and the Foreign, Commonwealth, and Development Office (FCDO) awarded £2.3 million towards a collaborative project between the ARTIC Network and the West African Center for Cell Biology of Infectious Pathogens (WACCBIP) at Legon, in Ghana. This project aims to improve viral sequencing capacity in West and Central Africa through supporting the scale-up of infrastructure, and providing expert training in sequencing and analysis to several spoke laboratories with varying levels of experience in molecular biology. With this infrastructure and training, the project aims to produce up to 10,000 more sequences through WACCBIP, and up to 1,000 from each of the seven spoke laboratory in the region.

The first stage of this project involved strengthening capacity at WACCBIP through installation of low cost technologies, such as GridION sequencers and OpenTron liquid handling robots. Staff at WACCBIP were given additional training to build on their existing knowledge of sequencing, and to enable staff to provide high level training to others at a later point. This prepared WACCBIP to act as a hub for viral sequencing at a national and regional level.

The second stage of this project has involved establishment of 7 spoke laboratories in Burkina Faso, Cameroon, Côte d’Ivoire, Guinea, Mali and Nigeria. A training workshop was held in August 2022 at WACCBIP, in which two people from each spoke laboratory were trained in the wet lab sequencing process, and one was trained in analysis using bioinformatics software. All training of the sequencing process was streamlined to ensure rapid support from the leading bodies, and to strengthen networks between the spoke laboratories.

Spoke laboratories

  1. African Center of Excellence for Population Health and Policy (ACEPHAP), Bayero University, Nigeria (Professor Hadiza Shehu Galadanci)
  2. Centre d’Excellence Africain pour la Prévention et le Contrôle des Maladies Transmissibles (CEA-PCMT), Conakry, Guinea (Professor Alexandre Delamou)
  3. Centre de Recherche sur les Filarioses et Autres Maladies Tropicales (CRFiLMT), Yaoundé, Cameroon (Dr Hugues Nana Djeunga)
  4. Centre Suisse de Recherche Scientifique (CSRS), Abijan, Côte d’Ivoire (Dr Solange Aka)
  5. Groupe de Recherche Action en Sante (GRAS), Ouagadougou, Burkina Faso (Dr Sodiomon B. Sirima)
  6. Institut de Recherche en Sciences de la Santé (IRSS) (ITEC-MTV), Bobo-Dioulasso, Burkina Faso (Professor Abdoulie Diabates)
  7. Malaria Research and Training Center (MRTC), Bamako, Mali (Professor Antoine Dara)

West Africa Center for Cell Biology of Infectious Pathogens (WACCBIP)

WACCBIP is an African Centre of Excellence (ACE) developed by faculty at the University of Ghana in the Department of Biochemistry, Cell and Molecular biology, and the Noguchi Memorial Institute for Medical Research. The Centre aims to tackle diseases affecting sub-Saharan Africa through excellent research and innovation, as well as providing high-quality training and development of scientific leaders across the continent.