Cambridge-Africa

SARS-CoV-2 sequencing network - West and Central Africa

At a glance

Grant: £2.3 million given by Wellcome Trust and FCDO for Epidemic Preparedness of SARS-CoV-2

Leading bodies: ARTIC Network (University of Cambridge, Edinburgh and Birmingham) and West Africa Center for Cell Biology of Infectious Pathogens (WACCBIP), Ghana.

Aims:

  • Establishment of a West African SARS-CoV-2 sequencing hub
  • Support sequencing across West and Central Africa through the establishment of 7 spoke partner laboratories (Burkina Faso, Cameroon, Côte d’Ivoire, Guinea, Mali and Nigeria)
  • Training, capacity strengthening and remote support of sequencing activities

 

Summary

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:

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

This project is led by a group of world renowned academics, including Professor Gordon Awandare (University of Ghana), Professor Ian Goodfellow (University of Cambridge), Professor Nicolas Lauman (University of Birmingham), Dr Osborne Quaye (University of Ghana), Dr Joshua Quick (University of Birmingham), and Professor Andrew Rambaut (University of Edinburgh).

 

ARTIC Network:

The ARTIC Network was established in 2017, following the West African Ebola outbreak. The aim of this was to bring about an end-to end system for processing viral samples and delivering real-time epidemiological information for public health response during outbreaks. One of the main focuses of this network is the ‘lab in a suitcase’ design, using portable Oxford Nanopore minION sequencers which can be deployed in remote and resource-limited settings for response against a range of viral diseases.

This network involves partners from the University of Edinburgh, the University of Birmingham, the University of Cambridge, KU Leuven, the University of Oxford, Fred Hutchinson Cancer Research Center, and the University of California Los Angeles.

 

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.