African COVID-19 preparedness (AFRICO19)


  • Prof Matthew Cotten

    MRC/UVRI and LSHTM Uganda Research Unit, Uganda

  • Dr Ke Yuan

    University of Glasgow, United Kingdom

  • Prof David Robertson

    University of Glasgow, United Kingdom

  • Prof James Nokes

    KEMRI-Wellcome Trust Research Programme, Kenya

  • Prof Martin Antonio

    London School of Hygiene and Tropical Medicine, United Kingdom

Project summary

Our project will enhance capacity to understand SARS-CoV-2/hCoV-19 infection in three regions of Africa (Kenya, The Gambia and Uganda) and globally. 

Building on existing infrastructures and collaborations, we will create a network to share knowledge on next generation sequencing (NGS), including Oxford Nanopore Technology (MinION), coronavirus biology and COVID-19 disease control. 

Our consortium links three African sites with support from the University of Glasgow on genomics and informatics to achieve three goals: 

  1. Support East and West African capacities for rapid diagnosis and sequencing of SARS-CoV-2 to help with contact tracing and quarantine measures. Novel diagnostic tools optimised for this virus will be deployed. An African COVID-19 case definition will be refined using machine learning for identification of SARS-CoV-2 infections. 
  2. Surveillance of SARS-CoV-2 will be performed in one cohort at each African site. The use of established cohorts will ensure that sampling begins quickly. A sampling plan optimised to detect initial moderate and severe cases, followed by household contact tracing, will be employed to obtain both mild to severe COVID-19 cases. 
  3. Provide improved understanding of SARS-CoV-2 biology and evolution using machine learning and novel bioinformatics analyses. Our results will be shared via a real-time analysis platform using the newly developed CoV-GLUE resource.