African COVID-19 preparedness (AFRICO19)
Year of award: 2020
Grantholders
Prof Matthew Cotten
MRC/UVRI and LSHTM Uganda Research Unit
Dr Ke Yuan
University of Glasgow
Prof David Robertson
University of Glasgow
Prof James Nokes
KEMRI-Wellcome Trust Research Programme
Prof Martin Antonio
London School of Hygiene and Tropical Medicine
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:
- 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.
- 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.
- 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.