African COVID-19 preparedness (AFRICO19)

The 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. 

The 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.

• Prospective Cohort
• Epidemiology, viral sequencing, phylogenetics, and machine learning to  develop novel diagnostics
• Description of  SARS-CoV-2 transmission as it enters and spreads through three African countries.

Enabling Technologies & Assays
Epidemiology

May 2020 — Apr 2022

$1.96M

Kenya
The Gambia
Uganda

Clinical Epidemiology of COVID-19 in Malaria Settings