Building capacity for public health bioinformatics in East Africa using a portable sequencing platform

George Githinji



The global spread of the SARS-CoV-2 virus epidemic over the last few months has generated unprecedented social and economic disruptions in developing countries compounded by weak healthcare facilities. Kenya, a lower-middle income country, lacks adequate resources for comprehensive preparedness to counter a large-scale epidemic similar to countries with large economies. To support the country’s epidemic preparations, we set up whole genome sequencing (WGS) of respiratory viruses using portable MinION technology to feed into public health control measures. We describe our approach in building capacity, understanding and informing public health agencies in tracking the spread of SARS-CoV-2 at the Kenyan Coast and the country in general.


George is a bioinformatician and a postdoctoral scientist at KEMRI-Wellcome Trust Research Programme in Kenya. His interests are in the application of genomic epidemiology in understanding transmission of respiratory viruses and in public health bioinformatics.