Establishing a genomic sequencing platform to inform public health response of SARS-CoV-2 in an LMIC

George Githinji

George Githinji, KEMRI-Wellcome Trust Research Programme, Kenya


Genomic surveillance of local SARS-CoV-2 genetic sequences has contributed to the COVID-19 outbreak response through spatial and temporal tracking of circulating diversity. Here we discuss the success and challenges of setting up a genomic sequencing platform using the Oxford Nanopore platform to inform public health efforts in low- and middle-income countries. We used this platform to describe the early introduction and seeding of SARS-CoV-2 in Kenya and in the region.


George is a bioinformatician at KEMRI-Wellcome Trust Research Programme in Kenya. His interests are in the application of genomic epidemiology of respiratory viruses and in the development of computational methods for public health bioinformatics. George is currently working on whole genome sequencing and genomic surveillance of SARS-CoV-2 in Kenya and in the region.