The Botswana Institute for Technology Research and Innovation (BITRI) in collaboration with the National Health Laboratory have successfully sequenced sixteen whole genomes of COVID-19 viruses that were first introduced into Botswana. This was achieved through a project funded by the National Institute for Health Research Global Health Research Unit Tackling Infections to Benefit Africa (TIBA).

TIBA is an Africa-led, wide-ranging, multi-disciplinary research programme that explores and draws lessons from the ways that different African health systems tackle infectious diseases. Through TIBA, the University of Edinburgh is working in partnerships with researchers from nine African countries, including Botswana, to generate new knowledge and inform comparative analyses of health systems. Whole genome sequencing of viruses has become a useful tool for understanding the ability of viruses to cause disease, track the evolution of viral genomes during transmission and at different time points of infections in individual patients.

By studying and comparing viral genomes from different countries, analysis of genetic mutations across the SARS-CoV-2 genomes can be used in the development of efficacious vaccines, novel treatments and improvement of diagnostic tests. To aid this effort, six local SARS-CoV-2 genomes have been uploaded to GISAID database, making Botswana the 16th African country to deposit SARS-CoV-2 genomes into the public database.

Nanopore sequencing technology is potable and generates sequences in real time. Therefore, this technology is appropriate for clinical diagnostics, epidemiological surveillance and can complement contact tracing by using the unique DNA sequences of viruses to track the source of infection, in cases in which the source is unclear. BITRI intends to build local capacity in Nanopore sequencing technology by training public health professionals and laboratory scientist in various Research and Academic Institutions.

Application of this technology will help monitor the genetic changes of the local circulating viral lineages and help understand the community transmission patterns of SARS-CoV-2 outbreaks in Botswana. This knowledge is vital in informing public health decision making and can help guide disease control and prevention strategies.