The epidemiology of COVID-19 in Ugandan settlements and neighbouring communities
Aligned with our mission to advance the understanding and impact of microbiology, the Society reached out to our community of microbiologists to share their experiences in responding to SARS-CoV-2. We aim to showcase the perspective of scientists during the COVID-19 pandemic and the variety of roles adopted to mitigate the global crisis.
This case study is written by Professor Richard Birtles, Chair of Biomedicine at the University of Salford, UK. Richard recounts his experience of establishing COVID-19 diagnostics facilities in Uganda, creating capacity for in situ SARS-CoV-2 whole genome sequencing, and how he used these new resources to clarify virus transmission routes. He also touches on the practical challenges that the project had to overcome, including supply chain issues and travel restrictions.
Along with other colleagues at Salford, we visited northern Uganda in 2018 and we were all profoundly moved by the scale of the public health challenges we saw out there. As the pandemic began to sweep across the globe, we immediately thought that whatever the threat of COVID-19 to the UK, the likely impact on the people of Uganda would be much worse. Uganda is a remarkable country in many ways; one reason for celebration is that, despite its small size and very recent history of civil war, it is Africa's largest refugee hosting country. Today, an estimated 1.5 million refugees, mainly from South Sudan and the Democratic Republic of Congo, live in Uganda, with most large settlements being in the remote far-north of the country. We speculated that the epidemiology of COVID-19 in these settlements and neighbouring Ugandan communities may be unusual and were able obtain funding from the UK Research and Innovation’s Global Challenges Research Fund to investigate.
Our project had 4 aims: first to establish COVID-19 real time polymerase chain reaction (RT-PCR)-based diagnostics in northern Uganda; second to follow this up by adding capacity for in situ SARS-CoV-2 whole genome sequencing; and third to use these new resources to clarify virus transmission routes into the refugee settlements and between settlements and adjacent Ugandan communities. At the heart of our project was capacity building and knowledge exchange with Ugandan colleagues (at the University of Gulu, Uganda), so our final aim was to improve supply chains for molecular microbiology in the country to make it easier for Ugandan scientists to continue to work when our funding finished.
We are now 18 months into the project and we’ve pretty much achieved aims 1 and 2. The diagnostic service has been in routine operation since May 2021 and we’ve tested over 10,000 samples now. We started sequencing in Gulu in the autumn and have just uploaded the first 150 genomes onto GISAID (a global resource providing open access to genomic data of influenza and coronaviruses). These numbers may not seem impressive compared to what’s happening in the UK, but then the UK doesn’t have to deal with almost daily power cuts and suchlike! We are currently in the middle of a large-scale survey of refugee communities in Lamwo District and we are just starting to process the samples we are collecting. Again, the logistical (and administrative) challenges of doing this work have been huge.
Finally, our supply chain work package has revealed a depressing insight into the struggles Ugandan scientists face; many of the reagents that we in the UK can buy for peanuts and get delivered within 24 hours are either unavailable in Uganda or are sold at hugely inflated prices by distributors. We have identified not-for-profit Ugandan distributors and we are now trying to connect them up with European biotech manufacturers (and convince these companies to be a bit more altruistic). We’ve had great success with Oxford Nanopore Technology, who now deliver to a Ugandan distributor to support our sequencing efforts.
The project has another 4 months to run and has been pretty exhausting, but really exciting to be part of. With all the lockdowns and red lists etc., we’ve struggled to get out to Uganda and/or get Ugandan scientists here for training as much as we hoped, but we’re getting there – we were really lucky to recruit a brilliant British-Kenyan postdoc as project manager based out in Gulu. Her incredible ability to find a way to get things done has saved us on many occasions.
Like many others now working on COVID-19, I had no direct experience of coronaviruses prior to the outbreak. Between us, we know a bit about molecular diagnostics and genomics but our pre-pandemic research focused on arthropod-borne bacteria and protozoa. We had some experience of working in sub-Saharan Africa (SSA), which served us well in understanding day to day hurdles and supporting the project manager in getting us over them. The project has strengthened our collaborative links with several Ugandan research institutions, the result of which is new work on neglected tropic diseases has started.
There are 101 huge public/veterinary/one health challenges to address in Uganda (and across SSA) that require microbiological expertise. These challenges should be addressed as much as possible in Uganda by Ugandan scientists. It is our responsibility to empower them to do so by capacity building and appropriate training and support. However, this training must address practicalities not just science – if we do not recognise that the way labs run in the UK is very different, is very much easier, than the way labs run in Uganda, then transfer of brilliant scientific skills will be futile.
About the author
Professor Richard Birtles is Chair of Biomedicine at the University of Salford, UK. His work explores the strategies adopted by infectious agents, at the individual and population level, to persist in nature, in particular those microorganisms that are transmitted by arthropods.