Community surveillance for COVID-19 and SARS-CoV-2 in Uganda

The Unit was uniquely placed to immediately contribute to the response in Uganda. Indeed, historically, the Unit was founded precisely to undertake such pandemic research – investigating dynamics and trends of HIV infection. The parallels with COVID-19 (such as the threat from people entering the country from outside and the profile of high-risk populations) are strikingly similar.

Research sites

Our strategically chosen study populations in Lukaya town (a truck-stop on the trans-African Highway) and the adjacent sub-county of Kyamulibwa (the site for our rural General Population Cohort (GPC)), gave us a unique opportunity to generate accurate data about how the virus was affecting the population.

Our staff had been active in these areas over many years and were well known, thereby ensuring good population level engagement and long-term follow-up of participants. We also had a wealth of existing data (e.g. socio-demographic factors, comorbidities); the areas had already been mapped and census data were available at a household level. In the GPC, routine vital registration of pregnancies, births, deaths and cause-specific mortality allowed for an assessment of COVID-19-related mortality, as well as mortality from other conditions, during the period of implementing pandemic mitigation strategies.

Findings

After 18 months of surveillance, we found

• no significant excess mortality from COVID, despite widespread infection (20% infected in the first wave);
• prevalent viral subtypes reflect global trends;
• serology reveals a lack of pre-existing protective immunity against SARS-CoV-2 and
• SARS-CoV-2 increases activity of certain cancer-causing infections, which has implications for long-term health of affected individuals. 

The future

This study is an important resource for much-needed population-level data on COVID-19 in rural Africa and for future studies of “long-COVID” in the region.

Publications

Mugisha, J., Mpairwe, B. and Newton, R. et al. SARS-CoV-2 Omicron BA.5 infections in vaccinated persons, rural Uganda. Emerging Infectious Diseases, 2023