Using outbreak data to estimate the dynamic COVID-19 landscape in Eastern Africa

Background The emergence of COVID-19 as a global pandemic presents a serious health threat to African countries and the livelihoods of its people. To mitigate the impact of this disease, intervention measures including self-isolation, schools and border closures were implemented to varying degrees of success. Moreover, there are a limited number of empirical studies on the effectiveness of non-pharmaceutical interventions (NPIs) to control COVID-19. In this study, we considered two models to inform policy decisions about pandemic planning and the implementation of NPIs based on case-death-recovery counts. Methods We applied an extended susceptible-infected-removed (eSIR) model, incorporating quarantine, antibody and vaccination compartments, to time series data in order to assess the transmission dynamics of COVID-19. Additionally, we adopted the susceptible-exposed-infectious-recovered (SEIR) model to investigate the robustness of the eSIR model based on case-death-recovery counts and the reproductive number (R-0). The prediction accuracy was assessed using the root mean square error and mean absolute error. Moreover, parameter sensitivity analysis was performed by fixing initial parameters in the SEIR model and then estimating R-0, beta and gamma. Results We observed an exponential trend of the number of active cases of COVID-19 since March 02 2020, with the pandemic peak occurring around August 2021. The estimated mean R-0 values ranged from 1.32 (95% CI, 1.17-1.49) in Rwanda to 8.52 (95% CI: 3.73-14.10) in Kenya. The predicted case counts by January 16/2022 in Burundi, Ethiopia, Kenya, Rwanda, South Sudan, Tanzania and Uganda were 115,505; 7,072,584; 18,248,566; 410,599; 386,020; 107,265, and 3,145,602 respectively. We show that the low apparent morbidity and mortality observed in EACs, is likely biased by underestimation of the infected and mortality cases. Conclusion The current NPIs can delay the pandemic pea and effectively reduce further spread of COVID-19 and should therefore be strengthened. The observed reduction in R-0 is consistent with the interventions implemented in EACs, in particular, lockdowns and roll-out of vaccination programmes. Future work should account for the negative impact of the interventions on the economy and food systems.

Automated summary

This study uses two models to assess the transmission dynamics of COVID-19 in African countries and the effectiveness of intervention measures. The results show that NPIs can delay the pandemic peak and reduce the spread of the virus. However, the observed morbidity and mortality may be underestimated.