Assessing the impact of non-pharmaceutical interventions (NPIs) and BCG vaccine cross-protection in the transmission dynamics of SARS-CoV-2 in eastern Africa

Abstract Objective: The outbreak of the novel coronavirus disease 2019 (COVID-19) is still affecting African countries. The pandemic presents challenges on how to measure governmental, and community responses to the crisis. Beyond health risks, the socio-economic implications of the pandemic motivated us to examine the transmission dynamics of COVID-19 and the impact of non-pharmaceutical interventions (NPIs). The main objective of this study was to assess the impact of BCG vaccination and NPIs enforced on COVID-19 case-death-recovery counts weighted by age-structured population in Ethiopia, Kenya, and Rwanda.We applied a semi-mechanistic Bayesian hierarchical model (BHM) combined with Markov Chain Monte Carlo (MCMC) simulation to the age-structured pandemic data obtained from the target countries. Results: The estimated mean effective reproductive number (Rt) for COVID-19 was 2.50 (C1:1.99 - 5.95), 3.51 (CI:2.28 - 7.28) and 3.53 (CI:2.97 - 5.60) in Ethiopia, Kenya and Rwanda respectively. Our results indicate that NPIs, lockdowns, and curfews had a large effect on reducing Rt. Current interventions have been effective in reducing Rt and thereby achieve control of the epidemic. Beyond age-structure and NPIs, we found no significant association between COVID-19 and BCG vaccine-induced protection. Continued interventions should be strengthened to control transmission of SARS-CoV-2.