COVID-19 and all-cause mortality in South Africa - the hidden deaths in the first four waves

Abstract

Accurate statistics are essential for policy guidance and decisions. However, the reported number of cases and COVID-19 deaths are known to be biased due to under-ascertainment of SARS-CoV-2 and incomplete reporting of deaths. Making use of death data from the National Population Register has made it possible to track in near-real time the number of excess deaths experienced in South Africa. These data reveal considerable provincial differences in the impact of COVID-19, likely associated with differences in population age structure and density, patterns of social mixing, and differences in the prevalence of known comorbidities such as diabetes, hypertension, and obesity. As the waves unfolded, levels of natural immunity together with vaccination began to reduce levels of mortality. Mortality rates during the second (Beta) wave were much higher than mortality in the third (Delta) wave, which were higher than in either the first or the fourth (Omicron) waves. However, the cumulative death toll during the second (Beta) wave was of a similar order of magnitude as that during the third (Delta) wave due to the longer duration of the Delta wave. Near-real time monitoring of all-cause deaths should be refined to provide more granular-level information to enable district-level policy support. In the meanwhile, there is an urgent need to re-engineer the civil registration and vital statistics system to enable more timely access to cause of death information for public health actions.