The National COVID-19 Epi Model (NCEM): Estimating cases, admissions and deaths for the first wave of COVID-19 in South Africa

The consortium coordinated mathematical modelling efforts, bringing together researchers from academic, non-profit, and government institutions. The goal was to provide, assess, and validate model projections to support planning by the South African government. The National COVID-19 Epi Model (NCEM) was developed jointly by disease modelling groups at the University of Cape Town, Stellenbosch University, and the University of the Witwatersrand. The model was initially developed as a deterministic compartmental model of SARS-Cov-2 transmission in the nine provinces of South Africa. However, it was adapted several times over the course of the first wave of infection in response to emerging local data and changing needs of government. The NCEM developed into a stochastic, spatially-explicit compartmental transmission model to estimate the total and reported incidence of COVID-19 across the 52 districts of South Africa. The model accounted for the clinical profile of SARS-COV-2, including asymptomatic, mild, severe, and critical cases, as well as avenues of treatment access. The model was updated 11 times between end-March and early September 2020, with four key releases to generate new sets of projections and scenario analyses. The NCEM was designed to incorporate a high level of local data to contextualize the model appropriately to address South Africa’s population and health system characteristics. The model was used to estimate cases, resource needs, and deaths due to COVID-19, and to assess the impact of interventions. The model was used to support planning by the South African government, and its projections were used to inform policy decisions. The NCEM was developed in response to the uncertainty surrounding the COVID-19 pandemic, including the prevalence, transmission, and clinical profile of SARS-COV-2. The model was designed to account for the uncertainty and to provide a framework for analyzing the transmission and impact of the disease. The NCEM was used in conjunction with the National COVID-19 Cost Model (NCCM) developed by the University of the Witwatersrand. The two models were used to provide a comprehensive understanding of the COVID-19 epidemic in South Africa. The NCEM and NCCM were used to estimate the economic and health impacts of the pandemic, and to inform policy decisions. The availability of data and local capacity for infectious disease modelling and economic analysis played a crucial role in the development and implementation of the NCEM. The model was used to provide strategic information to support policy makers in programme and funding decisions. The use of the NCEM and NCCM in South Africa highlights the importance of harnessing and developing local modelling capacity to address public health challenges.