Estimating the time-varying reproduction number for COVID-19 in South Africa during the first four waves using multiple measures of incidence for public and private sectors across four waves.

Objectives: The aim of this study was to quantify transmission trends in South Africa during the first four waves of the COVID-19 pandemic using estimates of the time-varying reproduction number (R) and to compare the robustness of R estimates based on three different data sources, and using data from public and private sector service providers.
Methods: R was estimated from March 2020 through April 2022, nationally and by province, based on time series of rt-PCR-confirmed cases, hospitalisations, and hospital-associated deaths, using a method that models daily incidence as a weighted sum of past incidence, as implemented in the R package EpiEstim. R was also estimated separately using public and private sector data.
Results: Nationally, the maximum case-based R following the introduction of lockdown measures was 1.55 (CI: 1.43-1.66), 1.56 (CI: 1.47-1.64), 1.46 (CI: 1.38-1.53) and 3.33 (CI: 2.84-3.97) during the first (Wuhan-Hu), second (Beta), third (Delta), and fourth (Omicron) waves, respectively. Estimates based on the three data sources (cases, hospitalisations, deaths) were generally similar during the first three waves, but higher during the fourth wave for case-based estimates. Public and private sector R estimates were generally similar except during the initial lockdowns and in case-based estimates during the fourth wave.
Conclusion: Agreement between R estimates using different data sources during the first three waves suggests that data from any of these sources could be used in the early stages of a future pandemic. The high R estimates for Omicron relative to earlier waves are interesting given a high level of exposure pre-Omicron. The agreement between public and private sector R estimates highlights that clients of the public and private sectors did not experience two separate epidemics, except perhaps to a limited extent during the strictest lockdowns in the first wave.
Competing Interests: CC has received grant support from Sanofi Pasteur, US CDC, Wellcome Trust, Programme for Applied Technologies in Health (PATH), Bill & Melinda Gates Foundation and South African Medical Research Council (SA-MRC). JRCP has received funding for COVID-related work from Bill & Melinda Gates Foundation, WHO AFRO, and Wellcome Trust and serves on the Ministerial Advisory Committee for COVID-19 for the South African National Department of Health. The other authors report no known conflicts of interest. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
(Copyright: © 2023 Bingham et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)