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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 (preprint)
medrxiv; 2022.
Preprint
em Inglês
| medRxiv | ID: ppzbmed-10.1101.2022.07.22.22277932
ABSTRACT
Objectives We aimed 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 We estimated R from March 2020 through April 2022, nationally and by province, based on time series of rt-PCR-confirmed cases, hospitalizations, and hospital-associated deaths, using a method which models daily incidence as a weighted sum of past incidence. We also estimated R 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 cases-based estimates were higher during the fourth wave. Public and private sector R estimates were generally similar except during the initial lockdowns and in case-based estimates during the fourth wave. Discussion Agreement between R estimates using different data sources during the first three waves suggests data from any of these sources could be used in early stages of a future pandemic. High R estimates for Omicron relative to earlier waves is interesting given a high level of exposure pre-Omicron. The agreement between public and private sector R estimates highlights the fact that clients of the public and private sectors did not experience two separate epidemics, except perhaps to a limited extent during the strictest lockdowns during the first wave.
Texto completo:
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Coleções:
Preprints
Base de dados:
medRxiv
Assunto principal:
Morte
/
COVID-19
Idioma:
Inglês
Ano de publicação:
2022
Tipo de documento:
Preprint
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