National average R for each consecutive lockdown level, with 2.5% and 97.5% credible intervals, based on cases (R_cases), admissions (R_admissions) and deaths (R_deaths).

National average R for each consecutive lockdown level, with 2.5% and 97.5% credible intervals, based on cases (Rcases), admissions (Radmissions) and deaths (Rdeaths).</p

Flow diagram of study participants.

<p>Flow diagram of study participants.</p

Province-level R estimates for each data endpoint from early March 2020 through 25 October 2022.

R estimated on 7-day sliding windows. Results reflect median values (between imputations) of median R estimates and associated 2.5% and 97.5% credible intervals. L = Level. Red-shaded areas indicate the period during which civil unrest caused severe disruptions to surveillance in KwaZulu-Natal and Gauteng provinces; grey-shaded areas indicate gradually diminishing effects on R estimates.</p

Toxicity outcomes during 12 months after initiation of TB co-treatment by modification made to the PI-containing regimen.

a<p>Toxicity outcomes in children on superboosted LPV/r significantly different to children taking ritonavir only if ≥ grade 1 is selected as the cut-off.</p

Additional results and analyses.

ObjectivesThe 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.MethodsR 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.ResultsNationally, 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.ConclusionAgreement 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.</div

R estimates by sector, based on rt-PCR-confirmed COVID-19 cases, hospitalisations, and deaths.

R estimates by sector, based on rt-PCR-confirmed COVID-19 cases (upper panel), hospitalisations (middle panel), and deaths (lower panel), South Africa. R estimates were generated using 7-day sliding windows. Results reflect median values (between imputations) of median R estimates and associated 2.5% and 97.5% credible intervals. L = Level. Red-shaded areas indicate the period during which civil unrest caused severe disruptions to surveillance in KwaZulu-Natal and Gauteng provinces; grey-shaded areas indicate gradually diminishing effects on R estimates.</p

R estimates for each data endpoint, based on national daily time series of rt-PCR-confirmed cases, hospitalisations, and deaths.

R estimates for each data endpoint (upper panel), South Africa, based on (lower panel) national daily time series of rt-PCR-confirmed cases, hospitalisations, and deaths. R estimated using 7-day sliding windows, from early March 2020 through 25 April. Results reflect median values (between imputations) of median R estimates and associated 2.5% and 97.5% credible intervals. L = Level. Red-shaded areas indicate the period during which civil unrest caused severe disruptions to surveillance in KwaZulu-Natal and Gauteng provinces; grey-shaded areas indicate gradually diminishing effects on R estimates.</p

Virologic, clinical and immunological outcomes at 6 and 12 months between children co-treated for TB stratified by the modifications made to their PI-based regimen and comparisons not co-treated for TB.

a<p>super-boosted LPV/r group significantly different from comparisons p<0.05,</p>b<p>double dose LPV/r group significantly different from comparisons p<0.05.</p>c<p>ritonavir group significantly different from Neverest comparisons.</p

Characteristics of children who initiated TB treatment by modification made to antiretroviral treatment (ART) regimen.

*<p>Percents add up to >100% because more than one type of TB or diagnostic intervention was possible in the same child.</p>**<p>Other diagnostic evaluations include lymph node biopsy (2), gastric washing (1).</p>***<p>Other medications include prednisone (3), ciprobay (3), ethambutol (3).</p

Pre-antiretroviral treatment (ART) characteristics stratified by the modification made to the ART regimen among 294 children treated for TB and 232 comparison children not treated for TB at each site.

a<p>Denominators in each group are as shown.</p>b<p>superboosted LPV/r group significantly different from Shezi comparisons p<0.05.</p>c<p>double dose LPV/r group significantly different from Shezi comparisons p<0.05.</p>d<p>ritonavir group significantly different from Neverest comparisons p<0.05.</p