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

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

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

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

Outcomes for select populations in each study evaluating TB patients co-infected with SARS-CoV-2 receiving corticosteroids or other immunomodulating treatment vs. not receiving such treatment (<i>Clinical Management Review)</i>.

Outcomes for select populations in each study evaluating TB patients co-infected with SARS-CoV-2 receiving corticosteroids or other immunomodulating treatment vs. not receiving such treatment (Clinical Management Review).</p

Characteristics of included studies.

BackgroundWhether SARS-CoV-2 infection and its management influence tuberculosis (TB) treatment outcomes is uncertain. We synthesized evidence on the association of SARS-CoV-2 coinfection (Coinfection Review) and its management (Clinical Management Review) on treatment outcomes among people with tuberculosis (TB) disease.MethodsWe systematically searched the literature from 1 January 2020 to 6 February 2022. Primary outcomes included: unfavorable (death, treatment failure, loss-to-follow-up) TB treatment outcomes (Coinfection and Clinical Management Review) and/or severe or critical COVID-19 or death (Clinical Management Review). Study quality was assessed with an adapted Newcastle Ottawa Scale. Data were heterogeneous and a narrative review was performed. An updated search was performed on April 3, 2023.FindingsFrom 9,529 records, we included 11 studies and 7305 unique participants. No study reported data relevant to our review in their primary publication and data had to be contributed by study authors after contact. Evidence from all studies was low quality. Eight studies of 5749 persons treated for TB (286 [5%] with SARS-CoV-2) were included in the Coinfection Review. Across five studies reporting our primary outcome, there was no significant association between SARS-CoV-2 coinfection and unfavorable TB treatment outcomes. Four studies of 1572 TB patients—of whom 291 (19%) received corticosteroids or other immunomodulating treatment—were included in the Clinical Management Review, and two addressed a primary outcome. Studies were likely confounded by indication and discordant findings existed among studies. When updating our search, we still did not identify any study reporting data relevant to this review in their primary publication.InterpretationNo study was designed to answer our research questions of interest. It remains unclear whether TB/SARS-CoV-2 and its therapeutic management are associated with unfavorable outcomes. Research is needed to improve our understanding of risk and optimal management of persons with TB and SARS-CoV-2 infection.Trial registrationRegistration: PROSPERO (CRD42022309818).</div

Additional details for each study as supplied by authors.

Additional details for each study as supplied by authors.</p

Risk of bias assessment.

BackgroundWhether SARS-CoV-2 infection and its management influence tuberculosis (TB) treatment outcomes is uncertain. We synthesized evidence on the association of SARS-CoV-2 coinfection (Coinfection Review) and its management (Clinical Management Review) on treatment outcomes among people with tuberculosis (TB) disease.MethodsWe systematically searched the literature from 1 January 2020 to 6 February 2022. Primary outcomes included: unfavorable (death, treatment failure, loss-to-follow-up) TB treatment outcomes (Coinfection and Clinical Management Review) and/or severe or critical COVID-19 or death (Clinical Management Review). Study quality was assessed with an adapted Newcastle Ottawa Scale. Data were heterogeneous and a narrative review was performed. An updated search was performed on April 3, 2023.FindingsFrom 9,529 records, we included 11 studies and 7305 unique participants. No study reported data relevant to our review in their primary publication and data had to be contributed by study authors after contact. Evidence from all studies was low quality. Eight studies of 5749 persons treated for TB (286 [5%] with SARS-CoV-2) were included in the Coinfection Review. Across five studies reporting our primary outcome, there was no significant association between SARS-CoV-2 coinfection and unfavorable TB treatment outcomes. Four studies of 1572 TB patients—of whom 291 (19%) received corticosteroids or other immunomodulating treatment—were included in the Clinical Management Review, and two addressed a primary outcome. Studies were likely confounded by indication and discordant findings existed among studies. When updating our search, we still did not identify any study reporting data relevant to this review in their primary publication.InterpretationNo study was designed to answer our research questions of interest. It remains unclear whether TB/SARS-CoV-2 and its therapeutic management are associated with unfavorable outcomes. Research is needed to improve our understanding of risk and optimal management of persons with TB and SARS-CoV-2 infection.Trial registrationRegistration: PROSPERO (CRD42022309818).</div

Additional results.

BackgroundWhether SARS-CoV-2 infection and its management influence tuberculosis (TB) treatment outcomes is uncertain. We synthesized evidence on the association of SARS-CoV-2 coinfection (Coinfection Review) and its management (Clinical Management Review) on treatment outcomes among people with tuberculosis (TB) disease.MethodsWe systematically searched the literature from 1 January 2020 to 6 February 2022. Primary outcomes included: unfavorable (death, treatment failure, loss-to-follow-up) TB treatment outcomes (Coinfection and Clinical Management Review) and/or severe or critical COVID-19 or death (Clinical Management Review). Study quality was assessed with an adapted Newcastle Ottawa Scale. Data were heterogeneous and a narrative review was performed. An updated search was performed on April 3, 2023.FindingsFrom 9,529 records, we included 11 studies and 7305 unique participants. No study reported data relevant to our review in their primary publication and data had to be contributed by study authors after contact. Evidence from all studies was low quality. Eight studies of 5749 persons treated for TB (286 [5%] with SARS-CoV-2) were included in the Coinfection Review. Across five studies reporting our primary outcome, there was no significant association between SARS-CoV-2 coinfection and unfavorable TB treatment outcomes. Four studies of 1572 TB patients—of whom 291 (19%) received corticosteroids or other immunomodulating treatment—were included in the Clinical Management Review, and two addressed a primary outcome. Studies were likely confounded by indication and discordant findings existed among studies. When updating our search, we still did not identify any study reporting data relevant to this review in their primary publication.InterpretationNo study was designed to answer our research questions of interest. It remains unclear whether TB/SARS-CoV-2 and its therapeutic management are associated with unfavorable outcomes. Research is needed to improve our understanding of risk and optimal management of persons with TB and SARS-CoV-2 infection.Trial registrationRegistration: PROSPERO (CRD42022309818).</div