The Impact of Non-Pharmaceutical Interventions on the First COVID-19 Epidemic Wave in South Africa

Mabuka, Thabo; Ncube, Nesisa; Ross, Michael J.; Silaji, Andrea; Macharia, Willie; Ndemera, Tinashe; Lemeke, Tlaleng

doi:10.1101/2021.06.29.21259625

Cited by 4 publications

(8 citation statements)

References 39 publications

(38 reference statements)

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“…South Africa’s COVID-19 NPI health policy response to the COVID-19 epidemic waves in South Africa was implemented in the form of National Lockdown Alert Level policies. The National Lockdown Alert Level policies were largely entry and exit screening at borders, limitations of movements and gatherings, closure and limitations of institutions and business activities, ban and limiting of alcohol and tobacco industries, isolation, quarantine of potentially infected persons, contact-tracing protocols, use of personal protective equipment, and hygienic protocols [ 38 , 42 ]. The adjustment in the alert levels resulted in eased movement restrictions compared with their predecessors.…”

Section: Resultsmentioning

confidence: 99%

“…The daily effective contact rate is the average number of adequate contacts per infective per day; it is directly proportional to the reproductive number [ 43 ]. Mabuka et al [ 38 ] showed through stochastic COVID-19 modeling that adjusting the NPIs by 1 Alert Level in South Africa translated into a reduction in the effective SARS-CoV-2 daily contact number by 4.13% to 14.6%. Thus, the relaxation of NPIs in South Africa after each consecutive COVID-19 epidemic wave could have possibly contributed to the increase in COVID-19 transmissibility in the COVID-19 epidemic waves.…”

Section: Discussionmentioning

confidence: 99%

“…The South African COVID-19 hospitalization data obtained in this study were composed of the number of facilities reporting, admission status data (daily COVID-19 hospital admission cases, hospitalized in high care, intensive care unit [ICU], isolation ward, on oxygen, and ventilator), cumulative COVID-19 admission age profile, cumulative COVID-19 hospital deaths age profile, and cumulative COVID-19 patients discharged alive. The COVID-19 hospital daily discharge rate (DR) and case fatality rate (CFR) were then calculated based on the methodology described in the study by Mabuka et al [ 38 ]. Weekly South African natural and excess (natural) deaths were obtained from the South African Medical Research Council [ 39 ] for the reporting period of December 29, 2019, to August 20, 2022.…”

Section: Methodsmentioning

confidence: 99%

“…Weekly South African natural and excess (natural) deaths were obtained from the South African Medical Research Council [ 39 ] for the reporting period of December 29, 2019, to August 20, 2022. The weekly unreported excess deaths (natural) to COVID-19 death ratio (ECDR) was then calculated based on the methodology in the study by Mabuka et al [ 38 ].…”

Section: Methodsmentioning

confidence: 99%

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The Impact of SARS-CoV-2 Lineages (Variants) and COVID-19 Vaccination on the COVID-19 Epidemic in South Africa: Regression Study

Mabuka¹,

Naidoo²,

Ncube³

et al. 2023

JMIRx Med

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Background Emerging SARS-CoV-2 variants have been attributed to the occurrence of secondary, tertiary, quaternary, and quinary COVID-19 epidemic waves threatening vaccine efforts owing to their immune invasiveness. Since the importation of SARS-CoV-2 in South Africa, with the first reported COVID-19 case on March 5, 2020, South Africa has observed 5 consecutive COVID-19 epidemic waves. The evolution of SARS-CoV-2 has played a major role in the resurgence of COVID-19 epidemic waves in South Africa and across the globe. Objective We aimed to conduct descriptive and inferential statistical analysis on South African COVID-19 epidemiological data to investigate the impact of SARS-CoV-2 lineages and COVID-19 vaccinations in South African COVID-19 epidemiology. Methods The general methodology involved the collation and stratification, covariance, regression analysis, normalization, and comparative inferential statistical analysis through null hypothesis testing (paired 2-tailed t tests) of South African COVID-19 epidemiological data. Results The mean daily positive COVID-19 tests in South Africa’s first, second, third, fourth, and fifth COVID-19 epidemic wave periods were 11.5% (SD 8.58%), 11.5% (SD 8.45%), 13.3% (SD 9.72%), 13.1% (SD 9.91%), and 14.3% (SD 8.49%), respectively. The COVID-19 transmission rate in the first and second COVID-19 epidemic waves in South Africa was similar, while the COVID-19 transmission rate was higher in the third, fourth, and fifth COVID-19 epidemic waves than in the aforementioned waves. Most COVID-19 hospitalized cases in South Africa were in the general ward (60%-79.1%). Patients with COVID-19 on oxygen were the second-largest admission status (11.2%-16.8%), followed by patients with COVID-19 in the intensive care unit (8.07%-16.7%). Most patients hospitalized owing to COVID-19 in South Africa’s first, second, third, and fourth COVID-19 epidemic waves were aged between 40 and 49 years (16.8%-20.4%) and 50 and 59 years (19.8%-25.3%). Patients admitted to the hospital owing to COVID-19 in the age groups of 0 to 19 years were relatively low (1.98%-4.59%). In general, COVID-19 hospital admissions in South Africa for the age groups between 0 and 29 years increased after each consecutive COVID-19 epidemic wave, while for age groups between 30 and 79 years, hospital admissions decreased. Most COVID-19 hospitalization deaths in South Africa in the first, second, third, fourth, and fifth COVID-19 epidemic waves were in the ages of 50 to 59 years (15.8%-24.8%), 60 to 69 years (15.9%-29.5%), and 70 to 79 years (16.6%-20.7%). Conclusions The relaxation of COVID-19 nonpharmaceutical intervention health policies in South Africa and the evolution of SARS-CoV-2 were associated with increased COVID-19 transmission and severity in the South African population. COVID-19 vaccination in South Africa was strongly associated with a decrease in COVID-19 hospitalization and severity in South Africa.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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The Impact of SARS-CoV-2 Lineages (Variants) and COVID-19 Vaccination on the COVID-19 Epidemic in South Africa: Regression Study

Mabuka¹,

Naidoo²,

Ncube³

et al. 2023

JMIRx Med

Self Cite

View full text Add to dashboard Cite

show abstract

“…The effectiveness of these lockdowns remains an ongoing debate among scholars. 4,5 A strict level 5 lockdown was implemented soon after on 26 March 2020. However, even the harsh restrictions on movement and social interactions under this alert level were not enough to contain or eliminate the virus and prevent the onward spread of infection.…”

Section: Covid-19 Epidemiological Trajectory and Outlookmentioning

confidence: 99%

Adding up the numbers: COVID-19 in South Africa

Suliman

Mtsweni

2022

S. Afr. J. Sci.

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The Impact of SARS-CoV-2 Lineages (Variants) on the COVID-19 Epidemic in South Africa

Mabuka¹,

Naidoo²,

Ncube³

et al. 2021

Preprint

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Emerging SARS-CoV-2 variants have been attributed to the occurrence of secondary and tertiary COVID-19 epidemic waves and also threatening vaccine efforts due to their immune invasiveness. Since the importation of SARS-CoV-2 in South Africa, with the first reported COVID-19 case on the 5th of March 2020, South Africa has observed 3 consecutive COVID-19 epidemic waves. The evolution of SARS-CoV-2 has played a significant role in the resurgence of COVID-19 epidemic waves in South Africa and across the globe. South Africa has a unique observation of the evolution of SARS-CoV-2, with distinct SARS-CoV-2 lineages dominating certain epidemic periods. This unique observation allows for an investigation of the detected SARS-CoV-2 lineages' impact on COVID-19 transmissibility and severity through analysis of epidemiological data. In this study, inferential statistical analysis was conducted on South African COVID-19 epidemiological data to investigate the impact of SARS-CoV-2 lineages in the South African COVID-19 epidemiology. The general methodology in this study involved the collation of South African COVID-19 epidemiological data, the regression and normalisation of the epidemiological data, and inferential statistical analysis. This study shows that the evolution of SARS-CoV-2 resulted in an increase in COVID-19 transmissibility and severity in South Africa. The Delta SARS-CoV-2 VOC resulted in increased COVID-19 transmissibility in the South African population by 53.9 to 54.8 % more than the Beta SARS-CoV-2 VOC and the predominantly B.1.1.54, B.1.1.56 C.1 SA SARS-CoV-2 lineage cluster. The Beta SARS-CoV-2 VOC resulted in more severe COVID-19 in South Africa than the Delta SARS-CoV-2 VOC. While, both the Beta and Delta SARS-CoV-2 VOC resulted in more severe COVID-19 than the initial SARS-CoV-2 lineages detected in the South African first epidemic wave period. The Delta, Beta SARS-CoV-2 VOCs, and the predominantly B.1.1.54, B.1.1.56 C.1 SA SARS-CoV-2 lineage cluster were observed to cause similar COVID-19 hospital case fatality and discharge rates in South African hospitals.

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The Impact of Non-Pharmaceutical Interventions on the First COVID-19 Epidemic Wave in South Africa

Cited by 4 publications

References 39 publications

The Impact of SARS-CoV-2 Lineages (Variants) and COVID-19 Vaccination on the COVID-19 Epidemic in South Africa: Regression Study

The Impact of SARS-CoV-2 Lineages (Variants) and COVID-19 Vaccination on the COVID-19 Epidemic in South Africa: Regression Study

Adding up the numbers: COVID-19 in South Africa

The Impact of SARS-CoV-2 Lineages (Variants) on the COVID-19 Epidemic in South Africa

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