On the 5th of March 2020, South Africa reported its first cases of COVID-19. This signalled the onset of the first COVID-19 epidemic wave in South Africa. The response by the Government of South Africa to the COVID-19 epidemic in South Africa was the use of non-pharmaceutical interventions (NPIs). In this study, a semi-reactive COVID-19 model, the ARI COVID-19 SEIR model, was used to investigate the impact of NPIs in South Africa to understand their effectiveness in the reduction of COVID-19 transmission in the South African population. This study also investigated the COVID-19 testing, reporting, hospitalised cases and excess deaths in the first COVID-19 epidemic wave in South Africa.

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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ObjectiveIn this study, we investigated the impact of COVID-19 NPIs in South Africa to understand their effectiveness in the reduction of transmission of COVID-19 in the South African population. This study also investigated the COVID-19 testing, reporting, hospitalised cases and excess deaths in the first wave of the COVID-19 epidemic in South Africa. MethodsA semi-reactive stochastic COVID-19 model, the ARI COVID-19 SEIR model, was used to investigate the impact of NPIs in South Africa to understand their effectiveness in the reduction of COVID-19 transmission in the South African population. COVID-19 testing, reporting, hospitalised cases and excess deaths in the first COVID-19 epidemic wave in South Africa were investigated using descriptive statistics.FindingsThe general trend in population movement in South African locations shows that the COVID-19 NPIs (National Lockdown Alert Levels 5,4,3,2) were approximately 30% more effective in reducing population movement concerning each increase by 1 Alert Level. The translated reduction in the effective SARS-CoV-2 daily contact number (β) was only 4.13 % to 14.6 % concerning increasing Alert Levels. Due to implemented NPIs, the effective SARS-CoV-2 daily contact number in the first COVID-19 epidemic wave in South Africa was reduced by 58.1-71.1 % while the peak was delayed by 84 days. The estimated COVID-19 reproductive number was between 1.98 to 0.40. During South Africa’s first COVID-19 epidemic wave, the estimated mean for the COVID-19 general ward, intensive care unit, on oxygen, high care, on ventilator, in isolation ward admission status in South African hospital was 58.5 %, 95% CI [58.1,59.0], 13.4 %, 95% CI [13.1,13.7], 13.3 %, 95% CI [12.6,14.0], 6.37 %, 95% CI [6.23,6.51], 6.29 %, 95% CI [6.02,6.55], 2.13 %, 95% CI [1.87,2.43] respectively. The estimated mean South African COVID-19 patient discharge rate was 11.9 days per patient. While the estimated mean of the South African COVID-19 patient case fatality rate (CFR) in hospital and outside the hospital was 2.06 %, 95% CI [1.86,2.25] (deaths per admitted patients) and 2.30 %, 95% CI [1.12,3.83](deaths per severe and critical cases) respectively.ConclusionThe results from this study show that the COVID-19 NPI policies implemented by the Government of South Africa played a significant role in the reduction of COVID-19 active, hospitalised cases and deaths in South Africa’s first COVID-19 epidemic wave.

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.