JMIR Publications

ABSTRACT

Background:

Emerging SARS-CoV-2 variants have been attributed to the occurrence of secondary, tertiary, and quaternary 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 5 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.

Objective:

In this study, descriptive and inferential statistical analysis was conducted 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 in this study involved the collation and stratification of South African COVID-19 epidemiological data, covariance, regression analysis of the epidemiological data, normalisation, and comparative inferential statistical analysis through null hypothesis testing (Paired T-tests).

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 were similar while the COVID-19 transmission rate was higher in the third, fourth, and fifth COVID-19 epidemic waves than in the aforementioned. Most COVID-19 hospitalised cases in South Africa were hospitalised in the general ward (60.0%-79.1%). COVID-19 patients on oxygen were the second-largest admission status (11.2%-16.8%) followed by the COVID-19 patients in the intensive care unit (8.07%-16.7%). Most COVID-19 hospitalised cases in South Africa’s first, second, third, and fourth COVID-19 epidemic wave period were in the ages of 40 to 49 years (16.8%-20.4%) and 50 to 59 years (19.8%-25.3%) respectively. COVID-19 admitted patients 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 years to 29 years increased after each consecutive COVID-19 epidemic wave while for age groups between 30 years to 79 years they decreased. Most COVID-19 hospitalised deaths in South Africa in the first, second, third, fourth, and fifth COVID-19 epidemic wave period were in the ages of 50 years to 59 years (15.8% to 24.8%), 60 years to 69 years (15.9% to 29.5% ) and 70 years to 79 years (16.6% to 20.7%) years respectively.

Conclusions:

The relaxation of COVID-19 NPI 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. While COVID-19 vaccination in South Africa was strongly associated with a decrease in COVID-19 hospitalisation and severity in South Africa.