The burden of SARS-CoV-2 Infection and Severe Illness in South Africa March 2020-August 2022: A synthesis of epidemiological data
Authors: Bolton Larisse , Tempia Stefano , Walaza Sibongile , Jassat Waasila , Sun Kaiyuan , Bradshaw Debbie , Dorrington Rob , Kleynhans Jackie , Martenson Neil , von Gottberg Anne , Wolter Nicole , Pulliam Juliet R.C. , Cohen Cheryl 
Published: November 2024

Introduction

Data on burden of SARS-CoV-2 infections by age group and for different severity levels are lacking. We estimated the South African SARS-CoV-2 disease burden and severity, describing changes in the shape of the disease burden pyramid with successive waves.

Methods

We estimated SARS-CoV-2 medically and non-medically attended illness stratified by severity (mild, severe non-fatal, and fatal) during the initial five waves, spanning 1 March 2020 through 13 August 2022. We utilised individual-level national surveillance, healthcare-utilisation and serosurvey data to calculate wave-specific hospitalisation-fatality (HFR) and infection-fatality ratios (IFR). We estimated wave-specific incidence rates per 100,000 population with 95% confidence intervals derived from bootstrapping the individual-level data.

Results

On 13 August 2022, the estimated cumulative number of SARS-CoV-2 infections in South Africa was 105 million, of which 399,886 (0.38%) were severe non-fatal and 258,754 (0.25%) fatal. 29% of severe non-fatal illness and 55% of deaths occurred outside hospital. The highest burden of severe and fatal illness was during the Delta wave (wave 3), and the HFR across the initial three waves was similar (range 31%-34%). Although there were more infections during the Omicron BA.1 wave (wave 4), there was a substantial reduction in HFR (14%). Successive waves saw a reduction in the rate of increase in mortality and hospitalisations with increasing age.

Conclusions

The substantial South African national burden of SARS-CoV-2 for the initial five waves contradicts the belief of minimal impact in Africa. A high proportion of severe non-fatal and fatal illness occurred outside of hospital, highlighting the importance of studies of health-seeking and vital registration systems to document the full burden of illness. Highest burden of severe illness and death was in the Delta wave. Following Omicron emergence severe illness reduced, and age-distribution for the incidence of medically attended severe non-fatal illness shifted to a J-shape, possibly reflecting the shift from widespread transmission to an endemic pattern.

KEY MESSAGES

What is already known on this topic?

As SARS-CoV-2 spread globally, initial assumptions painted a bleak picture for Africa due to its existing challenges in healthcare service delivery, multimorbidity, poverty and lack of resources needed to fight the infection. The number of cases and deaths reported during the pandemic seemed to contradict these initial assumptions. South Africa recorded over 4 million laboratory-confirmed cases of COVID-19 during the first three years of the pandemic. However, it is estimated that only a tenth of the cases were diagnosed. With the lack of testing, inconsistent healthcare-seeking behaviour, changes in attack, reinfection and symptomatic rates, the true burden of SARS-CoV-2 across the different age groups and severity levels were largely unknown. Although real-time epidemiological data was crucial for informing intervention strategies throughout the pandemic, it is now essential to quantify and describe the evolution of the epidemiology over successive pandemic waves as more information was made available.

What this study adds?

We found a high burden of severe illness and death in the first three waves of SARS-CoV-2, peaking in the third (Delta) wave. The emergence of the Omicron BA.1 variant was associated with very high rates of infection but substantial reductions in disease severity. Incidence of severe illness and hospitalisation fatality, generally increased with increasing age. Successive waves saw a reduction in the rate of the increase in mortality with increasing age and increases in hospitalisation fatality ratios in children below 5 years of age suggesting shift from the epidemic state to a J-shaped distribution in mortality, typical of seasonal respiratory viruses. Notably a high proportion of severe illness (29%) and death (55%) occurred outside hospital.

How this study might affect research, practice or policy?

Our study provides insights into the changes in patterns of infection and disease following introduction of a novel pathogen into a susceptible population which may be useful for future pandemic planning. The high proportion of undiagnosed and unreported illness and the high proportion of severe illness and death occurring outside of the hospital suggest that strengthening of access to diagnosis and care is needed in our setting.