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Difference in Mortality among Individuals Admitted to Hospital with COVID-19 during the First and Second Waves in South Africa: A Cohort Study

Our take —

This analysis examined factors associated with mortality among hospitalized persons with COVID-19 in South Africa during the first two pandemic waves (July 2020 and January 2021). The respective peaks of the first and second waves of the pandemic were in July 2020 and January 2021. The second wave was more severe, as evidenced by higher rates of cases, admissions, and deaths. The authors hypothesized that the severity of the second wave could be due to the predominance of the new Beta lineage of the virus. Using comprehensive national surveillance data, authors demonstrated that characteristics differed across patients hospitalized across waves, with Black individuals making up a higher percentage in the first vs second wave (78.6% vs. 68.1%). A major limitation of the paper is that while measures of disease frequency (e.g., odds) were reported separately for waves 1 and 2, measures of association (e.g., odds ratios) were only presented for wave 2, making it difficult to clearly decipher how associations between patient characteristics and clinical outcomes might have differed between the waves. Furthermore, some measures of frequency may be underestimates as people without access to care or who died outside of hospitals were not captured in the surveillance data. Notwithstanding, this paper presents important information on the dynamics of COVID-19 in South Africa, demonstrating a more severe second wave compared to the first and an overall high case-fatality risk among hospitalized patients.

Study design

Prospective Cohort

Study population and setting

This study examined characteristics and risk factors for mortality among patients hospitalized with COVID-19 in South Africa from March 5, 2020, to March 27, 2021 (the first two waves of the pandemic). Five distinct periods were defined: pre-wave 1 (March-June 6, 2020), wave 1 (June 7-Aug 22, 2020), post-wave 1 (Aug 23-Nov 14, 2020), wave 2 (Nov 15, 2020-Feb 6, 2021), and post-wave 2 (Feb 7-March 27, 2021). National active surveillance data of persons with SARS-CoV-2 positive RT-PCR or antigen test with hospital stay of at least one day was analyzed, regardless of a patient’s age or reason for hospitalization. Information on patients’ socio-demographic, occupational factors, and comorbidity was collected using a modified WHO COVID-19 case reporting tool. Odds ratios were obtained using multivariable logistic regression (with a random effect on admission facility). Incomplete or missing data were handled through imputation.

Summary of Main Findings

A total of 1,545,431 SARS-CoV-2 cases and 227,932 COVID-19 hospital admissions were reported within the period. Of 219,565 COVID-19 patients with information on in-hospital outcome (96.3%), 51,037 died (case fatality risk: 23.28%). The second wave was more severe than the first wave as evidenced by higher peak case fatality risk (29.34% vs. 21.80%, p < 0.0001), in-hospital deaths (8.3 deaths/100,000 people vs 3.6 deaths/100,000 people), admissions (27.9 admissions/100,000 people vs 16.1 admissions/100,000 people), average weekly growth rate of admissions (43% vs. 20%), and cases (240.4 cases/100,000 people vs 136.0 cases /100,000 people). Black individuals made up a higher proportion of COVID-19 hospitalizations in the first wave vs. the second (78.6% vs. 68.1%), while the reverse was true for individuals who identified as mixed race (7.1% vs. 13.6%); percentages were as follows for white individuals (9.2% vs. 11.6%) and Indian individuals (5.2% vs. 6.8%). Comorbidities were more common among admitted patients in the first wave compared to the second (60.7% vs. 55.0%). Compared to those < 40 years, risk of mortality was higher for those aged 40-64 years (OR: 3.17, 95% CI: 3.05-3.30) and those 65+ (OR: 7.89, 95% CI: 7.58-8.22) during the period. Overall, being male was associated with a 30% increased risk of mortality, while being Black, Mixed race, and of Indian race were respectively associated with 18%, 16%, 30% significantly increased risk of mortality compared to being white.

Study Strengths

Data came from a comprehensive national surveillance system that captured information from all South African hospitals that admitted COVID-19 patients and covered the entirety of the first and second waves of the pandemic in the country. In addition, the authors performed robust analyses that included adjustment for covariates and imputation for missing or incomplete data.


The reported measures of frequency are likely to be underestimates as information on persons without access to care or who died outside the hospital system were not captured, potentially leading to some bias in the findings. While the authors presented measures of disease frequency (e.g., odds of admission for the respective waves, comparisons of measures of association (odds ratios) across individuals were only presented for wave 2, making it difficult to unequivocally decipher how adjusted relationships between patient characteristics and the clinical outcomes differed across the waves. Obesity, and some other important factors could not be adjusted for, due to incomplete capturing of these data within the surveillance system. Despite these limitations, the use of national surveillance system data from all South African hospitals with COVID-19 patients provides, overall, a complete picture of changes in severity and mortality across waves.

Value added

This study improves understanding about changing dynamics of COVID-19 hospitalizations and death in South Africa, which currently has the highest number of recorded COVID-19 cases and deaths within sub-Saharan Africa.

This review was posted on: 15 August 2021