Changing character and waning impact of COVID-19 at a tertiary centre in Cape Town, South Africa

Lucas E Hermans; Petro Booysen; Linda Boloko; Marguerite Adriaanse; Timothy J de Wet; Aimee R Lifson; Naweed Wadee; Nectarios Papavarnavas; Gert Marais; Nei-Yuan Hsiao; Michael-Jon Rosslee; Gregory Symons; Gregory L Calligaro; Arash Iranzadeh; Robert J Wilkinson; Ntobeko A B Ntusi; Carolyn Williamson; Mary-Ann Davies; Graeme Meintjes; Sean Wasserman

doi:10.4102/sajid.v38i1.550

Changing character and waning impact of COVID-19 at a tertiary centre in Cape Town, South Africa

S Afr J Infect Dis. 2023 Dec 18;38(1):550. doi: 10.4102/sajid.v38i1.550. eCollection 2023.

Authors

Lucas E Hermans¹, Petro Booysen², Linda Boloko², Marguerite Adriaanse³, Timothy J de Wet⁴, Aimee R Lifson⁵, Naweed Wadee², Nectarios Papavarnavas⁶, Gert Marais^{7

8}, Nei-Yuan Hsiao⁷, Michael-Jon Rosslee⁹, Gregory Symons¹⁰, Gregory L Calligaro¹⁰, Arash Iranzadeh¹¹, Robert J Wilkinson^{2

12

13}, Ntobeko A B Ntusi^{1

14}, Carolyn Williamson¹⁵, Mary-Ann Davies^{16

17}, Graeme Meintjes^{1

2}, Sean Wasserman^{2

18}

Affiliations

¹ Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
² Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
³ Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa.
⁴ Department of Medical Microbiology, Faculty of Health Sciences, University of Cape town, Cape Town, South Africa.
⁵ Department of Medicine, Faculty of Internal Medicine, Groote Schuur Hospital, Cape Town, South Africa.
⁶ Institute of Infectious Disease and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa.
⁷ Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
⁸ Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
⁹ Department of Medicine, Victoria Hospital, Wynberg, Cape Town, South Africa.
¹⁰ Department of Medicine, Division of Pulmonology, Groote Schuur Hospital, Cape Town, South Africa.
¹¹ Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa.
¹² The Francis Crick Institute, London, United Kingdom.
¹³ Department of Infectious Disease, Imperial College, London, United Kingdom.
¹⁴ South African Medical Research Council, University of Cape Town Extramural Research Unit on the Intersection of Noncommunicable Diseases and Infectious Diseases, Cape Town, South Africa.
¹⁵ Department of Pathology, IDM and CIDRI-Africa, Division of Medical Virology, University of Cape Town, Cape Town, South Africa.
¹⁶ Department of Health and Wellness, Western Cape Government, Cape Town, South Africa.
¹⁷ Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape Town, Cape Town, South Africa.
¹⁸ Institute for Infection and Immunity, St George's, University of London, London, United Kingdom.

Abstract

Background: The emergence of genetic variants of SARS-CoV-2 was associated with changing epidemiological characteristics throughout coronavirus disease 2019 (COVID-19) pandemic in population-based studies. Individual-level data on the clinical characteristics of infection with different SARS-CoV-2 variants in African countries is less well documented.

Objectives: To describe the evolving clinical differences observed with the various SARS-CoV-2 variants of concern and compare the Omicron-driven wave in infections to the previous Delta-driven wave.

Method: We performed a retrospective observational cohort study among patients admitted to a South African referral hospital with COVID-19 pneumonia. Patients were stratified by epidemiological wave period, and in a subset, the variants associated with each wave were confirmed by genomic sequencing. Outcomes were analysed by Cox proportional hazard models.

Results: We included 1689 patients were included, representing infection waves driven predominantly by ancestral, Beta, Delta and Omicron BA1/BA2 & BA4/BA5 variants. Crude 28-day mortality was 25.8% (34/133) in the Omicron wave period versus 37.1% (138/374) in the Delta wave period (hazard ratio [HR] 0.68 [95% CI 0.47-1.00] p = 0.049); this effect persisted after adjustment for age, gender, HIV status and presence of cardiovascular disease (adjusted HR [aHR] 0.43 [95% CI 0.28-0.67] p < 0.001). Hospital-wide SARS-CoV-2 admissions and deaths were highest during the Delta wave period, with a decoupling of SARS-CoV-2 deaths and overall deaths thereafter.

Conclusion: There was lower in-hospital mortality during Omicron-driven waves compared with the prior Delta wave, despite patients admitted during the Omicron wave being at higher risk.

Contribution: This study summarises clinical characteristics associated with SARS-CoV-2 variants during the COVID-19 pandemic at a South African tertiary hospital, demonstrating a waning impact of COVID-19 on healthcare services over time despite epidemic waves driven by new variants. Findings suggest the absence of increasing virulence from later variants and protection from population and individual-level immunity.

Keywords: COVID-19; Delta; Omicron; SARS-CoV-2; clinical characteristics; observational study.

Abstract

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