Original Research

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
Southern African Journal of Infectious Diseases | Vol 38, No 1 | a550 | DOI: https://doi.org/10.4102/sajid.v38i1.550 | © 2023 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 | This work is licensed under CC Attribution 4.0
Submitted: 30 June 2023 | Published: 18 December 2023

About the author(s)

Lucas E. Hermans, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
Petro Booysen, Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
Linda Boloko, Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
Marguerite Adriaanse, Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
Timothy J. de Wet, Department of Medical Microbiology, Faculty of Health Sciences, University of Cape town, Cape Town, South Africa
Aimee R. Lifson, Department of Medicine, Faculty of Internal Medicine, Groote Schuur Hospital, Cape Town, South Africa
Naweed Wadee, Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
Nectarios Papavarnavas, Institute of Infectious Disease and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
Gert Marais, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; and, Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
Nei-yuan Hsiao, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
Michael-Jon Rosslee, Department of Medicine, Victoria Hospital, Wynberg, Cape Town, South Africa
Gregory Symons, Department of Medicine, Division of Pulmonology, Groote Schuur Hospital, Cape Town, South Africa
Gregory L. Calligaro, Department of Medicine, Division of Pulmonology, Groote Schuur Hospital, Cape Town, South Africa
Arash Iranzadeh, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
Robert J. Wilkinson, Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; and, The Francis Crick Institute, London, United Kingdom; and, Department of Infectious Disease, Imperial College, London, United Kingdom
Ntobeko A.B. Ntusi, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; and, 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
Carolyn Williamson, Department of Pathology, IDM and CIDRI-Africa, Division of Medical Virology, University of Cape Town, Cape Town, South Africa
Mary-Ann Davies, Department of Health and Wellness, Western Cape Government, Cape Town, South Africa; and, Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape Town, Cape Town, South Africa
Graeme Meintjes, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; and, Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
Sean Wasserman, Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; and, 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

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

Sustainable Development Goal

Goal 3: Good health and well-being

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