Southern African Journal of Infectious Diseases (Dec 2023)

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
https://doi.org/10.4102/sajid.v38i1.550
Journal volume & issue
Vol. 38, no. 1
pp. e1 – e9

Abstract

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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.

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