{"doi":"10.4102/sajid.v38i1.550","title":"Changing character and waning impact of COVID-19 at a tertiary centre in Cape Town, South Africa","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.","journal":"Southern African Journal of Infectious Diseases","year":2023,"id":415124,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8756,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1196950,"name":"Petro Booysen","orcid":"0009-0004-9170-0340","position":1,"is_corresponding":false},{"id":110199,"name":"Linda Boloko","orcid":"0000-0002-2418-0048","position":2,"is_corresponding":false},{"id":804016,"name":"Marguerite Adriaanse","orcid":"0009-0001-2895-8160","position":3,"is_corresponding":false},{"id":811666,"name":"Timothy J. de Wet","orcid":"0000-0002-3978-5322","position":4,"is_corresponding":false},{"id":811665,"name":"Aimee Lifson","orcid":"0009-0005-3253-0430","position":5,"is_corresponding":false},{"id":1196951,"name":"Naweed Wadee","orcid":"0000-0002-4204-6686","position":6,"is_corresponding":false},{"id":811667,"name":"Nectarios Papavarnavas","orcid":"0000-0001-9861-7428","position":7,"is_corresponding":false},{"id":634078,"name":"Gert Marais","orcid":"0000-0003-1477-6101","position":8,"is_corresponding":false},{"id":614572,"name":"Marvin Hsiao","orcid":"0000-0003-4926-6216","position":9,"is_corresponding":false},{"id":912606,"name":"Michael-Jon Rosslee","orcid":"0009-0006-9025-5710","position":10,"is_corresponding":false},{"id":1196952,"name":"Gregory Symons","orcid":"0009-0005-0440-7777","position":11,"is_corresponding":false},{"id":110204,"name":"Greg Calligaro","orcid":"0000-0001-7324-0775","position":12,"is_corresponding":false},{"id":621539,"name":"Arash Iranzadeh","orcid":"0000-0003-4413-2569","position":13,"is_corresponding":false},{"id":266683,"name":"Robert J. Wilkinson","orcid":"0000-0002-2753-1800","position":14,"is_corresponding":false},{"id":91456,"name":"Ntobeko A. B. Ntusi","orcid":"0000-0003-2347-7883","position":15,"is_corresponding":false},{"id":502204,"name":"Carolyn Williamson","orcid":null,"position":16,"is_corresponding":false},{"id":110157,"name":"Mary‐Ann Davies","orcid":"0000-0001-8496-6475","position":17,"is_corresponding":false},{"id":292884,"name":"Graeme Meintjes","orcid":"0000-0003-1196-4414","position":18,"is_corresponding":false},{"id":308893,"name":"Sean Wasserman","orcid":"0000-0002-3508-6719","position":19,"is_corresponding":false},{"id":1196949,"name":"Lucas E. Hermans","orcid":"0000-0002-8741-5852","position":0,"is_corresponding":true}],"reference_count":18,"raw_metadata":null,"created_at":"2026-07-19T01:22:08.814145Z","pmid":"38223432","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}