Evidence map›Paper›PMID 38223432›Full record

ArticleSouthern African journal of infectious diseases2023

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 and 10 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Southern African journal of infectious diseases, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact, top 47% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 0 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors at 7 institutions in 3 countries.

Lucas E HermansDepartment of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0002-8741-5852
Petro BooysenCentre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0009-0004-9170-0340
Linda BolokoCentre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0002-2418-0048
Marguerite AdriaanseDivision of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0009-0001-2895-8160
Timothy J de WetDepartment of Medical Microbiology, Faculty of Health Sciences, University of Cape town, Cape Town, South Africa.ORCID https://orcid.org/0000-0002-3978-5322
Aimee R LifsonDepartment of Medicine, Faculty of Internal Medicine, Groote Schuur Hospital, Cape Town, South Africa.ORCID https://orcid.org/0009-0005-3253-0430
Naweed WadeeCentre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0002-4204-6686
Nectarios PapavarnavasInstitute of Infectious Disease and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0001-9861-7428
Gert MaraisDivision of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0003-1477-6101
Nei-Yuan HsiaoDivision of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0003-4926-6216
Michael-Jon RossleeDepartment of Medicine, Victoria Hospital, Wynberg, Cape Town, South Africa.ORCID https://orcid.org/0009-0006-9025-5710
Gregory SymonsDepartment of Medicine, Division of Pulmonology, Groote Schuur Hospital, Cape Town, South Africa.ORCID https://orcid.org/0009-0005-0440-7777
Gregory L CalligaroDepartment of Medicine, Division of Pulmonology, Groote Schuur Hospital, Cape Town, South Africa.ORCID https://orcid.org/0000-0001-7324-0775
Arash IranzadehDepartment of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0003-4413-2569
Robert J WilkinsonCentre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0002-2753-1800
Ntobeko A B NtusiDepartment of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0003-2347-7883
Carolyn WilliamsonDepartment of Pathology, IDM and CIDRI-Africa, Division of Medical Virology, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0003-0125-1226
Mary-Ann DaviesDepartment of Health and Wellness, Western Cape Government, Cape Town, South Africa.ORCID https://orcid.org/0000-0001-8496-6475
Graeme MeintjesDepartment of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0003-1196-4414
Sean WassermanCentre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0002-3508-6719
University of Cape Town · ZAGroote Schuur Hospital · ZAWellcome Centre for Infectious Diseases Research in Africa · ZASouth African Medical Research Council · ZASt George's, University of London · GBThe Francis Crick Institute · GBVictoria Hospital · IN

Funding

Observational Antiretroviral Studies In Southern Africa (OASIS) CollaborationU01AI069924 · NIAID · UNIVERSITAT BERN · PI Cleophas Chimbetete, Mary-Ann Davies · 2006 to 2026
$55.9M
PRESCIENT: A phase IIc, open-label, randomized controlled trial of ultra-short course bedaquiline, clofazimine, pyrazinamide and delamanid versus standard therapy for drug-susceptible tuberculosisU01AI170426 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI SERENA Patricia KOENIG, Sean Wasserman · 2022 to 2026
$5.9M
Characterizing the pharmacokinetics of high dose rifampicin and linezolid in a randomized controlled trial for HIV-associated tuberculous meningitisK43TW011421 · FIC · UNIVERSITY OF CAPE TOWN · PI WASSERMAN, SEAN ADAM · 2019 to 2022
$404k
FIC NIH HHS K43 TW011421NIAID NIH HHS U01 AI069924NIAID NIH HHS U01 AI170426Wellcome Trust CC2112
6 · The paper itself

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] 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.

Indexed as

clinical characteristicsCOVID-19Deltaobservational studyOmicronSARS-CoV-2

Identifiers

PMID38223432
PMCPMC10784273
OpenAlexW4389922920

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.