Evidence map›Paper›PMID 35235826›Full record

ArticleInternational journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases2022

Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections - a survival analysis.

Hannah Hussey, Mary-Ann Davies, Alexa Heekes, Carolyn Williamson, Ziyaad Valley-Omar, Diana Hardie, Stephen Korsman, Deelan Doolabh, Wolfgang Preiser, Tongai Maponga and 16 more

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In one paragraph

Article in International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
19citing papers in PubMed, 1 pooled it
2.7field-weighted citation impact, top 8% 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

19 citing papers in PubMed, 1 synthesis or guideline pooled it, 25 citations in OpenAlex.

  1. Pooled it
  2. Article
  3. Article
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  5. Observational
  6. Deep Survival Analysis With Clinical Variables for COVID-19.IEEE journal of translational engineering in health and medicine · 2023
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  15. Observational
  16. Article
  17. Pathogenicity of SARS-CoV-2 Omicron.Clinical and translational medicine · 2022
    Article
  18. Review
  19. Article
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

26 authors at 5 institutions in 2 countries.

Hannah HusseyHealth Intelligence, Western Cape Government: Health, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa. Electronic address: hannah.hussey@westerncape.gov.za.
Mary-Ann DaviesHealth Intelligence, Western Cape Government: Health, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa.
Alexa HeekesHealth Intelligence, Western Cape Government: Health, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa.
Carolyn WilliamsonDivision of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.
Ziyaad Valley-OmarDivision of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa.
Diana HardieDivision of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa.
Stephen KorsmanDivision of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa.
Deelan DoolabhDivision of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa.
Wolfgang PreiserNational Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, South Africa.
Tongai MapongaNational Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, South Africa.
Arash IranzadehDivision of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa.
Sean WassermanWellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, South Africa.
Linda BolokoWellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa.
Greg SymonsDepartment of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa.
Peter RaubenheimerDepartment of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa.
Arifa ParkerDepartment of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa.
Neshaad SchruederDepartment of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa.
Wesley SolomonNational Department of Health, South Africa.
Petro RousseauNational Department of Health, South Africa.
Nicole WolterNational Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
Waasila JassatNational Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Cheryl CohenNational Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Richard LessellsKwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa.
Robert J WilkinsonWellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; The Francis Crick Institute, Midland Road, London, NW1 1AT, UK; Department of Infectious Diseases, Imperial College London, W12 0NN, UK.
Andrew BoulleHealth Intelligence, Western Cape Government: Health, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa.
Nei-Yuan HsiaoDivision of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.
National Health Laboratory Service · ZAUniversity of Cape Town · ZAWestern Cape Department of Health · ZAStellenbosch University · ZAUniversity of KwaZulu-Natal · ZA

Funding

Observational Antiretroviral Studies In Southern Africa (OASIS) CollaborationU01AI069924 · NIAID · UNIVERSITAT BERN · PI Cleophas Chimbetete, Mary-Ann Davies · 2006 to 2026
$55.9M
B positive_A population based evaluation of expanded ART access in pregnancyR01HD080465 · NICHD · UNIVERSITY OF CAPE TOWN · PI KALK, EMMA KATE · 2014 to 2019
$4.3M
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 AI069924NICHD NIH HHS R01 HD080465Wellcome Trust
6 · The paper itself

Abstract

backgroundAt present, it is unclear whether the extent of reduced risk of severe disease seen with SARS-Cov-2 Omicron variant infection is caused by a decrease in variant virulence or by higher levels of population immunity.

methodsRdRp target delay (RTD) in the Seegene Allplex

resultsA total of 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted hazard ratio [aHR], 0.56; 95% confidence interval [CI], 0.34-0.91). Complete vaccination was protective against admission, with an aHR of 0.45 (95% CI, 0.26-0.77).

conclusionOmicron has resulted in a lower risk of hospital admission compared with contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence.

Indexed as

COVID-19Hepatitis DHumansPolymerase Chain ReactionRNA-Dependent RNA PolymeraseSARS-CoV-2South AfricaSurvival AnalysisRNA-Dependent RNA Polymeraseclinical severityOmicron variantRdRp target delaySARS-CoV-2South Africa

Identifiers

PMID35235826
PMCPMC8882068
OpenAlexW4226018215

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.