International Journal of Infectious Diseases (May 2022)
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,
- Arash Iranzadeh,
- Sean Wasserman,
- Linda Boloko,
- Greg Symons,
- Peter Raubenheimer,
- Arifa Parker,
- Neshaad Schrueder,
- Wesley Solomon,
- Petro Rousseau,
- Nicole Wolter,
- Waasila Jassat,
- Cheryl Cohen,
- Richard Lessells,
- Robert J Wilkinson,
- Andrew Boulle,
- Nei-yuan Hsiao
Affiliations
- Hannah Hussey
- Health 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; Corresponding author: Hannah Hussey, Health 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. Postal address: Division of Public Health Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, Cape Town, South Africa.
- Mary-Ann Davies
- Health 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 Heekes
- Health 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 Williamson
- Division 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-Omar
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
- Diana Hardie
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
- Stephen Korsman
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
- Deelan Doolabh
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
- Wolfgang Preiser
- National Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, South Africa
- Tongai Maponga
- National Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, South Africa
- Arash Iranzadeh
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
- Sean Wasserman
- Wellcome 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 Boloko
- Wellcome 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 Symons
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa
- Peter Raubenheimer
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa
- Arifa Parker
- Department of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa
- Neshaad Schrueder
- Department of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa
- Wesley Solomon
- National Department of Health, South Africa
- Petro Rousseau
- National Department of Health, South Africa
- Nicole Wolter
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Waasila Jassat
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Cheryl Cohen
- National 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 Lessells
- KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
- Robert J Wilkinson
- Wellcome 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 Boulle
- Health 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 Hsiao
- Division 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
- Journal volume & issue
-
Vol. 118
pp. 150 – 154
Abstract
Background: At 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. Methods: RdRp target delay (RTD) in the Seegene AllplexTM 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections.Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene AllplexTM assay from November 1 to December 14, 2021 in the Western Cape Province, South Africa, in the public sector. Adjustments were made for vaccination status and prior diagnosis of infection. Results: A 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). Conclusion: Omicron 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.
