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

doi:10.1016/j.ijid.2022.02.051

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

Int J Infect Dis. 2022 May:118:150-154. doi: 10.1016/j.ijid.2022.02.051. Epub 2022 Feb 27.

Authors

Hannah Hussey¹, Mary-Ann Davies², Alexa Heekes³, Carolyn Williamson⁴, Ziyaad Valley-Omar⁵, Diana Hardie⁵, Stephen Korsman⁵, Deelan Doolabh⁵, Wolfgang Preiser⁶, Tongai Maponga⁶, Arash Iranzadeh⁵, Sean Wasserman⁷, Linda Boloko⁸, Greg Symons⁹, Peter Raubenheimer⁹, Arifa Parker¹⁰, Neshaad Schrueder¹⁰, Wesley Solomon¹¹, Petro Rousseau¹¹, Nicole Wolter¹², Waasila Jassat¹³, Cheryl Cohen¹⁴, Richard Lessells¹⁵, Robert J Wilkinson¹⁶, Andrew Boulle², Nei-Yuan Hsiao⁴

Affiliations

¹ 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. Electronic address: [email protected].
² 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.
³ 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.
⁴ 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.
⁵ Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa.
⁶ National Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, South Africa.
⁷ 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.
⁸ 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.
⁹ Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa.
¹⁰ Department of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa.
¹¹ National Department of Health, South Africa.
¹² National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
¹³ National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
¹⁴ 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.
¹⁵ KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa.
¹⁶ 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.

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 Allplex^TM 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 Allplex^TM 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.

Keywords: Omicron variant; RdRp target delay; SARS-CoV-2; South Africa; clinical severity.

MeSH terms

COVID-19* / diagnosis
Hepatitis D*
Humans
Polymerase Chain Reaction
RNA-Dependent RNA Polymerase
SARS-CoV-2 / genetics
South Africa / epidemiology
Survival Analysis

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

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