Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study

Hannah Hussey; Mary-Ann Davies; Alexa Heekes; Carolyn Williamson; Ziyaad Valley-Omar; Diana Hardie; Stephen Korsman; Deelan Doolabh; Wofgang Preiser; Tongai Maponga; Arash Iranzadeh; Susan Engelbrecht; Sean Wasserman; Neshaad Schrueder; Linda Boloko; Greg Symons; Peter Raubenheimer; Abraham Viljoen; Arifa Parker; Cheryl Cohen; Waasila Jasat; Richard Lessells; Robert J Wilkinson; Andrew Boulle; Marvin Hsiao

doi:10.12688/gatesopenres.13654.1

Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study

Gates Open Res. 2022 Aug 31:6:117. doi: 10.12688/gatesopenres.13654.1. eCollection 2022.

Authors

Hannah Hussey^{1

2}, Mary-Ann Davies^{1

3}, Alexa Heekes^{1

2}, Carolyn Williamson^{4

5

6}, Ziyaad Valley-Omar^{4

6}, Diana Hardie^{4

6}, Stephen Korsman^{4

6}, Deelan Doolabh^{4

6}, Wofgang Preiser^{6

7}, Tongai Maponga^{6

7}, Arash Iranzadeh^{4

6}, Susan Engelbrecht⁶, Sean Wasserman^{5

8}, Neshaad Schrueder⁹, Linda Boloko^{5

10}, Greg Symons¹⁰, Peter Raubenheimer¹⁰, Abraham Viljoen⁹, Arifa Parker⁹, Cheryl Cohen^{11

12}, Waasila Jasat¹¹, Richard Lessells¹³, Robert J Wilkinson^{5

14

15}, Andrew Boulle^{1

3}, Marvin Hsiao^{4

5

6}

Affiliations

¹ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa.
² Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
³ Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
⁴ Division of Medical Virology, University of Cape Town, Cape Town, South Africa.
⁵ Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
⁶ National Health Laboratory Service, Cape Town, South Africa.
⁷ Division of Medical Virology, Stellenbosch University, Cape Town, South Africa.
⁸ Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa.
⁹ Department of Medicine, Tygerberg Hospital,, Stellenbosch University, Cape Town, South Africa.
¹⁰ Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.
¹¹ National Institute for Communicable Diseases, Johannesburg, South Africa.
¹² School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹³ KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu Natal, Durban, South Africa.
¹⁴ The Francis Crick Institute, London, UK.
¹⁵ Department of Infectious Diseases, Imperial College London, London, UK.

Abstract

Background: The SARS-CoV-2 Delta variant (B.1.617.2) has been associated with more severe disease, particularly when compared to the Alpha variant. Most of this data, however, is from high income countries and less is understood about the variant's disease severity in other settings, particularly in an African context, and when compared to the Beta variant. Methods: A novel proxy marker, RNA-dependent RNA polymerase (RdRp) target delay in the Seegene Allplex ^TM 2019-nCoV (polymerase chain reaction) PCR assay, was used to identify suspected Delta variant infection in routine laboratory data. All cases diagnosed on this assay in the public sector in the Western Cape, South Africa, from 1 April to 31 July 2021, were included in the dataset provided by the Western Cape Provincial Health Data Centre (PHDC). The PHDC collates information on all COVID-19 related laboratory tests, hospital admissions and deaths for the province. Odds ratios for the association between the proxy marker and death were calculated, adjusted for prior diagnosed infection and vaccination status. Results: A total of 11,355 cases with 700 deaths were included in this study. RdRp target delay (suspected Delta variant) was associated with higher mortality (adjusted odds ratio [aOR] 1.45; 95% confidence interval [CI]: 1.13-1.86), compared to presumptive Beta infection. Prior diagnosed infection during the previous COVID-19 wave, which was driven by the Beta variant, was protective (aOR 0.32; 95%CI: 0.11-0.92) as was vaccination (aOR [95%CI] 0.15 [0.03-0.62] for complete vaccination [≥28 days post a single dose of Ad26.COV2.S or ≥14 days post second BNT162b2 dose]). Conclusion: RdRp target delay, a proxy for infection with the Delta variant, is associated with an increased risk of mortality amongst those who were tested for COVID-19 in our setting.

Keywords: B.1.617.2; Delta; RdRp target delay; SARS-CoV-2; South Africa; clinical severity.

Abstract

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