Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa

doi:10.1111/tmi.13752

. 2022 Jun;27(6):564-573.

doi: 10.1111/tmi.13752. Epub 2022 May 10.

Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa

Mary-Ann Davies^{1

2

3}, Reshma Kassanjee², Petro Rousseau⁴, Erna Morden^{1

3}, Leigh Johnson², Wesley Solomon⁴, Nei-Yuan Hsiao^{5

6}, Hannah Hussey^{1

3}, Graeme Meintjes^{7

8

9}, Masudah Paleker^{1

10}, Theuns Jacobs¹, Peter Raubenheimer^{7

8}, Alexa Heekes^{1

2}, Pierre Dane^{1

2}, Jamy-Lee Bam¹, Mariette Smith^{1

2}, Wolfgang Preiser^{6

11}, David Pienaar¹², Marc Mendelson^{7

13}, Jonathan Naude¹⁴, Neshaad Schrueder^{15

16}, Ayanda Mnguni¹⁷, Sue Le Roux^{18

19}, Kathleen Murie^{19

20}, Hans Prozesky^{15

21}, Hassan Mahomed^{10

20}, Liezel Rossouw¹⁹, Sean Wasserman^{7

9

13}, Deborah Maughan^{7

8}, Linda Boloko^{7

13}, Barry Smith^{18

19}, Jantjie Taljaard^{15

21}, Greg Symons^{7

8}, Ntobeko A B Ntusi^{7

8}, Arifa Parker^{15

21}, Nicole Wolter²², Waasila Jassat²², Cheryl Cohen^{22

23}, Richard Lessells²⁴, Robert J Wilkinson^{9

25

26}, Juanita Arendse¹⁹, Saadiq Kariem¹⁹, Melvin Moodley¹, Milani Wolmarans⁴, Keith Cloete¹⁹, Andrew Boulle^{1

2

3}; Western Cape and South African National Departments of Health in collaboration with the National Institute for Communicable Diseases in South Africa Affiliations

Affiliations

¹ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa.
² Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
³ Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
⁴ National Department of Health, Pretoria, South Africa.
⁵ Division of Medical Virology, University of Cape Town, Cape Town, South Africa.
⁶ National Health Laboratory Service, Cape Town, South Africa.
⁷ Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa.
⁸ Department of Medicine, University of Cape Town, Cape Town, South Africa.
⁹ Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
¹⁰ Division of Health Systems and Public Health, Department of Global Health, Stellenbosch University, Tygerberg, South Africa.
¹¹ Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa.
¹² Rural Health Services, Western Cape Government: Health, Cape Town, South Africa.
¹³ Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa.
¹⁴ Mitchells Plain Hospital, Western Cape Government: Health, Cape Town, South Africa.
¹⁵ Tygerberg Hospital, Western Cape Government: Health, Parow, South Africa.
¹⁶ Department of Medicine, Stellenbosch University, Stellenbosch, South Africa.
¹⁷ Khayelitsha District Hospital, Western Cape Government: Health, Khayelitsha, South Africa.
¹⁸ Karl Bremer Hospital, Western Cape Government: Health, Bellville, South Africa.
¹⁹ Western Cape Government: Health, Cape Town, South Africa.
²⁰ Metro Health Services, Western Cape Government: Health, Cape Town, South Africa.
²¹ Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Tygerberg, South Africa.
²² National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
²³ Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa.
²⁴ KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa.
²⁵ Francis Crick Institute, London, UK.
²⁶ Department of Infectious Diseases, Imperial College London, London, UK.

PMID: 35411997
PMCID: PMC9115442
DOI: 10.1111/tmi.13752

Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa

Mary-Ann Davies et al. Trop Med Int Health. 2022 Jun.

. 2022 Jun;27(6):564-573.

doi: 10.1111/tmi.13752. Epub 2022 May 10.

Authors

Affiliations

¹ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa.
² Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
³ Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
⁴ National Department of Health, Pretoria, South Africa.
⁵ Division of Medical Virology, University of Cape Town, Cape Town, South Africa.
⁶ National Health Laboratory Service, Cape Town, South Africa.
⁷ Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa.
⁸ Department of Medicine, University of Cape Town, Cape Town, South Africa.
⁹ Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
¹⁰ Division of Health Systems and Public Health, Department of Global Health, Stellenbosch University, Tygerberg, South Africa.
¹¹ Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa.
¹² Rural Health Services, Western Cape Government: Health, Cape Town, South Africa.
¹³ Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa.
¹⁴ Mitchells Plain Hospital, Western Cape Government: Health, Cape Town, South Africa.
¹⁵ Tygerberg Hospital, Western Cape Government: Health, Parow, South Africa.
¹⁶ Department of Medicine, Stellenbosch University, Stellenbosch, South Africa.
¹⁷ Khayelitsha District Hospital, Western Cape Government: Health, Khayelitsha, South Africa.
¹⁸ Karl Bremer Hospital, Western Cape Government: Health, Bellville, South Africa.
¹⁹ Western Cape Government: Health, Cape Town, South Africa.
²⁰ Metro Health Services, Western Cape Government: Health, Cape Town, South Africa.
²¹ Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Tygerberg, South Africa.
²² National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
²³ Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa.
²⁴ KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa.
²⁵ Francis Crick Institute, London, UK.
²⁶ Department of Infectious Diseases, Imperial College London, London, UK.

PMID: 35411997
PMCID: PMC9115442
DOI: 10.1111/tmi.13752

Abstract

Objectives: The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained.

Methods: In this cohort study, we included public sector patients aged ≥20 years with a laboratory-confirmed COVID-19 diagnosis between 14 November and 11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalisation or death and any hospitalisation or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection.

Results: We included 5144 patients from wave four and 11,609 from prior waves. The risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted hazard ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR: 0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58).

Conclusions: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for a modest reduction in risk of severe hospitalisation or death compared to the Delta-driven wave.

Keywords: COVID-19; Delta; immunity; omicron; prior infection; sub-Saharan Africa; vaccination.

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Conflict of interest statement

All authors declare that they have no conflicts of interest.

Figures

**FIGURE 1**
Daily new cases (7‐day moving average) by days since the start of each wave in (a) the Western Cape Province and (b) Khayelitsha subdistrict, Cape Town, South Africa from 10 March 2020 to 31 December 2021

**FIGURE 2**
Adjusted hazard ratio for associations between (a) vaccination and (b) prior diagnosed infection and different severe COVID‐19 outcomes adjusted for patient characteristics, subdistrict, vaccination and prior diagnosed infection using Cox regression

See this image and copyright information in PMC

Update of

Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa.
Davies MA, Kassanjee R, Rosseau P, Morden E, Johnson L, Solomon W, Hsiao NY, Hussey H, Meintjes G, Paleker M, Jacobs T, Raubenheimer P, Heekes A, Dane P, Bam JL, Smith M, Preiser W, Pienaar D, Mendelson M, Naude J, Schrueder N, Mnguni A, Roux SL, Murie K, Prozesky H, Mahomed H, Rossouw L, Wasserman S, Maughan D, Boloko L, Smith B, Taljaard J, Symons G, Ntusi N, Parker A, Wolter N, Jassat W, Cohen C, Lessells R, Wilkinson RJ, Arendse J, Kariem S, Moodley M, Vallabhjee K, Wolmarans M, Cloete K, Boulle A. Davies MA, et al. medRxiv [Preprint]. 2022 Jan 12:2022.01.12.22269148. doi: 10.1101/2022.01.12.22269148. medRxiv. 2022. Update in: Trop Med Int Health. 2022 Jun;27(6):564-573. doi: 10.1111/tmi.13752. PMID: 35043121 Free PMC article. Updated. Preprint.

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References

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[1] Scott L, Hsiao N‐y, Moyo S, Singh L, Tegally H, Dor G, et al. Track Omicron's spread with molecular data. Science. 2021;374(6574):1454–5. - PubMed

[2] Scott L, Hsiao N‐y, Moyo S, Singh L, Tegally H, Dor G, et al. Track Omicron's spread with molecular data. Science. 2021;374(6574):1454–5. - PubMed

[3] Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, et al. Rapid epidemic expansion of the SARS‐CoV‐2 Omicron variant in southern Africa. Nature. 2022;603:679–86. - PMC - PubMed

[4] Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, et al. Rapid epidemic expansion of the SARS‐CoV‐2 Omicron variant in southern Africa. Nature. 2022;603:679–86. - PMC - PubMed

[5] Cele S, Jackson L, Khan K, Khoury DS, Moyo‐Gwete T, Tegally H, et al. SARS‐CoV‐2 omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. Nature. 2022;602:654–56. - PubMed

[6] Cele S, Jackson L, Khan K, Khoury DS, Moyo‐Gwete T, Tegally H, et al. SARS‐CoV‐2 omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. Nature. 2022;602:654–56. - PubMed

[7] Pearson CAB, Silal SP, Li MWZ, Dushoff J, Bolker BM, Abbott S, et al. Bounding the levels of transmissibility and immune evasion of the omicron variant in South Africa. medRxiv. 2021. 10.1101/2021.12.19.21268038 - DOI

[8] Pearson CAB, Silal SP, Li MWZ, Dushoff J, Bolker BM, Abbott S, et al. Bounding the levels of transmissibility and immune evasion of the omicron variant in South Africa. medRxiv. 2021. 10.1101/2021.12.19.21268038 - DOI

[9] Pulliam JRC, van Schalkwyk C, Govender N, von Gottberg A, Cohen C, Groome MJ, et al. Increased risk of SARS‐CoV‐2 reinfection associated with emergence of the omicron variant in South Africa. Science 2021. 10.1126/science.abn4947 - DOI - PMC - PubMed

[10] Pulliam JRC, van Schalkwyk C, Govender N, von Gottberg A, Cohen C, Groome MJ, et al. Increased risk of SARS‐CoV‐2 reinfection associated with emergence of the omicron variant in South Africa. Science 2021. 10.1126/science.abn4947 - DOI - PMC - PubMed

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Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa

Affiliations

Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa

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