Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa

Mary-Ann Davies¹, Erna Morden², Petro Rousseau³, Juanita Arendse⁴, Jamy-Lee Bam⁵, Linda Boloko⁶, Keith Cloete⁴, Cheryl Cohen⁷, Nicole Chetty⁸, Pierre Dane⁸, Alexa Heekes⁸, Nei-Yuan Hsiao⁹, Mehreen Hunter², Hannah Hussey¹⁰, Theuns Jacobs⁵, Waasila Jassat¹¹, Saadiq Kariem⁴, Reshma Kassanjee¹², Inneke Laenen¹³, Sue Le Roux¹⁴, Richard Lessells¹⁵, Hassan Mahomed¹⁶, Deborah Maughan¹⁷, Graeme Meintjes¹⁷, Marc Mendelson⁶, Ayanda Mnguni¹⁸, Melvin Moodley⁵, Katy Murie¹⁹, Jonathan Naude²⁰, Ntobeko A B Ntusi²¹, Masudah Paleker¹³, Arifa Parker²², David Pienaar²³, Wolfgang Preiser²⁴, Hans Prozesky²⁵, Peter Raubenheimer¹⁷, Liezel Rossouw⁴, Neshaad Schrueder²⁶, Barry Smith¹⁴, Mariette Smith⁸, Wesley Solomon³, Greg Symons¹⁷, Jantjie Taljaard²⁵, Sean Wasserman²⁷, Robert J Wilkinson²⁸, Milani Wolmarans³, Nicole Wolter²⁹, Andrew Boulle³⁰

Affiliations

¹ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa. Electronic address: mary-ann.davies@uct.ac.za.
² Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
³ National Department of Health, Pretoria, South Africa.
⁴ Western Cape Government: Health, Cape Town, South Africa.
⁵ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa.
⁶ Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa; Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa.
⁷ National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁸ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
⁹ Division of Medical Virology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, South Africa.
¹⁰ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Metro Health Services, Western Cape Government: Health, Cape Town, South Africa.
¹¹ National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
¹² Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
¹³ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa.
¹⁴ Western Cape Government: Health, Cape Town, South Africa; Karl Bremer Hospital, Western Cape Government: Health, Cape Town, South Africa.
¹⁵ KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa.
¹⁶ Metro Health Services, Western Cape Government: Health, Cape Town, South Africa; Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa.
¹⁷ Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa; Department of Medicine, University of Cape Town, Cape Town, South Africa.
¹⁸ Khayelitsha District Hospital, Western Cape Government: Health, Cape Town, South Africa.
¹⁹ Western Cape Government: Health, Cape Town, South Africa; Metro Health Services, Western Cape Government: Health, Cape Town, South Africa.
²⁰ Mitchells Plain Hospital, Western Cape Government: Health, Cape Town, South Africa.
²¹ Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa; Department of Medicine, University of Cape Town, Cape Town, South Africa; South African Medical Research Council Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases, Cape Town, South Africa.
²² Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa; Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa; Division of General Medicine, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa.
²³ Rural Health Services, Western Cape Government: Health, Cape Town, South Africa.
²⁴ National Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, Stellenbosch, South Africa.
²⁵ Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa; Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa.
²⁶ Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa; Division of General Medicine, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa.
²⁷ Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa; Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
²⁸ The Francis Crick Institute, London, UK; Department of Infectious Diseases, Imperial College London, London, UK; Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
²⁹ National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
³⁰ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.

PMID: 36436752
PMCID: PMC9686046
DOI: 10.1016/j.ijid.2022.11.024

Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa

Mary-Ann Davies et al. Int J Infect Dis. 2023 Feb.

. 2023 Feb:127:63-68.

doi: 10.1016/j.ijid.2022.11.024. Epub 2022 Nov 24.

Authors

Affiliations

¹ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa. Electronic address: mary-ann.davies@uct.ac.za.
² Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
³ National Department of Health, Pretoria, South Africa.
⁴ Western Cape Government: Health, Cape Town, South Africa.
⁵ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa.
⁶ Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa; Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa.
⁷ National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁸ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
⁹ Division of Medical Virology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, South Africa.
¹⁰ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Metro Health Services, Western Cape Government: Health, Cape Town, South Africa.
¹¹ National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
¹² Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
¹³ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa.
¹⁴ Western Cape Government: Health, Cape Town, South Africa; Karl Bremer Hospital, Western Cape Government: Health, Cape Town, South Africa.
¹⁵ KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa.
¹⁶ Metro Health Services, Western Cape Government: Health, Cape Town, South Africa; Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa.
¹⁷ Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa; Department of Medicine, University of Cape Town, Cape Town, South Africa.
¹⁸ Khayelitsha District Hospital, Western Cape Government: Health, Cape Town, South Africa.
¹⁹ Western Cape Government: Health, Cape Town, South Africa; Metro Health Services, Western Cape Government: Health, Cape Town, South Africa.
²⁰ Mitchells Plain Hospital, Western Cape Government: Health, Cape Town, South Africa.
²¹ Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa; Department of Medicine, University of Cape Town, Cape Town, South Africa; South African Medical Research Council Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases, Cape Town, South Africa.
²² Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa; Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa; Division of General Medicine, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa.
²³ Rural Health Services, Western Cape Government: Health, Cape Town, South Africa.
²⁴ National Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, Stellenbosch, South Africa.
²⁵ Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa; Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa.
²⁶ Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa; Division of General Medicine, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa.
²⁷ Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa; Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
²⁸ The Francis Crick Institute, London, UK; Department of Infectious Diseases, Imperial College London, London, UK; Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
²⁹ National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
³⁰ Health Intelligence, Western Cape Government: Health, Cape Town, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.

PMID: 36436752
PMCID: PMC9686046
DOI: 10.1016/j.ijid.2022.11.024

Abstract

Objectives: We aimed to compare the clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection.

Methods: We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection.

Results: Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective.

Conclusion: Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.

Keywords: BA.4; BA.5; COVID-19; Death, Severe hospitalization; Omicron.

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Figures

**Figure 1**
Number of SARS-CoV-2 diagnosed infections, proportion of SARS-CoV-2 tests that are positive (PTP), number of specimens sequenced, and distribution of different SARS-CoV-2 variants and subvariants in the WC, South Africa by epidemiologic week from January 1, 2021, to June 25, 2022. Courtesy Network for Genomics Surveillance in South Africa. PTP, percentage testing positive; WC, Western Cape

See this image and copyright information in PMC

Update of

Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa.
Davies MA, Morden E, Rosseau P, Arendse J, Bam JL, Boloko L, Cloete K, Cohen C, Chetty N, Dane P, Heekes A, Hsiao NY, Hunter M, Hussey H, Jacobs T, Jassat W, Kariem S, Kassanjee R, Laenen I, Le Roux S, Lessells R, Mahomed H, Maughan D, Meintjes G, Mendelson M, Mnguni A, Moodley M, Murie K, Naude J, Ntusi NAB, Paleker M, Parker A, Pienaar D, Preiser W, Prozesky H, Raubenheimer P, Rossouw L, Schrueder N, Smith B, Smith M, Solomon W, Symons G, Taljaard J, Wasserman S, Wilkinson RJ, Wolmarans M, Wolter N, Boulle A. Davies MA, et al. medRxiv [Preprint]. 2022 Jul 1:2022.06.28.22276983. doi: 10.1101/2022.06.28.22276983. medRxiv. 2022. Update in: Int J Infect Dis. 2023 Feb;127:63-68. doi: 10.1016/j.ijid.2022.11.024. PMID: 35794899 Free PMC article. Updated. Preprint.

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Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa

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Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa

Authors

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Abstract

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