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[Preprint]. 2022 Jul 1:2022.06.28.22276983.

doi: 10.1101/2022.06.28.22276983.

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^{1

2

3}, Erna Morden^{1

3}, Petro Rosseau⁴, Juanita Arendse⁵, Jamy-Lee Bam¹, Linda Boloko^{6

7}, Keith Cloete⁵, Cheryl Cohen^{8

9}, Nicole Chetty^{1

2}, Pierre Dane^{1

2}, Alexa Heekes^{1

2}, Nei-Yuan Hsiao^{10

11}, Mehreen Hunter^{1

3}, Hannah Hussey^{1

3

12}, Theuns Jacobs¹, Waasila Jassat⁸, Saadiq Kariem⁵, Reshma Kassanjee², Inneke Laenen^{1

13}, Sue Le Roux^{5

14}, Richard Lessells¹⁵, Hassan Mahomed^{12

13}, Deborah Maughan^{6

16}, Graeme Meintjes^{6

16}, Marc Mendelson^{6

7}, Ayanda Mnguni¹⁷, Melvin Moodley¹, Katy Murie^{5

12}, Jonathan Naude¹⁸, Ntobeko A B Ntusi^{6

16

19}, Masudah Paleker^{1

13}, Arifa Parker^{20

21}, David Pienaar²², Wolfgang Preiser^{11

23}, Hans Prozesky^{20

21}, Peter Raubenheimer^{6

16}, Liezel Rossouw⁵, Neshaad Schrueder^{20

24}, Barry Smith^{5

14}, Mariette Smith^{1

2}, Wesley Solomon⁴, Greg Symons^{6

16}, Jantjie Taljaard^{20

21}, Sean Wasserman^{6

7}, Robert J Wilkinson^{25

26

27}, Milani Wolmarans⁴, Nicole Wolter^{8

28}, Andrew Boulle^{1

2

3}

Affiliations

¹ Health Intelligence, Western Cape Government: Health and Wellness, South Africa.
² Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa.
³ Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa.
⁴ National Department of Health, South Africa.
⁵ Western Cape Government: Health and Wellness, South Africa.
⁶ Groote Schuur Hospital, Western Cape Government: Health and Wellness, South Africa.
⁷ Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, South Africa.
⁸ National Institute for Communicable Diseases, National Health Laboratory Service, South Africa.
⁹ School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹⁰ Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa.
¹¹ National Health Laboratory Service, South Africa.
¹² Metro Health Services, Western Cape Government: Health and Wellness.
¹³ Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University.
¹⁴ Karl Bremer Hospital, Western Cape Government: Health and Wellness.
¹⁵ KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa.
¹⁶ Department of Medicine, University of Cape Town, South Africa.
¹⁷ Khayelitsha District Hospital, Western Cape Government: Health and Wellness.
¹⁸ Mitchells Plain Hospital, Western Cape Government: Health and Wellness.
¹⁹ South African Medical Research Council Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases.
²⁰ Tygerberg Hospital, Western Cape Government: Health and Wellness.
²¹ Division of Infectious Diseases, Department of Medicine, Stellenbosch University, South Africa.
²² Rural Health Services, Western Cape Government: Health and Wellness.
²³ Division of Medical Virology, University of Stellenbosch, South Africa.
²⁴ Division of General Medicine, Department of Medicine, Stellenbosch University, South Africa.
²⁵ The Francis Crick Institute, Midland Road, London, NW1 1AT, UK.
²⁶ Department of Infectious Diseases, Imperial College London, W12 0NN, UK.
²⁷ Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.
²⁸ School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.

PMID: 35794899
PMCID: PMC9258293
DOI: 10.1101/2022.06.28.22276983

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. medRxiv. 2022.

[Preprint]. 2022 Jul 1:2022.06.28.22276983.

doi: 10.1101/2022.06.28.22276983.

Authors

Affiliations

¹ Health Intelligence, Western Cape Government: Health and Wellness, South Africa.
² Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa.
³ Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa.
⁴ National Department of Health, South Africa.
⁵ Western Cape Government: Health and Wellness, South Africa.
⁶ Groote Schuur Hospital, Western Cape Government: Health and Wellness, South Africa.
⁷ Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, South Africa.
⁸ National Institute for Communicable Diseases, National Health Laboratory Service, South Africa.
⁹ School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹⁰ Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa.
¹¹ National Health Laboratory Service, South Africa.
¹² Metro Health Services, Western Cape Government: Health and Wellness.
¹³ Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University.
¹⁴ Karl Bremer Hospital, Western Cape Government: Health and Wellness.
¹⁵ KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa.
¹⁶ Department of Medicine, University of Cape Town, South Africa.
¹⁷ Khayelitsha District Hospital, Western Cape Government: Health and Wellness.
¹⁸ Mitchells Plain Hospital, Western Cape Government: Health and Wellness.
¹⁹ South African Medical Research Council Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases.
²⁰ Tygerberg Hospital, Western Cape Government: Health and Wellness.
²¹ Division of Infectious Diseases, Department of Medicine, Stellenbosch University, South Africa.
²² Rural Health Services, Western Cape Government: Health and Wellness.
²³ Division of Medical Virology, University of Stellenbosch, South Africa.
²⁴ Division of General Medicine, Department of Medicine, Stellenbosch University, South Africa.
²⁵ The Francis Crick Institute, Midland Road, London, NW1 1AT, UK.
²⁶ Department of Infectious Diseases, Imperial College London, W12 0NN, UK.
²⁷ Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.
²⁸ School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.

PMID: 35794899
PMCID: PMC9258293
DOI: 10.1101/2022.06.28.22276983

Update in

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, Rousseau 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, Roux SL, 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. Int J Infect Dis. 2023 Feb;127:63-68. doi: 10.1016/j.ijid.2022.11.024. Epub 2022 Nov 24. Int J Infect Dis. 2023. PMID: 36436752 Free PMC article.

Abstract

Objective: We aimed to compare 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 â‰¥20 years with laboratory-confirmed COVID-19 between 1-21 May 2022 (BA.4/BA.5 wave) and equivalent prior 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 prior infection.

Results: Among 3,793 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 lower risk of severe outcomes than previous waves. Prior infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for boosted vs. no vaccine) were protective.

Conclusion: Disease severity was similar amongst 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 prior infection and vaccination, both of which were strongly protective.

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Conflict of interest statement

Conflict of interest

All authors declare that they have no conflicts of interest.

References

1. Bingham J, Cable R, Coleman C, Glatt TN, Grebe E, Mhlanga L, et al. Estimates of prevalence of anti-SARS-CoV-2 antibodies among blood donors in South Africa in March 2022. Res Sq 2022. doi: 10.21203/rs.3.rs-1687679/v1. - DOI
1. Boulle A, Heekes A, Tiffin N, Smith M, Mutemaringa T, Zinyakatira N, et al. Data Centre Profile: The Provincial Health Data Centre of the Western Cape Province, South Africa. International Journal of Population Data Science 2019;4(2). - PMC - PubMed
1. Callaway E. What Omicron’s BA.4 and BA.5 variants mean for the pandemic. Nature 2022;23 June 2022. doi: 10.1038/d41586-022-01730-y. - DOI - PubMed
1. Davies MA, Kassanjee R, Rousseau P, Morden E, Johnson L, Solomon W, et al. 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. Trop Med Int Health 2022; 27(6):564–73. - PMC - PubMed
1. Hussey H, Davies MA, Heekes A, Williamson C, Valley-Omar Z, Hardie D, et al. 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;118:150–4. - PMC - PubMed

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This is a preprint.

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

Affiliations

Update in

Abstract

Conflict of interest statement

References

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