Clinical severity of SARS-CoV-2 Omicron BA.4 and BA.5 lineages compared to BA.1 and Delta in South Africa

Nicole Wolter^{1

2}, Waasila Jassat^{3

4}, Sibongile Walaza^{5

6}, Richard Welch^{3

4}, Harry Moultrie^{7

8}, Michelle J Groome^{7

3}, Daniel Gyamfi Amoako^{5

9}, Josie Everatt⁵, Jinal N Bhiman^{10

11}, Cathrine Scheepers^{10

11}, Naume Tebeila⁵, Nicola Chiwandire⁵, Mignon du Plessis^{5

7}, Nevashan Govender³, Arshad Ismail^{12

13}, Allison Glass^{7

14}, Koleka Mlisana^{7

15

16}, Wendy Stevens^{7

15}, Florette K Treurnicht^{7

15}, Kathleen Subramoney^{7

15}, Zinhle Makatini^{7

15}, Nei-Yuan Hsiao^{15

17}, Raveen Parboosing^{7

15

18}, Jeannette Wadula^{7

15

19}, Hannah Hussey²⁰, Mary-Ann Davies²⁰, Andrew Boulle²⁰, Anne von Gottberg^#^{5

7}, Cheryl Cohen^#^{5

6}

Affiliations

¹ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa. nicolew@nicd.ac.za.
² School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. nicolew@nicd.ac.za.
³ Division of Public Health Surveillance and Response, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa.
⁴ Right to Care, Pretoria, South Africa.
⁵ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa.
⁶ School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁷ School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁸ Centre for Tuberculosis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa.
⁹ School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa.
¹⁰ Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
¹¹ SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹² Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa.
¹³ Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
¹⁴ Lancet Laboratories, Johannesburg, South Africa.
¹⁵ National Health Laboratory Service (NHLS), Johannesburg, South Africa.
¹⁶ School of Laboratory Medicine and Medical Sciences, University of KwaZulu Natal, Durban, South Africa.
¹⁷ Division of Medical Virology, University of Cape Town, Cape Town, South Africa.
¹⁸ Department of Virology, University of KwaZulu-Natal, Durban, South Africa.
¹⁹ Department of Clinical Microbiology & Infectious Diseases, CH Baragwanath Academic Hospital, Johannesburg, South Africa.
²⁰ Western Cape Government: Health and Wellness, and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.

^# Contributed equally.

PMID: 36195617
PMCID: PMC9531215
DOI: 10.1038/s41467-022-33614-0

Clinical severity of SARS-CoV-2 Omicron BA.4 and BA.5 lineages compared to BA.1 and Delta in South Africa

Nicole Wolter et al. Nat Commun. 2022.

. 2022 Oct 4;13(1):5860.

doi: 10.1038/s41467-022-33614-0.

Authors

Affiliations

¹ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa. nicolew@nicd.ac.za.
² School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. nicolew@nicd.ac.za.
³ Division of Public Health Surveillance and Response, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa.
⁴ Right to Care, Pretoria, South Africa.
⁵ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa.
⁶ School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁷ School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁸ Centre for Tuberculosis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa.
⁹ School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa.
¹⁰ Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
¹¹ SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹² Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa.
¹³ Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
¹⁴ Lancet Laboratories, Johannesburg, South Africa.
¹⁵ National Health Laboratory Service (NHLS), Johannesburg, South Africa.
¹⁶ School of Laboratory Medicine and Medical Sciences, University of KwaZulu Natal, Durban, South Africa.
¹⁷ Division of Medical Virology, University of Cape Town, Cape Town, South Africa.
¹⁸ Department of Virology, University of KwaZulu-Natal, Durban, South Africa.
¹⁹ Department of Clinical Microbiology & Infectious Diseases, CH Baragwanath Academic Hospital, Johannesburg, South Africa.
²⁰ Western Cape Government: Health and Wellness, and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.

^# Contributed equally.

PMID: 36195617
PMCID: PMC9531215
DOI: 10.1038/s41467-022-33614-0

Abstract

Omicron lineages BA.4 and BA.5 drove a fifth wave of COVID-19 cases in South Africa. Here, we use the presence/absence of the S-gene target as a proxy for SARS-CoV-2 variant/lineage for infections diagnosed using the TaqPath PCR assay between 1 October 2021 and 26 April 2022. We link national COVID-19 individual-level data including case, laboratory test and hospitalisation data. We assess severity using multivariable logistic regression comparing the risk of hospitalisation and risk of severe disease, once hospitalised, for Delta, BA.1, BA.2 and BA.4/BA.5 infections. After controlling for factors associated with hospitalisation and severe outcome respectively, BA.4/BA.5-infected individuals had a similar odds of hospitalisation (aOR 1.24, 95% CI 0.98-1.55) and severe outcome (aOR 0.72, 95% CI 0.41-1.26) compared to BA.1-infected individuals. Newly emerged Omicron lineages BA.4/BA.5 showed similar severity to the BA.1 lineage and continued to show reduced clinical severity compared to the Delta variant.

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Conflict of interest statement

C.C. has received grant support from South African Medical Research Council, UK Foreign, Commonwealth and Development Office and Wellcome Trust, US Centers for Disease Control and Prevention and Sanofi Pasteur. NW has received grant support from Sanofi Pasteur and the Bill and Melinda Gates Foundation. AvG has received grant support from US Centers for Disease Control and Prevention, Africa Centres for Disease Control and Prevention, African Society for Laboratory Medicine (ASLM), South African Medical Research Council, WHO AFRO, The Fleming Fund and Wellcome Trust. SW has received grant support from US Centers for Disease Control and Prevention. RW declares personal shareholding in the following companies: Adcock Ingram Holdings Ltd, Dischem Pharmacies Ltd, Discovery Ltd, Netcare Ltd, Aspen Pharmacare Holdings Ltd. All other authors declare no conflict of interest.

References

1. Network for Genomics Surveillance in South Africa (NGS-SA). SARS-CoV-2 Genomic Surveillance Update (3 June 2022). https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/sars-co... (2022).
1. Tegally, H. et al. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat. Med. 10.1038/s41591-022-01911-2 (2022). - PMC - PubMed
1. Department of Health. COVID-19 Online Resources and News portal. Latest Vaccine Statistics https://sacoronavirus.co.za/latest-vaccine-statistics/ (2022).
1. Tuekprakhon A, et al. Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum. Cell. 2022;185:2422–2433.e13. doi: 10.1016/j.cell.2022.06.005. - DOI - PMC - PubMed
1. European Centre for Disease Prevention and Control. Epidemiological update: SARS-CoV-2 Omicron sub-lineages BA.4 and BA.5. https://www.ecdc.europa.eu/en/news-events/epidemiological-update-sars-co... (2022).

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Clinical severity of SARS-CoV-2 Omicron BA.4 and BA.5 lineages compared to BA.1 and Delta in South Africa

Affiliations

Clinical severity of SARS-CoV-2 Omicron BA.4 and BA.5 lineages compared to BA.1 and Delta in South Africa

Authors

Affiliations

Abstract

Conflict of interest statement

References

Publication types

MeSH terms

Supplementary concepts

Grants and funding

LinkOut - more resources

Full Text Sources

Medical

Miscellaneous