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

Nicole Wolter; Waasila Jassat; Sibongile Walaza; Richard Welch; Harry Moultrie; Michelle J Groome; Daniel Gyamfi Amoako; Josie Everatt; Jinal N Bhiman; Cathrine Scheepers; Naume Tebeila; Nicola Chiwandire; Mignon du Plessis; Nevashan Govender; Arshad Ismail; Allison Glass; Koleka Mlisana; Wendy Stevens; Florette K Treurnicht; Kathleen Subramoney; Zinhle Makatini; Nei-Yuan Hsiao; Raveen Parboosing; Jeannette Wadula; Hannah Hussey; Mary-Ann Davies; Andrew Boulle; Anne von Gottberg; Cheryl Cohen

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

Nat Commun. 2022 Oct 4;13(1):5860. doi: 10.1038/s41467-022-33614-0.

Authors

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.

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.

Publication types

Research Support, U.S. Gov't, P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / epidemiology
Humans
SARS-CoV-2* / genetics
South Africa / epidemiology

Supplementary concepts

SARS-CoV-2 variants

Abstract

Publication types

MeSH terms

Supplementary concepts

Grants and funding