Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study
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Abstract
BACKGROUND: The SARS-CoV-2 omicron variant of concern was identified in South Africa in November, 2021, and was associated with an increase in COVID-19 cases. We aimed to assess the clinical severity of infections with the omicron variant using S gene target failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy. METHODS: We did data linkages for national, South African COVID-19 case data, SARS-CoV-2 laboratory test data, SARS-CoV-2 genome data, and COVID-19 hospital admissions data. For individuals diagnosed with COVID-19 via TaqPath PCR tests, infections were designated as either SGTF or non-SGTF. The delta variant was identified by genome sequencing. Using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with SGTF versus non-SGTF infections diagnosed between Oct 1 and Nov 30, 2021, and we further assessed disease severity by comparing SGTF-infected individuals diagnosed between Oct 1 and Nov 30, 2021, with delta variant-infected individuals diagnosed between April 1 and Nov 9, 2021. FINDINGS: From Oct 1 (week 39), 2021, to Dec 6 (week 49), 2021, 161 328 cases of COVID-19 were reported in South Africa. 38 282 people were diagnosed via TaqPath PCR tests and 29 721 SGTF infections and 1412 non-SGTF infections were identified. The proportion of SGTF infections increased from two (3·2%) of 63 in week 39 to 21 978 (97·9%) of 22 455 in week 48. After controlling for factors associated with hospitalisation, individuals with SGTF infections had significantly lower odds of admission than did those with non-SGTF infections (256 [2·4%] of 10 547 vs 121 [12·8%] of 948; adjusted odds ratio [aOR] 0·2, 95% CI 0·1-0·3). After controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with SGTF versus non-SGTF infections (42 [21%] of 204 vs 45 [40%] of 113; aOR 0·7, 95% CI 0·3-1·4). Compared with individuals with earlier delta variant infections, SGTF-infected individuals had a significantly lower odds of severe disease (496 [62·5%] of 793 vs 57 [23·4%] of 244; aOR 0·3, 95% CI 0·2-0·5), after controlling for factors associated with disease severity. INTERPRETATION: Our early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity. FUNDING: The South African Medical Research Council, the South African National Department of Health, US Centers for Disease Control and Prevention, the African Society of Laboratory Medicine, Africa Centers for Disease Control and Prevention, the Bill & Melinda Gates Foundation, the Wellcome Trust, and the Fleming Fund.
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Case numbers were insufficient to estimate the duration of protection against COVID-19 hospitalization and death for each Omicron subvariant separately.
“With the lower severity of Omicron infections24,25 and the young population of Qatar15,26, case numbers were insufficient to estimate the duration of protection against COVID-19 hospitalization and death for each subvariant separately.”
From Duration of mRNA vaccine protection against SARS-CoV-2 Omicron BA.1 and BA.2 subvariants in Qatar (2022) · cites this paper as [24]
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- Authors
- Wolter, N., Jassat, W., Walaza, S., Welch, R., Moultrie, H., Groome, M., Amoako, D. G., Everatt, J., Bhiman, J. N., Scheepers, C., Tebeila, N., Chiwandire, N., du Plessis, M., Govender, N., Ismail, A., Glass, A., Mlisana, K., Stevens, W., Treurnicht, F. K., Makatini, Z., Hsiao, N.-Y., Parboosing, R., Wadula, J., Hussey, H., Davies, M.-A., Boulle, A., von Gottberg, A., & Cohen, C.
- Affiliations
- National Health Laboratory Service (ZA)
- Lancet Laboratories (ZA)
- University of Cape Town (ZA)
- Corresponding author
- Wolter, Nicole
- Cohen, Cheryl
- ORCID
- Venue
- The Lancet
- Publisher
- Elsevier BV
- Published
- 2022-01
- Volume
- 399
- Issue
- 10323
- Pages
- 437-446
- ISSN
- 0099-5355 (ISSN-L)
- 0140-6736
- PMC
- PMC8769664
- OpenAlex
- W4206027538
- Cited by
- 1,041
- References
- 10
- Citations by year
- 2026: 24 · 2025: 60 · 2024: 131 · 2023: 270 · 2022: 545 · 2021: 10
- FWCI
- 123.20
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- The Lancet (publishedVersion, cc-by)
- medRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- World Health Organization
- Foreign, Commonwealth and Development Office
- South African Medical Research Council
- Centers for Disease Control and Prevention (5 U01IP001048\u201305\u201300, AF-NICD-001/2021)
- National Department of Health
- National Institutes of Health
- National Health Laboratory Service
- Department of Health and Social Care
- Sanofi Pasteur
- Bill and Melinda Gates Foundation (INV-018978)
- Fogarty International Center
- Wellcome Trust (203135/Z/16/Z, 221003/Z/20/Z, 222754)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Keywords
- S-gene target failure, Delta variant, hospitalization, disease severity, South Africa, SARS-CoV-2 genome sequencing, data linkage, Omicron BA.1, Omicron BA.2
- MeSH terms
- COVID-19, SARS-CoV-2, COVID-19 Nucleic Acid Testing, Adolescent, Adult, Child, Child, Preschool, Female, Hospitalization, Humans, Male, Middle Aged, Severity of Illness Index, South Africa, Multivariate Analysis, Logistic Models, Odds Ratio, Information Storage and Retrieval, Genome, Viral, Young Adult
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