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Johnson R, Mangwana N, Sharma JR, Muller CJF, Malemela K, Mashau F, Dias S, Ramharack P, Kinnear C, Glanzmann B, Viraragavin A, Louw J, Surujlal-Naicker S, Nkambule S, Webster C, Mdhluli M, Gray G, Mathee A, Preiser W, Vorster A, Dalvie S, Street R. Delineating the spread and prevalence of SARS-CoV-2 Omicron sub-lineages (BA.1- BA.5) and Deltacron using wastewater in the Western Cape, South Africa. J Infect Dis 2022; 226:1418-1427. [PMID: 36017801 PMCID: PMC9574669 DOI: 10.1093/infdis/jiac356] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022] Open
Abstract
This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive correlation between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA in wastewater samples and clinical cases (r = 0.7749, P < .0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven third wave, was significantly higher than during the Omicron-driven fourth wave. Whole-genome sequencing confirmed presence of Omicron lineage defining mutations in wastewater with the first occurrence reported 23 November 2021 (BA.1 predominant). The variant spread rapidly, with prevalence of Omicron-positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sublineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. These findings demonstrate the value of wastewater-based epidemiology to monitor the spatiotemporal spread and potential origin of new Omicron sublineages.
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Affiliation(s)
- Rabia Johnson
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,Centre for Cardio-metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Noluxabiso Mangwana
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa
| | - Jyoti R Sharma
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,Centre for Cardio-metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Christo J F Muller
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,Centre for Cardio-metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa.,Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa
| | - Kholofelo Malemela
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa
| | - Funanani Mashau
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa
| | - Stephanie Dias
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa
| | - Pritika Ramharack
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Craig Kinnear
- Genomics Centre, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Brigitte Glanzmann
- Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Amsha Viraragavin
- Genomics Centre, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa
| | - Johan Louw
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa
| | - Swastika Surujlal-Naicker
- Scientific Services, Water and Sanitation Department, City of Cape Town Metropolitan Municipality, Cape Town, South Africa
| | - Sizwe Nkambule
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
| | - Candice Webster
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), JohannesburgSouth Africa
| | - Mongezi Mdhluli
- Chief Research Operations Office, South African Medical Research Council, Tygerberg 7050, South Africa
| | - Glenda Gray
- Office of the President, South African Medical Research Council, Tygerberg 7050, South Africa
| | - Angela Mathee
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), JohannesburgSouth Africa
| | - Wolfgang Preiser
- Division of Medical Virology at NHLS Tygerberg Hospital and Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Alvera Vorster
- Central Analytical Facilities, Stellenbosch University, South Africa
| | - Shareefa Dalvie
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,SAMRC, Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Renee Street
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
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