One Year of Wastewater Surveillance in South Africa Supporting COVID-19 Clinical Findings Across Two Waves of Infection

Renée Street; Angela Mathee; Tarylee Reddy; Nomfundo T Mahlangeni; Noluxabiso Mangwana; Sizwe Nkambule; Candice Webster; Stephanie Dias; Jyoti Rajan Sharma; Pritika Ramharack; Johan Louw; Swastika Surujlal-Naicker; Natacha Berkowitz; Mongezi Mdhluli; Glenda Gray; Christo Muller; Rabia Johnson

doi:10.3390/microorganisms12112230

One Year of Wastewater Surveillance in South Africa Supporting COVID-19 Clinical Findings Across Two Waves of Infection

Microorganisms. 2024 Nov 4;12(11):2230. doi: 10.3390/microorganisms12112230.

Authors

Renée Street^{1

2}, Angela Mathee^{2

3}, Tarylee Reddy⁴, Nomfundo T Mahlangeni¹, Noluxabiso Mangwana^{5

6}, Sizwe Nkambule¹, Candice Webster¹, Stephanie Dias⁵, Jyoti Rajan Sharma^{5

7}, Pritika Ramharack^{5

8}, Johan Louw^{5

9}, Swastika Surujlal-Naicker¹⁰, Natacha Berkowitz¹¹, Mongezi Mdhluli¹², Glenda Gray¹³, Christo Muller^{5

7

9}, Rabia Johnson⁵

Affiliations

¹ Environment & Health Research Unit, South African Medical Research Council (SAMRC), Cape Town 7505, South Africa.
² Environmental Health Department, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2028, South Africa.
³ Environment & Health Research Unit, South African Medical Research Council (SAMRC), Johannesburg 2028, South Africa.
⁴ Biostatistics Unit, South African Medical Research Council (SAMRC), Durban 4091, South Africa.
⁵ Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.
⁶ Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa.
⁷ Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch 7600, South Africa.
⁸ Discipline of Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa.
⁹ Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa.
¹⁰ Scientific Services, Water and Sanitation Department, City of Cape Town Metropolitan Municipality, Cape Town 8000, South Africa.
¹¹ Community Service and Health, City Health, City of Cape Town, Hertzog Boulevard, Cape Town 8000, South Africa.
¹² Chief Research Operations Office, South African Medical Research Council, Tygerberg 7050, South Africa.
¹³ Office of the President, South African Medical Research Council, Tygerberg 7050, South Africa.

Abstract

Wastewater-based epidemiology (WBE) has been an important tool for the detection of COVID-19 outbreaks. The retrospective analysis of COVID-19 data is vital to understand the spread and impact of the virus as well as to inform future planning and response efforts. In this study, we evaluated the SARS-CoV-2 RNA levels in wastewater from 21 wastewater treatment plants (WWTPs) in the City of Cape Town (South Africa) over a period of 12 months and compared the (inactive) SARS-CoV-2 viral RNA in wastewater between wave 2 (November 2020 to January 2021) and wave 3 (June 2021 to September 2021). The SARS-CoV-2 RNA expression was quantified in wastewater using quantitative real-time PCR (qRT-PCR) by targeting the nucleocapsid (N) gene, and the resultant signal was normalized to the WWTP design capacity and catchment size. Our findings show that the maximum SARS-CoV-2 RNA signal was significantly higher in wave 3 than in wave 2 (p < 0.01). The duration of wave 3 (15 weeks) was longer than that of wave 2 (10 weeks), and the wastewater surveillance data supported the clinical findings, as evidenced by the two distinct waves. Furthermore, the data demonstrated the importance of long-term wastewater surveillance as a key indicator of changing trends.

Keywords: COVID-19; SARS-CoV-2; South Africa; environmental epidemiology; viral RNA; wastewater.

Abstract

Grants and funding