Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1-BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

Rabia Johnson; Noluxabiso Mangwana; Jyoti R Sharma; Christo J F Muller; Kholofelo Malemela; Funanani Mashau; Stephanie Dias; Pritika Ramharack; Craig Kinnear; Brigitte Glanzmann; Amsha Viraragavan; Johan Louw; Swastika Surujlal-Naicker; Sizwe Nkambule; Candice Webster; Mongezi Mdhluli; Glenda Gray; Angela Mathee; Wolfgang Preiser; Alvera Vorster; Shareefa Dalvie; Renee Street

doi:10.1093/infdis/jiac356

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1-BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

J Infect Dis. 2022 Oct 17;226(8):1418-1427. doi: 10.1093/infdis/jiac356.

Authors

Rabia Johnson^{1

2}, Noluxabiso Mangwana¹, Jyoti R Sharma^{1

2}, Christo J F Muller^{1

2

3}, Kholofelo Malemela¹, Funanani Mashau¹, Stephanie Dias¹, Pritika Ramharack^{1

4}, Craig Kinnear^{5

6}, Brigitte Glanzmann⁴, Amsha Viraragavan⁵, Johan Louw^{1

3}, Swastika Surujlal-Naicker⁷, Sizwe Nkambule⁸, Candice Webster⁹, Mongezi Mdhluli¹⁰, Glenda Gray¹¹, Angela Mathee⁹, Wolfgang Preiser¹², Alvera Vorster¹³, Shareefa Dalvie^{1

14}, Renee Street⁸

Affiliations

¹ Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
² Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardio-metabolic Research in Africa, Stellenbosch University, Tygerberg, South Africa.
³ Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa.
⁴ Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
⁵ Genomics Centre, South African Medical Research Council, Tygerberg, South Africa.
⁶ Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.
⁷ Scientific Services, Water, and Sanitation Department, City of Cape Town Metropolitan Municipality, Cape Town, South Africa.
⁸ Environment and Health Research Unit, South African Medical Research Council, Durban, South Africa.
⁹ Environment and Health Research Unit, South African Medical Research Council, Johannesburg, South Africa.
¹⁰ Chief Research Operations Office, South African Medical Research Council, Tygerberg, South Africa.
¹¹ Office of the President, South African Medical Research Council, Tygerberg, South Africa.
¹² Division of Medical Virology, National Health Laboratory Services Tygerberg Hospital, and Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
¹³ Central Analytical Facilities, Stellenbosch University, Cape Town, South Africa.
¹⁴ Department of Psychiatry and Neuroscience Institute, South African Medical Research Council, Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa.

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.

Keywords: B.1.5.9 (Omicron); B.1.617.2 (Delta) lineages; BA.1; BA.2; BA.3; SARS-CoV-2; and BA.5; genotyping; wastewater-based epidemiology.

Publication types

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

MeSH terms

COVID-19* / epidemiology
Humans
Prevalence
RNA, Viral / genetics
SARS-CoV-2* / genetics
South Africa / epidemiology
Wastewater

Substances

RNA, Viral
Waste Water