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.

Journal: The Journal of infectious diseases

Volume: 226

Issue: 8

Year of Publication: 2022

Affiliated Institutions:  Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa. Genomics Centre, South African Medical Research Council, Tygerberg, South Africa. Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa. Scientific Services, Water, and Sanitation Department, City of Cape Town Metropolitan Municipality, Cape Town, South Africa. Environment and Health Research Unit, South African Medical Research Council, Durban, South Africa. Environment and Health Research Unit, South African Medical Research Council, Johannesburg, South Africa. Chief Research Operations Office, South African Medical Research Council, Tygerberg, South Africa. Office of the President, South African Medical Research Council, Tygerberg, South Africa. Division of Medical Virology, National Health Laboratory Services Tygerberg Hospital, and Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa. Central Analytical Facilities, Stellenbosch University, Cape Town, South Africa.

Abstract summary 

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.

Authors & Co-authors:  Johnson Rabia R Mangwana Noluxabiso N Sharma Jyoti R JR Muller Christo J F CJF Malemela Kholofelo K Mashau Funanani F Dias Stephanie S Ramharack Pritika P Kinnear Craig C Glanzmann Brigitte B Viraragavan Amsha A Louw Johan J Surujlal-Naicker Swastika S Nkambule Sizwe S Webster Candice C Mdhluli Mongezi M Gray Glenda G Mathee Angela A Preiser Wolfgang W Vorster Alvera A Dalvie Shareefa S Street Renee R

Study Outcome 

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Citations :  Tong C, Shi W, Zhang A, Shi Z. Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa. Travel Med Infect Dis 2022; 46:102252.
Authors :  22
Identifiers
Doi : 10.1093/infdis/jiac356
SSN : 1537-6613
Study Population
Male,Female
Mesh Terms
COVID-19
Other Terms
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
Study Design
Cross Sectional Study
Study Approach
Country of Study
South Africa
Publication Country
United States