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

Overview

Journal J Infect Dis

Publisher Oxford University Press

Specialty Infectious Diseases

Date 2022 Aug 26

PMID 36017801

Authors

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

Affiliations

Soon will be listed here.

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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