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 exists between SARS-CoV-2 viral RNA in wastewater samples and clinical cases (r = 0.7749, p < 0.0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven 3rd wave, was significantly higher than during the Omicron-driven 4th wave, p < 0.005. Whole-genome sequencing confirmed the presence of Omicron lineage defining mutations in wastewater with the first occurrence reported on 23 November 2021 (BA.1 predominant). The variant rapidly spread, with the prevalence of Omicron positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sub-lineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. Taken together, these findings demonstrate the value of WBE to monitor the spatiotemporal spread and potential origination of new Omicron sub-lineages of SARS-CoV-2.

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Anti-tuberculosis drugs are a two-edged sword.