Clinical data of hospitalized COVID-19 cases from Gauteng Province from April 2020-July 2022 were obtained from the national surveillance system, DATCOV, and linked to laboratory data from the National Health Laboratory Service data repository. The study period was divided into pandemic waves: Asp614Gly/wave1(7 June to 22 Aug 2020); beta/wave2(15 Nov 2020 to 6 Feb 2021); delta/wave3(9 May to 18 Sept 2021) and omicron/wave4(21 Nov 2021 to 22 Jan 2022).  Only Ct values of SARS-CoV-2 specific genes were used in the analysis: ORF gene(Roche), N2 gene(GeneXpert) and RdRp gene(Abbott). Ct values were categorized as low (30).