Comparison of SARS-CoV-2 molecular results from the first two COVID-19 waves in Gauteng

Background: Laboratory-based molecular assays return cycle threshold (Ct) values for each gene target. There is limited hyperlocal information describing the Ct, age and sex trends during the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) waves in South Africa. Objectives: To analyse the demographic and Ct value trends of SARS-CoV-2 molecular assays from two South African hospitals. Method: The Seegene Allplex 2019-nCoVTM results from the first two waves (June-July 2020 and November 2020-January 2021) from two major hospitals in Gauteng, South Africa, were extracted from the laboratory information system. Demographic variables and Ct values were analysed. Results: Overall, 2391 samples were analysed over two waves. In both waves, more women were tested than men; 68.4% versus 31.2% in the first wave and 59.8% versus 39.7% in the second wave. Differences in Ct values among the age groups were non-significant overall; however, most median Ct values in all age groups were < 30. Men had lower median Ct values in the first wave, but this trend reversed in the second wave (p < 0.001). The first wave had significantly lower mean and median Ct values per gene target (p < 0.001). Conclusion: Patients tested in the first wave had lower Ct values. All age groups in both waves demonstrated infectivity potential; the demographic analysis agreed with South Africa's coronavirus disease 2019 (COVID-19) epidemiological trends in both waves. Contribution: Granular insight into the basic demographic variables and Ct trends of SARS-CoV-2 real-time polymerase chain reaction (RT-PCR) results within and between SARS-CoV-2 waves in South Africa.