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...
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| Language: | English |
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AOSIS
2024-11-01
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| Series: | Southern African Journal of Infectious Diseases |
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| Online Access: | https://sajid.co.za/index.php/sajid/article/view/647 |
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| author | Kreshalen Govender Rendani T. Mafuyeka Azwidowi Lukhwareni Pieter Meyer |
| author_facet | Kreshalen Govender Rendani T. Mafuyeka Azwidowi Lukhwareni Pieter Meyer |
| author_sort | Kreshalen Govender |
| collection | DOAJ |
| description | 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-nCoV™ 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. |
| format | Article |
| id | doaj-art-4cd3d051d68b4321ac76df41f75f61f6 |
| institution | OA Journals |
| issn | 2312-0053 2313-1810 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | AOSIS |
| record_format | Article |
| series | Southern African Journal of Infectious Diseases |
| spelling | doaj-art-4cd3d051d68b4321ac76df41f75f61f62025-08-20T02:38:51ZengAOSISSouthern African Journal of Infectious Diseases2312-00532313-18102024-11-01391e1e710.4102/sajid.v39i1.647323Comparison of SARS-CoV-2 molecular results from the first two COVID-19 waves in GautengKreshalen Govender0Rendani T. Mafuyeka1Azwidowi Lukhwareni2Pieter Meyer3Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; and, Department of Virology, Tshwane Academic Division, National Health Laboratory Service, PretoriaDepartment of Molecular Virology, Faculty of Virology, Ampath Laboratories Inc., PretoriaDepartment of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; and, Department of Virology, Tshwane Academic Division, National Health Laboratory Service, PretoriaDepartment of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; and, Department of Immunology, Tshwane Academic Division, National Health Laboratory Service, PretoriaBackground: 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-nCoV™ 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.https://sajid.co.za/index.php/sajid/article/view/647sars-cov-2rt‒pcrcycle thresholddemographicscovid‒19. |
| spellingShingle | Kreshalen Govender Rendani T. Mafuyeka Azwidowi Lukhwareni Pieter Meyer Comparison of SARS-CoV-2 molecular results from the first two COVID-19 waves in Gauteng Southern African Journal of Infectious Diseases sars-cov-2 rt‒pcr cycle threshold demographics covid‒19. |
| title | Comparison of SARS-CoV-2 molecular results from the first two COVID-19 waves in Gauteng |
| title_full | Comparison of SARS-CoV-2 molecular results from the first two COVID-19 waves in Gauteng |
| title_fullStr | Comparison of SARS-CoV-2 molecular results from the first two COVID-19 waves in Gauteng |
| title_full_unstemmed | Comparison of SARS-CoV-2 molecular results from the first two COVID-19 waves in Gauteng |
| title_short | Comparison of SARS-CoV-2 molecular results from the first two COVID-19 waves in Gauteng |
| title_sort | comparison of sars cov 2 molecular results from the first two covid 19 waves in gauteng |
| topic | sars-cov-2 rt‒pcr cycle threshold demographics covid‒19. |
| url | https://sajid.co.za/index.php/sajid/article/view/647 |
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