How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality

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dc.contributor.authorScott, Lesley Erica
dc.contributor.authorHsiao, Nei-yuan
dc.contributor.authorDor, Graeme
dc.contributor.authorHans, Lucia
dc.contributor.authorMarokane, Puleng
dc.contributor.authorda Silva, Manuel Pedro
dc.contributor.authorPreiser, Wolfgang
dc.contributor.authorVreede, Helena
dc.contributor.authorTsoka, Jonathan
dc.contributor.authorMlisana, Koleka
dc.contributor.authorStevens, Wendy Susan
dc.date.accessioned2023-09-20T09:55:44Z
dc.date.available2023-09-20T09:55:44Z
dc.date.issued2023-08-01
dc.date.updated2023-08-11T14:33:39Z
dc.description.abstractThe high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID-19 pandemic resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms being implemented. Ongoing monitoring of the performance of these multiple and varied systems required novel approaches, especially during the circulation of variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from 6 commonly used PCR assays in 36 months, and visually monitored changes in their median Ct within a 28-day centered moving average for each assays’ gene targets. This continuous quality monitoring rapidly identified delayed hybridization of in the Allplex & trade; SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; gene target failure in the TaqPath & trade; COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently gene delayed hybridization in the Xpress SARS-CoV-2 due to XBB.1.5. This near ;real-time; monitoring helped inform the need for sequencing and the importance of multiplex molecular nucleic acid amplification technology designs used in diagnostics for patient care. This continuous quality monitoring approach at the granularity of Ct values should be included in ongoing surveillance and with application to other disease use cases that rely on molecular diagnostics.
dc.identifierdoi: 10.3390/diagnostics13152554
dc.identifier.apacitationScott, L. E., Hsiao, N., Dor, G., Hans, L., Marokane, P., da Silva, M. P., ... Stevens, W. S. (2023). How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality. <i>Diagnostics</i>, 13(15), 2554. http://hdl.handle.net/11427/38794en_ZA
dc.identifier.chicagocitationScott, Lesley Erica, Nei-yuan Hsiao, Graeme Dor, Lucia Hans, Puleng Marokane, Manuel Pedro da Silva, Wolfgang Preiser, et al "How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality." <i>Diagnostics</i> 13, 15. (2023): 2554. http://hdl.handle.net/11427/38794en_ZA
dc.identifier.citationScott, L.E., Hsiao, N., Dor, G., Hans, L., Marokane, P., da Silva, M.P., Preiser, W. & Vreede, H. et al. 2023. How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality. <i>Diagnostics.</i> 13(15):2554. http://hdl.handle.net/11427/38794en_ZA
dc.identifier.risTY - Journal Article AU - Scott, Lesley Erica AU - Hsiao, Nei-yuan AU - Dor, Graeme AU - Hans, Lucia AU - Marokane, Puleng AU - da Silva, Manuel Pedro AU - Preiser, Wolfgang AU - Vreede, Helena AU - Tsoka, Jonathan AU - Mlisana, Koleka AU - Stevens, Wendy Susan AB - The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID-19 pandemic resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms being implemented. Ongoing monitoring of the performance of these multiple and varied systems required novel approaches, especially during the circulation of variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from 6 commonly used PCR assays in 36 months, and visually monitored changes in their median Ct within a 28-day centered moving average for each assays&rsquo; gene targets. This continuous quality monitoring rapidly identified delayed hybridization of <i>RdRp</i> in the Allplex&trade; SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; <i>S</i>-gene target failure in the TaqPath&trade; COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently <i>E</i>-gene delayed hybridization in the Xpert<sup>&reg;</sup> Xpress SARS-CoV-2 due to XBB.1.5. This near &ldquo;real-time&rdquo; monitoring helped inform the need for sequencing and the importance of multiplex molecular nucleic acid amplification technology designs used in diagnostics for patient care. This continuous quality monitoring approach at the granularity of Ct values should be included in ongoing surveillance and with application to other disease use cases that rely on molecular diagnostics. DA - 2023-08-01 DB - OpenUCT DP - University of Cape Town IS - 15 J1 - Diagnostics LK - https://open.uct.ac.za PY - 2023 T1 - How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality TI - How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality UR - http://hdl.handle.net/11427/38794 ER -en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/38794
dc.identifier.vancouvercitationScott LE, Hsiao N, Dor G, Hans L, Marokane P, da Silva MP, et al. How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality. Diagnostics. 2023;13(15):2554. http://hdl.handle.net/11427/38794.en_ZA
dc.publisherMultidisciplinary Digital Publishing Institute
dc.publisher.departmentMedical Virology
dc.publisher.facultyHealth Science
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.sourceDiagnostics
dc.source.journalissue15
dc.source.journalvolume13
dc.source.pagination2554
dc.source.urihttps://www.mdpi.com/journal/diagnostics
dc.titleHow South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality
dc.typeJournal Article
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