Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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

Lesley Erica Scott
* ORCID logo ,
Nei-yaun Hsiao
,
Graeme Dor
,
Lucia Hans
ORCID logo ,
Puleng Marokane
,
Pedro Da Silva
ORCID logo ,
Wolfgang Preiser
ORCID logo ,
Heleen Vreede
ORCID logo ,
Jonathan Tsoka
ORCID logo ,
Koleka Mlisana
,
Wendy Susan Stevens
Version 1 : Received: 5 June 2023 / Approved: 6 June 2023 / Online: 6 June 2023 (05:35:27 CEST)

A peer-reviewed article of this Preprint also exists.

Scott, L.E.; Hsiao, N.-Y.; Dor, G.; Hans, L.; Marokane, P.; da Silva, M.P.; Preiser, W.; Vreede, H.; Tsoka, J.; Mlisana, K.; Stevens, W.S. How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality. Diagnostics 2023, 13, 2554. Scott, L.E.; Hsiao, N.-Y.; Dor, G.; Hans, L.; Marokane, P.; da Silva, M.P.; Preiser, W.; Vreede, H.; Tsoka, J.; Mlisana, K.; Stevens, W.S. How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality. Diagnostics 2023, 13, 2554.

Abstract

The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID19 pandemic, resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms. Novel approaches were required to monitor test quality especially during the introduction of newly circulating variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from six 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 RdRp in the Allplex™ SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; S-gene target failure in the TaqPath™ COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently E-gene delayed hybridization in the Xpert® 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.

Keywords

SARS-CoV-2; COVID19; Laboratory diagnostics; Cycle threshold; PCR platforms; median Ct; moving average; variants; continuous quality monitoring

Subject

Public Health and Healthcare, Public Health and Health Services

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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