Samenvatting
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic triggered the implementation of large-scale screenings in the health care and in the general population. Consequently, medical laboratories have to apply lean laboratory management to design workflows that are able to process large batches within short turnaround times while maintaining flexibility to use different SARS-CoV-2 reverse transcription polymerase chain reactions (RT-PCRs) and to be able to process a variety of clinical samples. We validated two SARS-CoV-2 PCR assays on the STARlet workflow: Allplex SARS-CoV-2 PCR kit and RealAccurate Quadruplex SARS-CoV-2 PCR kit. Furthermore, we optimized and validated the STARlet workflow for semi-automatic screening for SARS-CoV-2 in upper respiratory swabs and deep respiratory materials (sputa, bronchoalveolar lavage, and aspirate). Strikingly, guanidine-containing lysis buffers allow for easy processing and can enhance sensitivity of SARS-COV-2 screening since sampling in these buffers may preserve viral transcripts as evident by the higher copy numbers of the SARS-CoV-2 N gene. Moreover, using the principles of lean laboratory management, several bottlenecks that are typical for medical laboratories were addressed. We show that lean laboratory management resulted in significant reduction of the turnaround times of the SARS-CoV-2 PCR in our laboratory. This report thus describes a useful framework for laboratories to implement similar semi-automated workflows.IMPORTANCEThe SARS-CoV-2 pandemic triggered the implementation of large-scale screenings in the health care and in the general population. Consequently, medical laboratories had to adapt and evolve workflows that are able to process large batches within short turnaround times while maintaining flexibility to use different assays and to be able to process a variety of clinical samples. We describe how the need for increased outputs and greater flexibility was addressed with respect to clinical samples and assays (Allplex SARS-CoV-2 PCR and RealAccurate Quadruplex SARS-CoV-2 PCR). Strikingly, we found that upper respiratory swabs collected in guanidine-containing lysis buffers both improved the ease of processing as well as enhanced the sensitivity of the SARS-CoV-2 screening. This report thus describes a useful framework for laboratories to implement and optimize similar semi-automated workflows.
| Originele taal-2 | Engels |
|---|---|
| Artikelnummer | e03296-23 |
| Aantal pagina's | 15 |
| Tijdschrift | Microbiology Spectrum |
| Volume | 12 |
| Nummer van het tijdschrift | 2 |
| DOI's | |
| Status | Gepubliceerd - 6 feb. 2024 |
Financiering
The authors gratefully acknowledge all efforts from all colleagues of the Laboratory for Medical Microbiology and Immunology (Rijnstate Hospital, Velp) and the Laboratory for Clinical Chemistry (Rijnstate Hospital, Arnhem). Ron Bosboom (Rijnstate Hospital, Arnhem), Karel Knez and Maxine Vanvuchelen (Accuramed, Halen, Belgium), Antoinette Brink (PathoFinder, Maastricht, the Netherlands), and Jeroen Poodt (Labhelp International B.V., Bladel, the Netherlands) are acknowledged for their valuable input, adapting the equipment, assays, and middleware, respectively. Adam Meijer and colleagues from the National Institute for Public Health and Environment (Bilthoven, the Netherlands) are acknowledged for organizing quality assurances. J.F. conceived, designed, and analyzed the data. A.T.T. and C.M.A.S. contributed to designation and analysis of the work. D.T., N.X.J.B., R.P., H.J.V., and J.M. contributed to acquisition of the data. J.F. wrote the manuscript. All authors read and approved the final version.
| Financiers | Financiernummer |
|---|---|
| Labhelp International B.V. | |
| Laboratory for Clinical Chemistry | |
| National Institute for Public Health and the Environment (RIVM) |
Duurzame ontwikkelingsdoelstellingen van de VN
Deze output draagt bij aan de volgende duurzame ontwikkelingsdoelstelling(en)
