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. 2021 Nov 1;6(6):1441-1451.
doi: 10.1093/jalm/jfab079.

Implementation of an Extraction-Free COVID Real-Time PCR Workflow in a Pediatric Hospital Setting

Rebekah E Dumm  1   2 , Michael Elkan  1 , Jeffrey Fink  1 , Melissa Richard-Greenblatt  1   2 , Amrom E Obstfeld  1   3 , Rebecca M Harris  1   2
Affiliations

Implementation of an Extraction-Free COVID Real-Time PCR Workflow in a Pediatric Hospital Setting

Rebekah E Dumm et al. J Appl Lab Med. .

Abstract

Background: This study outlines the development, implementation, and impact of a laboratory-developed, extraction-free real-time PCR assay as the primary diagnostic test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a pediatric hospital.

Methods: Clinical specimens from both upper and lower respiratory tract sources were validated, including nasopharyngeal aspirates, nasopharyngeal swabs, anterior nares swabs, and tracheal aspirates (n = 333 clinical samples). Testing volumes and laboratory turnaround times were then compared before and after implementation to investigate effects of the workflow changes.

Results: Compared to magnetic-bead extraction platforms, extraction-free real-time PCR demonstrated ≥95% positive agreement and ≥97% negative agreement across all tested sources. Implementation of this workflow reduced laboratory turnaround time from an average of 8.8 (+/-5.5) h to 3.6 (+/-1.3) h despite increasing testing volumes (from 1515 to 4884 tests per week over the reported period of testing).

Conclusions: The extraction-free workflow reduced extraction reagent cost for SARS-CoV-2 testing by 97%, shortened sample handling time, and significantly alleviated supply chain scarcities due to the elimination of specialized extraction reagents for routine testing. Overall, this assay is a viable option for laboratories to increase efficiency and navigate reagent shortages for SARS-CoV-2 diagnostic testing.

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Figures

Fig. 1
Fig. 1
Schematic of SARS-CoV2 testing workflow in the IDDL. Samples were extracted using either magnetic bead extraction on the MagNA Pure LC 2.0 extraction platform or heat inactivated using extraction-free platform. Graphics were created with Biorender.com.
Fig. 2
Fig. 2
Comparison of methods for samples extracted on the MagNA Pure compared to extraction-free protocols. Sources tested include (A) anterior nares swabs, (B) nasopharyngeal swabs, (C) nasopharyngeal aspirates, and (D) tracheal aspirates. Descriptive statistics include mean and SD between samples run on both platforms. A Student’s t-test was used to determine significant differences between protocols.
Fig. 3
Fig. 3
SARS-CoV-2 testing performance analysis in the IDDL. (A) Daily volume of testing performed by the laboratory developed real-time PCR assay .(B) Laboratory turnaround time in hours from receipt of samples to resulting. Data were compiled from 6 weeks prior to and post implementation of the extraction-free workflow in the laboratory. Boxplot data are shown with minimum, maximum, sample median, and quartiles plotted, and outliers are shown as dots.
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