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Implementation of an extraction-free COVID RT-PCR workflow in a pediatric hospital setting.


ABSTRACT:

Background

This study outlines the development, implementation, and impact of a laboratory-developed, extraction-free real-time polymerase chain reaction (RT-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 RT-PCR demonstrated ≥ 95% positive percent agreement and ≥ 97% negative percent agreement across all tested sources. Implementation of this workflow reduced laboratory turnaround time from an average of 8.8 (+/- 5.5) hours to 3.6 (+/- 1.3) hours 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.

SUBMITTER: Dumm RE 

PROVIDER: S-EPMC8394822 | biostudies-literature |

REPOSITORIES: biostudies-literature

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