Development and Performance Evaluation of T-prep24: A Novel Automated Nucleic Acid Extraction System Based on Silica Magnetic Beads

Abstract

Background: Rapid molecular detection of infectious pathogen with high sensitivity and specificity has become increasingly important in clinical microbiology laboratories. The need to develop domestically produced nucleic acid extraction equipment has grown since COVID-19 pandemic in South Korea. In this study, we developed a new magnetic bead-based automated nucleic acid extraction system, T-Prep24 system, and the performance of the new system was evaluated with many clinical specimens. Methods: A total of 180 respiratory specimens were collected, and nucleic acids were extracted using three different systems, the T-Prep24 system, TANBead system, and Qiagen system. The quality and concentration of extracted nucleic acid were evaluated by spectrophotometer and Qubit fluorometer. Qualitative determination for SARS-CoV-2 was performed by PowerChek SARS-CoV-2 Real-time PCR kit. Results: The median concentration of nucleic acid extracted by T-Prep24 system and measured by a fluorescence-based method was 0.685 ng/mu L (first to third interquartile range, 0.258-1.493 ng/mu L), which was lower than that of nucleic acid extracted by TANBead system (median value, 0.985 ng/mu L; first to third interquartile range, 0.610-1.583 ng/mu L; p < 0.001), and that of nucleic acid extracted by Qiagen system (median value, 4.710 ng/<mu>L; first to third interquartile range, 3.783-5.810 ng/mu L; p < 0.001). The Cq values of PCR assays using nucleic acid extracted by T-prep24 showed minimal systematic bias (slope = 1.015) when compared with those using nucleic acid extracted by TANBead, but significant proportional constant bias (slope = 0.907) when compared with those using nucleic acid extracted by Qiagen. The results of PCR assays using nucleic acid extracted by the T-Prep24 system were identical to those of PCR assays using nucleic acid extracted by TANBead system, and two discrepant results were identified when comparing with those by the Qiagen system. Conclusions: T-Prep24 system is a reliable and effective tool for nucleic acid extraction in clinical settings. Future investigations should be carried out to widen the applicability to a range of pathogens and sample types.