Evaluation of Three Automated Extraction Systems for the Detection of SARS-CoV-2 from Clinical Respiratory Specimens

Lim, Ho Jae; Jung, Hye-Soo; Park, Min-Young; Baek, Yong-Hyeon; Kannappan, Balaji; Park, Jin‐Young; Yang, Jae-Hyun; Seol, Ja-Hwan; Lee, Minwoo; Jung, Sung-Cherl; Lee, Sun-Hwa; Park, Jung-Eun; Yang, Yong

doi:10.3390/life12010068

Cited by 15 publications

(20 citation statements)

References 33 publications

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“…It demonstrated a sensitivity of 100 % compared to the reference laboratory method and viral detection down to 2.80 copies μl −1 (2800 copies ml –1 ) [9]. There are a range of other well-established commercial extraction platforms used in pathogen diagnostics for the molecular detection of SARS-CoV-2 in respiratory samples, and all of the major commercial methods tested have been found to have good agreement, with recommendations that they could be interchanged [10–13]. The difficulties experienced worldwide in procuring laboratory equipment and reagents have necessitated diagnostic microbiology laboratories to explore other extraction and testing platforms on the market.…”

Section: Discussionmentioning

confidence: 99%

A comparison of SARS-CoV-2 RNA extraction with the QuickGene-810 Nucleic Acid Isolation System compared to the EZ1 Advanced DSP Virus Kit

Phan

Stephenson

Cai

et al. 2022

Access Microbiology

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The QuickGene-810 Nucleic Acid Isolation System is a semi-automated extraction platform which may be used for RNA extraction. New methods were required to support the rapid increase in respiratory virus testing during the SARS-CoV-2 pandemic. The aim of this study was to assess SARS-CoV-2 RNA extraction using the QuickGene-810 kit compared to the EZ1 Advanced Extraction Platform for use on the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well RT-PCR assay. Qualitative results from all clinical samples were concordant between the QuickGene-810 and the EZ1 extraction methods, demonstrating that the QuickGene-810 kit is suitable for use in pathogen diagnostics. However, there was an average difference of approximately two cycles between the cycle threshold (Ct) values for both SARS-CoV-2 targets, suggesting that the EZ1 kit yields a higher concentration of nucleic acid extract, possibly related to its use of carrier RNA and/or smaller elution volume, which infers the possibility of false negative results for samples with very low viral loads.

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Section: Discussionmentioning

confidence: 99%

A comparison of SARS-CoV-2 RNA extraction with the QuickGene-810 Nucleic Acid Isolation System compared to the EZ1 Advanced DSP Virus Kit

Phan

Stephenson

Cai

et al. 2022

Access Microbiology

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“…Based on the collection site, ALLTM and SELTM universal transport media were classified into two sets of swabs. Nucleic acids were simultaneously extracted from HCW- and self-collected specimens using the automated MagNA Pure 96 system (Roche, Inc., Basel, Switzerland), as described previously [ 23 ]. Following the Pathogen Universal 200 protocol, 200 µL of the samples was processed using magnetic beads for nucleic acid extraction.…”

Section: Methodsmentioning

confidence: 99%

Performance Analysis of Self-Collected Nasal and Oral Swabs for Detection of SARS-CoV-2

Lim

Baek²,

Park³

et al. 2022

Diagnostics

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third highly pathogenic human coronavirus and is rapidly transmitted by infected individuals regardless of their symptoms. During the COVID-19 pandemic, owing to the dearth of skilled healthcare workers (HCWs) to collect samples for early diagnosis, self-collection emerged as a viable alternative. To evaluate the reliability of self-collection, we compared the virus detection rate using 3990 self-collected swabs and HCW-collected swabs, procured from the same individuals and collected immediately after the self-collection. The results of multiplex reverse-transcription quantitative polymerase chain reaction revealed that the viral load in the HCW-collected swabs was marginally (18.4–28.8 times) higher than that in self-collected swabs. Self-collection showed no significant difference in sensitivity and specificity from HCW-collection (κ = 0.87, McNemar’s test; p = 0.19), indicating a comparable performance. These findings suggest that self-collected swabs are acceptable substitutes for HCW-collected swabs, and that their use improved the specimen screening efficiency and reduced the risk of SARS-CoV-2 infection among HCWs during and after the COVID-19 pandemic.

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“…Three SARS-CoV-2-positive samples were selected for stability assessment, and 72 vials of additional samples were prepared in each medium. All samples were processed using an automated nucleic acid extraction system (MagNA Pure 96; Roche, Basel, Switzerland), in accordance with the “Pathogen Universal 200” protocol described in a previous study [ 21 ]. In brief, the MagNA Pure 96 DNA and Viral NA Small Volume kit (Roche) was used, and 200 μ L of each sample was transferred to the cartridge.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, we compared the three media to evaluate the stability of incubation conditions and storage duration. [21].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Alternative Transport Media for RT-qPCR-Based SARS-CoV-2 Testing

Baek¹,

Park²,

Lim

et al. 2022

International Journal of Analytical Chemistry

Self Cite

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), is still rapidly spreading as of March 2022. An accurate and rapid molecular diagnosis is essential to determine the exact number of confirmed cases. Currently, the viral transport medium (VTM) required for testing is in short supply due to a sharp increase in the laboratory tests performed, and alternative VTMs are needed to alleviate the shortage. Guanidine thiocyanate-based media reportedly inactivate SARS-CoV-2 and are compatible with quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays, but the compatibility and the viral detection capacity have not been fully validated. To evaluate the guanidine thiocyanate-based Gene Transport Medium (GeneTM) as an alternative VTM, we prepared 39 SARS-CoV-2-positive and 7 SARS-CoV-2-negative samples in GeneTM, eNAT™, and phosphate-buffered saline (PBS). The cycle threshold (Ct) values of three SARS-CoV-2 targets (the S, RdRP, and N genes) were analyzed using RT-qPCR testing. The comparison of Ct values from the positive samples showed a high correlation (R2= 0.95–0.96) between GeneTM and eNAT™, indicating a comparable viral detection capacity. The delta Ct values of the SARS-CoV-2 genes in each transport medium were maintained for 14 days at cold (4°C) or room (25°C) temperatures, suggesting viral samples were stably preserved in the transport media for 14 days. Together, GeneTM is a potential alternative VTM with comparable RT-qPCR performance and stability to those of standard media.

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Evaluation of Three Automated Extraction Systems for the Detection of SARS-CoV-2 from Clinical Respiratory Specimens

Cited by 15 publications

References 33 publications

A comparison of SARS-CoV-2 RNA extraction with the QuickGene-810 Nucleic Acid Isolation System compared to the EZ1 Advanced DSP Virus Kit

A comparison of SARS-CoV-2 RNA extraction with the QuickGene-810 Nucleic Acid Isolation System compared to the EZ1 Advanced DSP Virus Kit

Performance Analysis of Self-Collected Nasal and Oral Swabs for Detection of SARS-CoV-2

Evaluation of Alternative Transport Media for RT-qPCR-Based SARS-CoV-2 Testing

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