Evaluation of ExiPrep16 Automated System for the Extraction of Nucleic Acids from Nasopharyngeal Swabs for the Detection of Respiratory Viruses

Koung Sun Lee; Do Sim Park; Kui Hyun Yoon; Young Jin Lee; Ji Hyun Cho

doi:10.3343/lmo.2013.3.4.227

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Lee, Park, Yoon, Lee, and Cho: Evaluation of ExiPrep16 Automated System for the Extraction of Nucleic Acids from Nasopharyngeal Swabs for the Detection of Respiratory Viruses

Original Article

Clinical Microbiology

Laboratory Medicine Online 2013; 3(4): 227-233.

Published online: 1 October 2013

DOI: https://doi.org/10.3343/lmo.2013.3.4.227

Evaluation of ExiPrep16 Automated System for the Extraction of Nucleic Acids from Nasopharyngeal Swabs for the Detection of Respiratory Viruses

Koung Sun Lee, M.D.¹, Do Sim Park, M.D.¹, Kui Hyun Yoon, M.D.², Young Jin Lee, M.D.¹, Ji Hyun Cho, M.D.¹

¹Department of Laboratory Medicine, School of Medicine, Wonkwang University, Iksan, Korea.

²Department of Laboratory Medicine, Wonkwang University Sanbon Hospital, Gunpo, Korea.

Corresponding author: Ji Hyun Cho. Department of Laboratory Medicine, School of Medicine, Wonkwang University, 895 Muwang-ro, Iksan 570-711, Korea. Tel: +82-63-859-1861, Fax: +82-63-842-3786, cjh@wonkwang.ac.kr

Received 21 August 2012 Revised 9 November 2012 Accepted 12 November 2012

(open-access):

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background

Automated nucleic acid extraction offers a standardized sample treatment method, low error rate, and avoids sample nucleic acid contamination for use in molecular diagnostics. Here, we evaluated the performance of automated ExiPrep16 system (Bioneer Co.) in comparison with the manual Viral Gene-spin Viral DNA/RNA Extraction kit (VGspin; iNtRON Biotechnology Inc.) for the detection of respiratory viruses from nasopharyngeal flocked swabs.

Methods

To compare the agreement rate and analytical sensitivity between ExiPrep16 and VGspin, previously collected 78 patient samples and 11 pooled samples of each respiratory viruses and their serially diluted samples (until 1/10⁸), were tested by multiplex reverse-transcriptase PCR (Seeplex RV 12 ACE Detection kit; SeeGene Inc.). In addition, we repeatedly analyzed the threshold cycle of the pooled and 1/10³ dilution of adenovirus (ADV) and influenza virus A (Flu-A) by using real-time PCR to evaluate the precision and crossover of the ExiPrep16 system.

Results

The analytical sensitivity of the ExiPrep16 was comparable to that of VGspin, and the highest detectable dilution varied in the range of 1/10 to 1/10⁶ depending on the viruses. The total, overall positive and negative percent agreements of ExiPrep16 in comparison with VGspin were 95.7%, 96.2%, and 95.2%, respectively. The mean (CV%) of pooled and 1/10³ dilution of ADV were, respectively, 19.2 cycle (2.1%) and 31.6 cycle (4.3%) and those for Flu-A were 22.6 cycle (3.1%) and 35.5 cycle (2.6%). No carryover was detected.

Conclusions

Compared to the manual VGspin, ExiPrep16 ensured nucleic acid extraction for efficient detection of respiratory viruses.

Keywords: Nucleic acid amplification, Molecular diagnostics, respiratory virus

Figures and Tables

Table 1

Comparison of the analytical sensitivity between manual Viral gene-spin Viral DNA/RNA Extraction kit (VGspin) and automatic ExiPrep16 system

+: thick band, w+: thin band confirmed repeatedly, ww+: thin band, but cannot be confirmed repeatedly.

Abbreviations: ADV, adenovirus; Flu-A, influenza virus A; Flu-B, influenza virus B; PIV, parainfluenza virus; RSV, respiratory syncytial virus; hMPV, human metapneumovirus; hRV, human rhinovirus.

Table 2

Agreement rate between manual VGspin kitand automatic ExiPrep16 system for the detection of respiratory viruses in flocked nasopharyngeal swabs

^*Measurement of agreement (K) between ExiPrep16 and VGspin was 0.914; ^†including 1 case of RSV-A and 1 case of hRV-A; ^‡including 1 case of hMPV and 1 case of ADV.

Table 3

Reproducibility of Ct values analysed by real-time PCR using nucleic acid extracted by automatic ExiPrep16 system

Abbreviations: Ct, threshold cycle; CI, confidence interval.

Notes

This article is available from http://www.labmedonline.org

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