Comparison of the new fully automated extraction platform eMAG to the MagNA PURE 96 and the well-established easyMAG for detection of common human respiratory viruses

RESEARCH ARTICLE Comparison of the new fully automated extraction platform eMAG to the MagNA PURE 96 and the well-established easyMAG for detection of common human respiratory viruses Musa Hindiyeh1,2☯, Orna Mor ID1,2☯, Rakefet Pando1,3, Batya Mannasse1, Areej Kabat1,2, Hadar Assraf-Zarfati1, Ella Mendelson1,2, Danit Sofer1, Michal Mandelboim ID1,2* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel, 2 Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel, 3 The Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Israel ☯ These authors contributed equally to this work. * Abstract OPEN ACCESS Citation: Hindiyeh M, Mor O, Pando R, Mannasse B, Kabat A, Assraf-Zarfati H, et al. (2019) Comparison of the new fully automated extraction platform eMAG to the MagNA PURE 96 and the well-established easyMAG for detection of common human respiratory viruses. PLoS ONE 14(2): e0211079. https://doi.org/10.1371/journal. pone.0211079 Editor: Olivier Terrier, Centre International de Recherche en Infectiologie, FRANCE Received: October 15, 2018 Accepted: January 7, 2019 Published: February 19, 2019 Copyright: © 2019 Hindiyeh et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Respiratory viral infections constitute the majority of samples tested in the clinical virology laboratory during the winter season, and are mainly diagnosed using molecular assays, namely real-time PCR (qPCR). Therefore, a high-quality extraction process is critical for successful, reliable and sensitive qPCR results. Here we aimed to evaluate the performance of the newly launched eMAG compared to the fully automated MagNA PURE 96 (Roche, Germany) and to the semi-automated easyMAG (bioMerieux, France) extraction platforms. For this analysis, we assessed and compared the analytic and clinical performance of the three platforms, using 262 archived respiratory samples positive or negative to common viruses regularly examined in our laboratory (influenza A, B, H1N1pdm, Respiratory Syncytial Virus (RSV), human Metapneumovirus (hMPV), parainfluenza-3, adenovirus and negative samples). In addition, quantitated virus controls were used to determine the limit of detection of each extraction method. In all categories tested, eMAG results were comparable to those of the easyMAG and MagNa PURE 96, highly sensitive for all viruses and over 98% clinical specificity and sensitivity for all viruses tested. Together with its high level of automation, the bioMerieux eMAG is a high-quality extraction platform enabling effective molecular analysis and is mostly suitable for medium-sized laboratories. Data Availability Statement: All relevant data are within the manuscript. Funding: The authors received no funding for this work. Introduction Competing interests: The authors have declared that no competing interests exist. Respiratory viral infections are a major cause of morbidity and mortality worldwide [1] and have been shown to be the etiological agents of more than 70% of respiratory tract infections PLOS ONE | https://doi.org/10.1371/journal.pone.0211079 February 19, 2019 1/9 Comparison of the new fully automated extraction platforms (RTIs) [2]. Nucleic acid-based tests, mostly performed in multiplexes by real-time PCR (qPCR) platforms, are the most common and efficient means of detecting viral infections, and support rapid and simultaneous detection of many viruses [3,4]. The nucleic acids extraction process is one of the most significant steps dictating the accuracy and sensitivity of viral infection diagnosis and virus type determination. Moreover, efficient extraction allows for the detection of different viral agents including DNA and RNA viruses, from a single extraction tube. Using qPCR technology, the Israeli Central Virology Laboratory performs viral detection on more than 10,000 respiratory samples each year, which constitute the majority of samples requiring nucleic acid extraction process in our laboratory. NUCLISENS easyMAG (bioMérieux, France) is a second-generation silica-based semiautomatic platform that was first launched in 2005. It was specifically optimized for total nucleic acid extraction from biological samples. The system automates enhanced magnetic silica-based extraction based on the BOOM technology, a gold standard for the universal extraction of RNA and DNA based on the ability of silica to bind DNA and RNA in high salt concentrations [5]. eMAG (bioMérieux, France) is a new, fully automated nucleic acid extraction platform that enables simultaneous extraction of 48 specimens from primary tubes, either into PCR strips ready for qPCR analysis or into storage tubes. eMAG also utilizes the already well-established BOOM technology as the easyMAG [5]. MagNA PURE 96 (Roche, Germany), which was launched in 2009, was also shown to have excellent nucleic acid extraction efficiency for clinical samples [6]. This system is a fully automated extraction system that enables simultaneous extraction of 96 specimens using magnetic bead technology, from a 96 deep-well plate to a PCR plate. The performance of the semi-automated easyMAG system has been extensively investigated; the platform was shown to efficiently extract viral nucleic acid [7,8]. In a study that compared the performance of the new eMAG and the easyMAG systems, eMAG was shown to perform equally well on several types of clinical samples including respiratory samples [9]. However, no large-scale study has simultaneously compared the performance of the eMAG to that of easyMAG and MagNA PURE 96 in nucleic acid extraction from respiratory samples. In this study, we performed an evaluation of the newly launched eMAG as compared to both easyMAG and the fully automated MagNA PURE 96, with emphasis on the detection of influenza viruses (A, H1N1pdm09 and B), respiratory syncytial virus (RSV), parainfluenza-3, human metapneumovirus (hMPV) and adenovirus, using an in-house-developed qPCR assay [3]. Evaluations were performed using archived clinical samples collected at Sheba Medical Center in Israel, as well as calibrated controls for each virus. Materials and methods Clinical specimens and extraction platform properties Archived nasopharyngeal samples (including Bronchoalveolar lavage (BAL) (N = 8), tracheal aspirations (N = 32) or nasopharyngeal swabs (N = 403)) of patients hospitalized at Chaim Sheba Medical Center, collected into Virocult liquid viral transport medium (LVTM) (Medical Wire & Equipment Co, Wiltshire, United Kingdom) and stored at -70˚C, were used to evaluate the performance of the three extraction systems. Representative samples (...truncated)