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      Evaluation of the automated cartridge-based ARIES SARS-CoV-2 Assay (RUO) against automated Cepheid Xpert Xpress SARS-CoV-2 PCR as gold standard

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          Abstract

          Introduction

          To evaluate the automated cartridge-based PCR approach ARIES SARS-CoV-2 Assay targeting the ORF-sequence and the N-gene of SARS-CoV-2.

          Methods

          In line with the suggestions by Rabenau and colleagues, the automated ARIES SARS-CoV-2 Assay was challenged with strongly positive samples, weakly positive samples and negative samples. Further, intra-assay and inter-assay precision as well as the limit-of-detection (lod) were defined with quantified target RNA and DNA. The Cepheid Xpert Xpress SARS-Cov-2 Assay was used as gold standard.

          Results

          Concordance between the ARIES assay and the Cepheid assay was 100% for strongly positive samples and for negative samples, respectively. For weakly positive samples as confirmed applying the Cepheid assay, a relevant minority of 4 out of 15 samples (26.7%) went undetected by the ARIES assay. Intra- and inter-assay precision were satisfactory, while the lod was in the 10 3 DNA copies/reaction-range, in the 10 3 virus copies/reaction-range, or in the 10 3-10 4 free RNA copies/reaction-range in our hands.

          Conclusions

          The automated ARIES assay shows comparable test characteristics as the Cepheid assay focusing on strongly positive and negative samples but a slightly reduced sensitivity with weakly positive samples. Decisions on diagnostic use should include considerations on the lod.

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          Most cited references20

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          A pneumonia outbreak associated with a new coronavirus of probable bat origin

          Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1–4 . Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5–7 . Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.
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            Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

            Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. Aim We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. Methods Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. Results The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project. Conclusion The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.
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              The measurement of observer agreement for categorical data.

              This paper presents a general statistical methodology for the analysis of multivariate categorical data arising from observer reliability studies. The procedure essentially involves the construction of functions of the observed proportions which are directed at the extent to which the observers agree among themselves and the construction of test statistics for hypotheses involving these functions. Tests for interobserver bias are presented in terms of first-order marginal homogeneity and measures of interobserver agreement are developed as generalized kappa-type statistics. These procedures are illustrated with a clinical diagnosis example from the epidemiological literature.
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                Author and article information

                Journal
                Eur J Microbiol Immunol (Bp)
                Eur J Microbiol Immunol (Bp)
                EUJMI
                European Journal of Microbiology & Immunology
                Akadémiai Kiadó (Budapest )
                2062-509X
                2062-8633
                17 August 2020
                14 October 2020
                : 10
                : 3
                : 156-164
                Affiliations
                [1 ] Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg , Hamburg, Germany
                [2 ] Department of Laboratory Medicine, Bundeswehr Hospital Hamburg , Hamburg, Germany
                [3 ] Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock , Rostock, Germany
                Author notes
                *Corresponding author. Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Bernhard Nocht Str. 74, D-20359 Hamburg, Germany E-mail: Frickmann@ 123456bni-hamburg.de
                Article
                10.1556/1886.2020.00017
                7592518
                32804668
                98a175ae-2fb1-48cb-92a8-889bf51cf321
                © 2020, The Authors

                Open Access statement. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted use, distribution, and reproduction in any medium for non-commercial purposes, provided the original author and source are credited, a link to the CC License is provided, and changes - if any - are indicated.

                Page count
                Figures: 0, Tables: 8, Equations: 0, References: 24, Pages: 9
                Categories
                Original Research Paper

                sars-cov-2,covid-19,point-of-care-testing,automated pcr,molecular rapid testing,testing comparison

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