Evaluation of three commercial assays for SARS-CoV-2 molecular detection in upper respiratory tract samples
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ORIGINAL ARTICLE
Evaluation of three commercial assays for SARS-CoV-2 molecular detection in upper respiratory tract samples Flora Marzia Liotti 1,2 & Giulia Menchinelli 1,2 & Simona Marchetti 2 & Grazia Angela Morandotti 2 & Maurizio Sanguinetti 1,2 & Brunella Posteraro 1,3 & Paola Cattani 1,2 Received: 28 May 2020 / Accepted: 26 August 2020 # The Author(s) 2020
Abstract The increasing COVID-19 widespread has created the necessity to assess the diagnostic accuracy of newly introduced (RT-PCR based) assays for SARS-CoV-2 RNA detection in respiratory tract samples. We compared the results of the Allplex™ 2019nCoV assay with those of the Simplexa™ COVID-19 Direct assay and the Quanty COVID-19 assay, respectively, all performed on 125 nasal/oropharyngeal swab samples of patients with COVID-19 suspicion. Fifty-four samples were positive, and 71 were negative with the Allplex™ assay, whereas 47 of 54 samples were also positive with the Simplexa™ assay. The Quanty assay detected 55 positive samples, including the 54 positive samples with the Allplex™ assay and 1 sample that was Allplex™ negative but Simplexa™ positive. Using a consensus result criterion as the reference standard allowed to resolve the eight samples with discordant results (one Allplex™ negative and seven Simplexa™ negative) as truly false negative. Interestingly, a Spearman’s negative association was found between the viral RNA loads quantified by the Quanty assay and the CT values of RT PCRs performed with either the Allplex™ assay or the Simplexa™ assay. However, the strength of this association was higher for the Allplex™ assay (N gene, ρ = − 0.92; RdRP gene, ρ = − 0.91) than for the Simplexa™ assay (ORF1ab gene, ρ = − 0.65; S gene, ρ = − 0.80). The Allplex™ 2019-nCoV, the Simplexa™ COVID-19 Direct, and the Quanty COVID-19 assays yielded comparable results. However, the role these assays might play in future clinical practice warrants larger comparison studies. Keywords SARS-CoV-2 . COVID-19 . Molecular assay . Viral RNA load . Respiratory samples
Introduction Flora Marzia Liotti, Giulia Menchinelli, Brunella Posteraro and Paola Cattani contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10096-020-04025-0) contains supplementary material, which is available to authorized users. * Maurizio Sanguinetti [email protected] 1
Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
2
Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
3
Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
Since first isolation on December 2019 [1], the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—initially called 2019-nCoV—which causes the illness referred to as coronavirus disease 2019 (COVID-19) has in
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