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™ 2019-nCoV 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.
Highlights
Flora Marzia Liotti, Giulia Menchinelli, Brunella Posteraro and Paola Cattani contributed to this work.Electronic supplementary material The online version of this article contains supplementary material, which is available to authorized users.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 increasingly spread worldwide
Real-time reverse transcription-polymerase chain reaction (RT-PCR)-based assay performed on upper respiratory tract (URT) samples is the current diagnostic strategy to
The aim of this study was to perform a comparative evaluation of the AllplexTM 2019-nCoV (Arrow Diagnostics S.r.l., Genova, Italy), the SimplexaTM COVID-19 Direct (DiaSorin Molecular, Saluggia, Vercelli, Italy), and the Quanty COVID19 (Clonit S.r.l, Milan, Italy) assays on nasal/oropharyngeal swab (NOS) samples of patients screened for SARS-CoV-2 infection
Summary
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 increasingly spread worldwide. By 29 April 2020, the number of confirmed cases reported by the World Health Organization (WHO) had reached 3,023,788 (https://covid19.who.int/), representing an unprecedented viral pandemic. To prevent virus transmission and/or ensure appropriate management of COVID-19 patients [2], clinical microbiology laboratories are constantly requested to implement relatively quick and sensitive diagnostic assays for SARS-CoV-2 RNA detection in clinical samples [3]. Real-time reverse transcription-polymerase chain reaction (RT-PCR)-based assay performed on upper respiratory tract (URT) samples (e.g., nasopharyngeal and/or oropharyngeal swabs) is the current diagnostic strategy to
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