Abstract
Purpose: 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.Methods: We compared the results of the Allplex™ 2019-nCoV assay with those of the Simplexa™ COVID-19 Direct assay, both performed on 125 nasal/oropharyngeal swab samples of patients with COVID-19 suspicion.Results: Fifty-four samples tested positive (CT below 40) and 71 negative (CT above 40) with the Allplex™ 2019-nCoV assay, whereas 47 of 54 samples were also positive with the Simplexa™ COVID-19 Direct assay. Eight results were discordant, resulting in 93.6% agreement between the assays. We used the Quanty COVID-19 assay—developed to detect and quantify SARS–CoV-2 in respiratory tract samples—to arbitrate these results. One Allplex™ 2019-nCoV negative (but Simplexa™ COVID-19 positive) and seven Simplexa™ COVID-19 negative samples were truly false negative. Interestingly, a Spearman’s negative association was found between the viral RNA loads quantified by the Quanty COVID-19 assay and the CT values of RT PCRs performed with either the Allplex™ 2019–nCoV assay or the Simplexa™ COVID-19 Direct assay. However, the strength of this association was higher for the Allplex™ 2019–nCoV assay (N gene, ρ = −0.92; RdRP gene, ρ = −0.91) than for the Simplexa™ COVID-19 Direct assay (ORF1ab gene, ρ = −0.65; S gene, ρ = −0.80).Conclusion: The Allplex™ 2019–nCoV and Simplexa™ COVID-19 Direct assays yielded comparable results. However, the role these assays might play in future clinical practice warrants larger comparison studies.