Performance of RT-qPCR detection of SARS-CoV-2 in unextracted nasopharyngeal samples using the Seegene AllplexTM 2019-nCoV protocol

•SARS-CoV-2 RNA detection in unextracted nasopharyngeal swabs save time and costs.•The modified Allplex protocol is a rapid and efficient method to detect SARS-CoV-2.•A Ct cut-off of 35 increased the NPA between the modified Allplex and USA CDC tests. The rapid spread of the Severe Acute Respiratory...

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Published in:Journal of virological methods 2022-02, Vol.300, p.114429-114429, Article 114429
Main Authors: Barros, Flavia R.O., Leite, Deborah C.A., Guimarães, Larissa J., Lopes, Juliana M.H., Vasconcelos, Marina W., Ferreira, Luciane X., Gonçalves, Sandrieli, Pastre, Victor G.F., Pereira, Gabriela, Trentin, Alex B., Gabiatti, Naiana C., Kuhn, Betty C., Perseguini, Juliana M.K.C., Wendt, Simone N., Ghisi, Nédia C.
Format: Article
Language:English
Subjects:
Coronavirus
COVID-19
Ct cut-off
Molecular diagnostics
Protocols
Real time PCR
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Summary:•SARS-CoV-2 RNA detection in unextracted nasopharyngeal swabs save time and costs.•The modified Allplex protocol is a rapid and efficient method to detect SARS-CoV-2.•A Ct cut-off of 35 increased the NPA between the modified Allplex and USA CDC tests. The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led the world to a pandemic. Therefore, rapid, sensitive, and reproducible diagnostic tests are essential to indicate which measures should be taken during pandemics. We retrospectively tested unextracted nasopharyngeal samples from consecutive patients with suspected SARS-CoV-2 infection (n = 334), and compared two different Ct cut-off values for interpretation of results using a modified Allplex protocol. Its performance was evaluated using the USA Centers for Disease Control and Prevention (CDC) as reference. The reduction on Ct cut-off to 35 increased the test NPA from 79.65 to 88.00 %, reducing the number of false positives, from 10.48 to 6.29 %, resulting in an almost perfect agreement between the Allplex and the CDC protocol (Cohen’s Kappa coefficient = 0.830 ± 0.032). This study demonstrates that the Seegene Allplex™ 2019-nCoV protocol skipping the viral RNA extraction step using the Ct cut-off of 35 is a rapid and efficient method to detect SARS-CoV-2 in nasopharyngeal samples.
ISSN:0166-0934
1879-0984
DOI:10.1016/j.jviromet.2021.114429