Journal of virological methods · 2021
Performance of RT-qPCR detection of SARS-CoV-2 in unextracted nasopharyngeal samples using the Seegene AllplexTM 2019-nCoV protocol.
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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
Аннотация
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.