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

• Published in: Journal of virological methods Vol. 300; p. 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: Journal Article
• Language: English
• Published: Netherlands 01-02-2022
• Subjects: COVID-19; Diagnostic Tests, Routine; Humans; Nasopharynx; Retrospective Studies; RNA, Viral - genetics; SARS-CoV-2; Sensitivity and Specificity; COVID-19; Molecular diagnostics; Coronavirus; Real time PCR; Ct cut-off
• ISSN: 1879-0984

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.