tetano
Editor, Senior Moderator
J Virol Methods
. 2021 Dec 14;300:114429.
doi: 10.1016/j.jviromet.2021.114429. Online ahead of print.
Performance of RT-qPCR detection of SARS-CoV-2 in unextracted nasopharyngeal samples using the Seegene Allplex [SUP]TM[/SUP] 2019-nCoV protocol
Flavia R O Barros[SUP] 1 [/SUP], Deborah C A Leite[SUP] 2 [/SUP], Larissa J Guimarães[SUP] 3 [/SUP], Juliana M H Lopes[SUP] 3 [/SUP], Marina W Vasconcelos[SUP] 3 [/SUP], Luciane X Ferreira[SUP] 3 [/SUP], Sandrieli Gonçalves[SUP] 3 [/SUP], Victor G F Pastre[SUP] 3 [/SUP], Gabriela Pereira[SUP] 3 [/SUP], Alex B Trentin[SUP] 3 [/SUP], Naiana C Gabiatti[SUP] 3 [/SUP], Betty C Kuhn[SUP] 3 [/SUP], Juliana M K C Perseguini[SUP] 3 [/SUP], Simone N Wendt[SUP] 3 [/SUP], Nédia C Ghisi[SUP] 4 [/SUP]
Affiliations
Abstract
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.
Keywords: COVID-19; Coronavirus; Ct cut-off; Molecular diagnostics; Real time PCR.
. 2021 Dec 14;300:114429.
doi: 10.1016/j.jviromet.2021.114429. Online ahead of print.
Performance of RT-qPCR detection of SARS-CoV-2 in unextracted nasopharyngeal samples using the Seegene Allplex [SUP]TM[/SUP] 2019-nCoV protocol
Flavia R O Barros[SUP] 1 [/SUP], Deborah C A Leite[SUP] 2 [/SUP], Larissa J Guimarães[SUP] 3 [/SUP], Juliana M H Lopes[SUP] 3 [/SUP], Marina W Vasconcelos[SUP] 3 [/SUP], Luciane X Ferreira[SUP] 3 [/SUP], Sandrieli Gonçalves[SUP] 3 [/SUP], Victor G F Pastre[SUP] 3 [/SUP], Gabriela Pereira[SUP] 3 [/SUP], Alex B Trentin[SUP] 3 [/SUP], Naiana C Gabiatti[SUP] 3 [/SUP], Betty C Kuhn[SUP] 3 [/SUP], Juliana M K C Perseguini[SUP] 3 [/SUP], Simone N Wendt[SUP] 3 [/SUP], Nédia C Ghisi[SUP] 4 [/SUP]
Affiliations
- PMID: 34919975
- DOI: 10.1016/j.jviromet.2021.114429
Abstract
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.
Keywords: COVID-19; Coronavirus; Ct cut-off; Molecular diagnostics; Real time PCR.