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

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 nasoph...

Full description

Saved in:
Bibliographic Details
Published in:Journal of virological methods 2022-02, 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: Article
Language:English
Subjects:
COVID-19
Diagnostic Tests, Routine
Humans
Nasopharynx
Retrospective Studies
RNA, Viral - genetics
SARS-CoV-2
Sensitivity and Specificity
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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:1879-0984