Performance of RT-qPCR Detection of SARS-CoV-2 in Unextracted Nasopharyngeal Samples Using the Seegene Allplex 2019-nCoV Protocol

Overview

Journal J Virol Methods

Specialty Microbiology

Date 2021 Dec 17

PMID 34919975

Authors

Flavia R O Barros

Deborah C A Leite

Larissa J Guimaraes

Juliana M H Lopes

Marina W Vasconcelos

Luciane X Ferreira

Sandrieli Goncalves

Victor G F Pastre

Gabriela Pereira

Alex B Trentin

Naiana C Gabiatti

Betty C Kuhn

Juliana M K C Perseguini

Simone N Wendt

Nedia C Ghisi

Affiliations

Soon will be listed here.

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.

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