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Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants

The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant...

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Autores principales: De Pace, Vanessa, Bruzzone, Bianca, Orsi, Andrea, Ricucci, Valentina, Domnich, Alexander, Guarona, Giulia, Randazzo, Nadia, Stefanelli, Federica, Battolla, Enrico, Dusi, Pier Andrea, Lillo, Flavia, Icardi, Giancarlo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8876857/
https://www.ncbi.nlm.nih.gov/pubmed/35208761
http://dx.doi.org/10.3390/microorganisms10020306
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author De Pace, Vanessa
Bruzzone, Bianca
Orsi, Andrea
Ricucci, Valentina
Domnich, Alexander
Guarona, Giulia
Randazzo, Nadia
Stefanelli, Federica
Battolla, Enrico
Dusi, Pier Andrea
Lillo, Flavia
Icardi, Giancarlo
author_facet De Pace, Vanessa
Bruzzone, Bianca
Orsi, Andrea
Ricucci, Valentina
Domnich, Alexander
Guarona, Giulia
Randazzo, Nadia
Stefanelli, Federica
Battolla, Enrico
Dusi, Pier Andrea
Lillo, Flavia
Icardi, Giancarlo
author_sort De Pace, Vanessa
collection PubMed
description The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant panel (n = 72) of SARS-CoV-2-positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild-type strains circulating in Liguria (Italy) from January to August 2021. First, NGS libraries of study samples were prepared and mapped to the reference genome. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. The overall accuracy of these assays ranged from 96.9% to 100%. Specificity and sensitivity were 100% and 96–100%, respectively. We highly recommend the use of these assays as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics, as they are accurate, user friendly, low cost, may identify specific mutations in about 2–3 h and, therefore, optimize the surveillance of SARS-CoV-2 variants.
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spelling pubmed-88768572022-02-26 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants De Pace, Vanessa Bruzzone, Bianca Orsi, Andrea Ricucci, Valentina Domnich, Alexander Guarona, Giulia Randazzo, Nadia Stefanelli, Federica Battolla, Enrico Dusi, Pier Andrea Lillo, Flavia Icardi, Giancarlo Microorganisms Article The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant panel (n = 72) of SARS-CoV-2-positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild-type strains circulating in Liguria (Italy) from January to August 2021. First, NGS libraries of study samples were prepared and mapped to the reference genome. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. The overall accuracy of these assays ranged from 96.9% to 100%. Specificity and sensitivity were 100% and 96–100%, respectively. We highly recommend the use of these assays as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics, as they are accurate, user friendly, low cost, may identify specific mutations in about 2–3 h and, therefore, optimize the surveillance of SARS-CoV-2 variants. MDPI 2022-01-27 /pmc/articles/PMC8876857/ /pubmed/35208761 http://dx.doi.org/10.3390/microorganisms10020306 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
De Pace, Vanessa
Bruzzone, Bianca
Orsi, Andrea
Ricucci, Valentina
Domnich, Alexander
Guarona, Giulia
Randazzo, Nadia
Stefanelli, Federica
Battolla, Enrico
Dusi, Pier Andrea
Lillo, Flavia
Icardi, Giancarlo
Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants
title Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants
title_full Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants
title_fullStr Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants
title_full_unstemmed Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants
title_short Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants
title_sort comparative analysis of five multiplex rt-pcr assays in the screening of sars-cov-2 variants
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8876857/
https://www.ncbi.nlm.nih.gov/pubmed/35208761
http://dx.doi.org/10.3390/microorganisms10020306
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