SARS-CoV-2 variants of concern surveillance including Omicron using RT-PCR–based genotyping offers comparable performance to whole genome sequencing

Known SARS-CoV-2 variants of concern (VOCs) can be detected and differentiated using an RT-PCR–based genotyping approach, which offers quicker time to result, lower cost, higher flexibility, and use of the same laboratory instrumentation for detection of SARS-CoV-2 when compared with whole genome se...

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Autores principales: Vanoni, Simone, Matulevicius, Arnoldas, Avdiu, Besard, Scantamburlo, Giada, Ulekleiv, Camilla, Brzoska, Pius M., Furtado, Manohar R., Feenstra, Jelena D. M., Rico, Alain, Gandhi, Manoj, Giacobazzi, Elisabetta, Masi, Elisa, Paulmichl, Markus, Nofziger, Charity
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Cellular and Infection Microbiology
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9670535/
https://www.ncbi.nlm.nih.gov/pubmed/36405967
http://dx.doi.org/10.3389/fcimb.2022.960065
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author Vanoni, Simone
Matulevicius, Arnoldas
Avdiu, Besard
Scantamburlo, Giada
Ulekleiv, Camilla
Brzoska, Pius M.
Furtado, Manohar R.
Feenstra, Jelena D. M.
Rico, Alain
Gandhi, Manoj
Giacobazzi, Elisabetta
Masi, Elisa
Paulmichl, Markus
Nofziger, Charity
author_facet Vanoni, Simone
Matulevicius, Arnoldas
Avdiu, Besard
Scantamburlo, Giada
Ulekleiv, Camilla
Brzoska, Pius M.
Furtado, Manohar R.
Feenstra, Jelena D. M.
Rico, Alain
Gandhi, Manoj
Giacobazzi, Elisabetta
Masi, Elisa
Paulmichl, Markus
Nofziger, Charity
author_sort Vanoni, Simone
collection PubMed
description Known SARS-CoV-2 variants of concern (VOCs) can be detected and differentiated using an RT-PCR–based genotyping approach, which offers quicker time to result, lower cost, higher flexibility, and use of the same laboratory instrumentation for detection of SARS-CoV-2 when compared with whole genome sequencing (WGS). In the current study, we demonstrate how we applied a genotyping approach for identification of all VOCs and that such technique can offer comparable performance to WGS for identification of known SARS-CoV-2 VOCs, including more recent strains, Omicron BA.1 and BA.2.
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spelling pubmed-96705352022-11-18 SARS-CoV-2 variants of concern surveillance including Omicron using RT-PCR–based genotyping offers comparable performance to whole genome sequencing Vanoni, Simone Matulevicius, Arnoldas Avdiu, Besard Scantamburlo, Giada Ulekleiv, Camilla Brzoska, Pius M. Furtado, Manohar R. Feenstra, Jelena D. M. Rico, Alain Gandhi, Manoj Giacobazzi, Elisabetta Masi, Elisa Paulmichl, Markus Nofziger, Charity Front Cell Infect Microbiol Cellular and Infection Microbiology Known SARS-CoV-2 variants of concern (VOCs) can be detected and differentiated using an RT-PCR–based genotyping approach, which offers quicker time to result, lower cost, higher flexibility, and use of the same laboratory instrumentation for detection of SARS-CoV-2 when compared with whole genome sequencing (WGS). In the current study, we demonstrate how we applied a genotyping approach for identification of all VOCs and that such technique can offer comparable performance to WGS for identification of known SARS-CoV-2 VOCs, including more recent strains, Omicron BA.1 and BA.2. Frontiers Media S.A. 2022-11-03 /pmc/articles/PMC9670535/ /pubmed/36405967 http://dx.doi.org/10.3389/fcimb.2022.960065 Text en Copyright © 2022 Vanoni, Matulevicius, Avdiu, Scantamburlo, Ulekleiv, Brzoska, Furtado, Feenstra, Rico, Gandhi, Giacobazzi, Masi, Paulmichl and Nofziger https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cellular and Infection Microbiology
Vanoni, Simone
Matulevicius, Arnoldas
Avdiu, Besard
Scantamburlo, Giada
Ulekleiv, Camilla
Brzoska, Pius M.
Furtado, Manohar R.
Feenstra, Jelena D. M.
Rico, Alain
Gandhi, Manoj
Giacobazzi, Elisabetta
Masi, Elisa
Paulmichl, Markus
Nofziger, Charity
SARS-CoV-2 variants of concern surveillance including Omicron using RT-PCR–based genotyping offers comparable performance to whole genome sequencing
title SARS-CoV-2 variants of concern surveillance including Omicron using RT-PCR–based genotyping offers comparable performance to whole genome sequencing
title_full SARS-CoV-2 variants of concern surveillance including Omicron using RT-PCR–based genotyping offers comparable performance to whole genome sequencing
title_fullStr SARS-CoV-2 variants of concern surveillance including Omicron using RT-PCR–based genotyping offers comparable performance to whole genome sequencing
title_full_unstemmed SARS-CoV-2 variants of concern surveillance including Omicron using RT-PCR–based genotyping offers comparable performance to whole genome sequencing
title_short SARS-CoV-2 variants of concern surveillance including Omicron using RT-PCR–based genotyping offers comparable performance to whole genome sequencing
title_sort sars-cov-2 variants of concern surveillance including omicron using rt-pcr–based genotyping offers comparable performance to whole genome sequencing
topic Cellular and Infection Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9670535/
https://www.ncbi.nlm.nih.gov/pubmed/36405967
http://dx.doi.org/10.3389/fcimb.2022.960065
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