Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay

ABSTRACT: Background: The emergence of SARS-CoV-2 variants of concern (VOCs) for increased transmissibility and being potentially capable of immune-escape mandates for epidemiological surveillance. Genomic alterations present in VOCs can affect the results of RT-qPCR assays for routine diagnostic p...

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Autores principales:	Nicla Giovacchini, Marco Coppi, Noemi Aiezza, Ilaria Baccani, Francesca Malentacchi, Simona Pollini, Alberto Antonelli, Gian Maria Rossolini
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Rapid screening method SARS-CoV-2 VOC B.1.1.7 lineage Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/9b93b829cdeb4dc6a29ec67c887d7169
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spelling	oai:doaj.org-article:9b93b829cdeb4dc6a29ec67c887d71692021-11-10T04:21:22ZRapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay1201-971210.1016/j.ijid.2021.10.005https://doaj.org/article/9b93b829cdeb4dc6a29ec67c887d71692021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S120197122100792Xhttps://doaj.org/toc/1201-9712ABSTRACT: Background: The emergence of SARS-CoV-2 variants of concern (VOCs) for increased transmissibility and being potentially capable of immune-escape mandates for epidemiological surveillance. Genomic alterations present in VOCs can affect the results of RT-qPCR assays for routine diagnostic purposes, leading to peculiar profiles that can be used for rapid screening of variants. This study reports a peculiar profile observed with the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay and VOC-Alpha (202012/01, lineage B.1.1.7, also named VOC-UK), which was the first identified SARS-CoV-2 VOC. Methods: Samples were analyzed by two RT-qPCR assays: the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay (ASFR, Seegene Technologies Inc; Seoul, South Korea) and the TaqPath COVID-19 RT-PCR (Thermo Fisher Scientific, USA). Definition of the SARS-CoV-2 variant was carried out by Sanger sequencing of the relevant S-gene regions and, in some cases, by whole genome sequencing (WGS) using the ARTIC-nCoV workflow on a MiniION (Oxford Nanopore Technologies, Oxford, UK) or a Illumina MiSeq platform (San Diego, California, USA). Results: Of the 173 SARS-CoV-2-positive specimens, all those of lineage B.1.1.7 (N=71) showed an average Cq difference between the N and S genes of +11±2 (range, +8/+15). None of the other specimens, including several different lineages (Wild-type for the analyzed regions, N=22; Gamma, N=63; Delta, N=9; B.1.258Δ, N=3; B.1.160, N=3; B.1.177.7, N=1; B.1.1.420, N=1), exhibited a similar difference in Cq values. Conclusions: The peculiar pattern of delayed N gene positivity could constitute a convenient method for VOC-Alpha screening, simultaneous to viral detection, when using the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay.Nicla GiovacchiniMarco CoppiNoemi AiezzaIlaria BaccaniFrancesca MalentacchiSimona PolliniAlberto AntonelliGian Maria RossoliniElsevierarticleRapid screening methodSARS-CoV-2 VOCB.1.1.7 lineageInfectious and parasitic diseasesRC109-216ENInternational Journal of Infectious Diseases, Vol 113, Iss , Pp 207-209 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Rapid screening method SARS-CoV-2 VOC B.1.1.7 lineage Infectious and parasitic diseases RC109-216
spellingShingle	Rapid screening method SARS-CoV-2 VOC B.1.1.7 lineage Infectious and parasitic diseases RC109-216 Nicla Giovacchini Marco Coppi Noemi Aiezza Ilaria Baccani Francesca Malentacchi Simona Pollini Alberto Antonelli Gian Maria Rossolini Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay
description	ABSTRACT: Background: The emergence of SARS-CoV-2 variants of concern (VOCs) for increased transmissibility and being potentially capable of immune-escape mandates for epidemiological surveillance. Genomic alterations present in VOCs can affect the results of RT-qPCR assays for routine diagnostic purposes, leading to peculiar profiles that can be used for rapid screening of variants. This study reports a peculiar profile observed with the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay and VOC-Alpha (202012/01, lineage B.1.1.7, also named VOC-UK), which was the first identified SARS-CoV-2 VOC. Methods: Samples were analyzed by two RT-qPCR assays: the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay (ASFR, Seegene Technologies Inc; Seoul, South Korea) and the TaqPath COVID-19 RT-PCR (Thermo Fisher Scientific, USA). Definition of the SARS-CoV-2 variant was carried out by Sanger sequencing of the relevant S-gene regions and, in some cases, by whole genome sequencing (WGS) using the ARTIC-nCoV workflow on a MiniION (Oxford Nanopore Technologies, Oxford, UK) or a Illumina MiSeq platform (San Diego, California, USA). Results: Of the 173 SARS-CoV-2-positive specimens, all those of lineage B.1.1.7 (N=71) showed an average Cq difference between the N and S genes of +11±2 (range, +8/+15). None of the other specimens, including several different lineages (Wild-type for the analyzed regions, N=22; Gamma, N=63; Delta, N=9; B.1.258Δ, N=3; B.1.160, N=3; B.1.177.7, N=1; B.1.1.420, N=1), exhibited a similar difference in Cq values. Conclusions: The peculiar pattern of delayed N gene positivity could constitute a convenient method for VOC-Alpha screening, simultaneous to viral detection, when using the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay.
format	article
author	Nicla Giovacchini Marco Coppi Noemi Aiezza Ilaria Baccani Francesca Malentacchi Simona Pollini Alberto Antonelli Gian Maria Rossolini
author_facet	Nicla Giovacchini Marco Coppi Noemi Aiezza Ilaria Baccani Francesca Malentacchi Simona Pollini Alberto Antonelli Gian Maria Rossolini
author_sort	Nicla Giovacchini
title	Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay
title_short	Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay
title_full	Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay
title_fullStr	Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay
title_full_unstemmed	Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay
title_sort	rapid screening for sars-cov-2 voc-alpha (202012/01, b.1.1.7) using the allplex™ sars-cov-2/flua/flub/rsv assay
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/9b93b829cdeb4dc6a29ec67c887d7169
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Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay

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