Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

doi:10.1371/journal.pbio.3001236

Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

,

Microbiology, Immunology, and Molecular Genetics

Research output: Contribution to journal › Article › peer-review

170 Scopus citations

Abstract

With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath Coronavirus Disease 2019 (CAU OVID-19): PCR assay because a key deletion in these viruses, spike Δ69–70, would cause a “spike gene target failure” (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69–70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675–3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675–3677 as the primary target and spike Δ69–70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.

Original language	English
Article number	e3001236
Journal	PLoS Biology
Volume	19
Issue number	5 May
DOIs	https://doi.org/10.1371/journal.pbio.3001236
State	Published - May 2021

Bibliographical note

Publisher Copyright:
© 2021 Vogels et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding

This work was funded by CTSA Grant Number TL1 TR001864 (TA and MEP), Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z; NRF), a Medical Research Council-São Paulo Research Foundation CADDE partnership award (MR/S0195/1 and FAPESP 18/ 14389-0; NRF), Fast Grant from Emergent Ventures at the Mercatus Center at George Mason University (NDG), and CDC Contract # 75D30120C09570 (NDG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Funders	Funder number
National Research Foundation of Korea
National Center for Advancing Translational Sciences (NCATS)	UL1TR001863, TL1TR001864
Royal Society Sir Henry Dale Fellowship	204311/Z/16/Z
Fundação de Amparo à Pesquisa do Estado de São Paulo	18/ 14389-0
Medical Research Council-São Paulo Research Foundation	MR/S0195/1
Centers for Disease Control and Prevention	75D30120C09570
UK Medical Research Council, Engineering and Physical Sciences Research Council	MR/R015600/1
Wellcome Trust	204311

ASJC Scopus subject areas

General Neuroscience
General Immunology and Microbiology
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences

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10.1371/journal.pbio.3001236

Cite this

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title = "Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2",

abstract = "With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath Coronavirus Disease 2019 (CAU OVID-19): PCR assay because a key deletion in these viruses, spike Δ69–70, would cause a “spike gene target failure” (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69–70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675–3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675–3677 as the primary target and spike Δ69–70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.",

author = "Vogels, \{Chantal B.F.\} and Breban, \{Mallery I.\} and Ott, \{Isabel M.\} and Tara Alpert and Petrone, \{Mary E.\} and Watkins, \{Anne E.\} and Kalinich, \{Chaney C.\} and Rebecca Earnest and Rothman, \{Jessica E.\} and \{de Jesus\}, \{Jaqueline Goes\} and Claro, \{Ingra Morales\} and Ferreira, \{Giulia Magalh{\~a}es\} and Crispim, \{Myuki A.E.\} and Lavanya Singh and Houriiyah Tegally and Anyaneji, \{Ugochukwu J.\} and Hodcroft, \{Emma B.\} and Mason, \{Christopher E.\} and Gaurav Khullar and Jessica Metti and Dudley, \{Joel T.\} and MacKay, \{Matthew J.\} and Megan Nash and Jianhui Wang and Chen Liu and Pei Hui and Steven Murphy and Caleb Neal and Eva Laszlo and Landry, \{Marie L.\} and Anthony Muyombwe and Randy Downing and Jafar Razeq and \{de Oliveira\}, Tulio and Faria, \{Nuno R.\} and Sabino, \{Ester C.\} and Neher, \{Richard A.\} and Fauver, \{Joseph R.\} and Grubaugh, \{Nathan D.\} and \{da Silva Sales\}, \{Flavia Cristina\} and Ramundo, \{Mariana Severo\} and Candido, \{Darlan S.\} and Silva, \{Camila Alves Maia\} and \{de Pinho\}, \{Mariana Cardoso\} and Coletti, \{Thais de Moura\} and Andrade, \{P{\^a}mela dos Santos\} and \{de Souza\}, \{Leandro Menezes\} and Rocha, \{Esm{\^e}nia Coelho\} and \{Gomes Jardim\}, \{Ana Carolina\} and \{de Souza\}, \{William Marciel\}",

note = "Publisher Copyright: {\textcopyright} 2021 Vogels et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",

year = "2021",

month = may,

doi = "10.1371/journal.pbio.3001236",

language = "English",

volume = "19",

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T1 - Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

AU - Vogels, Chantal B.F.

AU - Breban, Mallery I.

AU - Ott, Isabel M.

AU - Alpert, Tara

AU - Petrone, Mary E.

AU - Watkins, Anne E.

AU - Kalinich, Chaney C.

AU - Earnest, Rebecca

AU - Rothman, Jessica E.

AU - de Jesus, Jaqueline Goes

AU - Claro, Ingra Morales

AU - Ferreira, Giulia Magalhães

AU - Crispim, Myuki A.E.

AU - Singh, Lavanya

AU - Tegally, Houriiyah

AU - Anyaneji, Ugochukwu J.

AU - Hodcroft, Emma B.

AU - Mason, Christopher E.

AU - Khullar, Gaurav

AU - Metti, Jessica

AU - Dudley, Joel T.

AU - MacKay, Matthew J.

AU - Nash, Megan

AU - Wang, Jianhui

AU - Liu, Chen

AU - Hui, Pei

AU - Murphy, Steven

AU - Neal, Caleb

AU - Laszlo, Eva

AU - Landry, Marie L.

AU - Muyombwe, Anthony

AU - Downing, Randy

AU - Razeq, Jafar

AU - de Oliveira, Tulio

AU - Faria, Nuno R.

AU - Sabino, Ester C.

AU - Neher, Richard A.

AU - Fauver, Joseph R.

AU - Grubaugh, Nathan D.

AU - da Silva Sales, Flavia Cristina

AU - Ramundo, Mariana Severo

AU - Candido, Darlan S.

AU - Silva, Camila Alves Maia

AU - de Pinho, Mariana Cardoso

AU - Coletti, Thais de Moura

AU - Andrade, Pâmela dos Santos

AU - de Souza, Leandro Menezes

AU - Rocha, Esmênia Coelho

AU - Gomes Jardim, Ana Carolina

AU - de Souza, William Marciel

N1 - Publisher Copyright: © 2021 Vogels et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2021/5

Y1 - 2021/5

N2 - With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath Coronavirus Disease 2019 (CAU OVID-19): PCR assay because a key deletion in these viruses, spike Δ69–70, would cause a “spike gene target failure” (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69–70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675–3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675–3677 as the primary target and spike Δ69–70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.

AB - With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath Coronavirus Disease 2019 (CAU OVID-19): PCR assay because a key deletion in these viruses, spike Δ69–70, would cause a “spike gene target failure” (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69–70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675–3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675–3677 as the primary target and spike Δ69–70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.

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JO - PLoS Biology

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ER -

Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

Abstract

Bibliographical note

Funding

ASJC Scopus subject areas

Access to Document

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