TY - JOUR
T1 - Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
AU - Brazil-UK CADDE Genomic Network
AU - Network for Genomic Surveillance in South Africa
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.
UR - http://www.scopus.com/inward/record.url?scp=85105881839&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85105881839&partnerID=8YFLogxK
U2 - 10.1371/journal.pbio.3001236
DO - 10.1371/journal.pbio.3001236
M3 - Article
C2 - 33961632
AN - SCOPUS:85105881839
SN - 1544-9173
VL - 19
JO - PLoS Biology
JF - PLoS Biology
IS - 5 May
M1 - e3001236
ER -