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

Vogels, Chantal B. F. and Breban, Mallery I. and Ott, Isabel M. and Alpert, Tara and Petrone, Mary E. and Watkins, Anne E. and Kalinich, Chaney C. and Earnest, Rebecca and Rothman, Jessica E. and Goes de Jesus, Jaqueline and Morales Claro, Ingra and Magalhães Ferreira, Giulia and Crispim, Myuki A. E. and Brazil-UK Cadde Genomic Network, and Singh, Lavanya and Tegally, Houriiyah and Anyaneji, Ugochukwu J. and Network for Genomic Surveillance in South Africa, and Hodcroft, Emma B. and Mason, Christopher E. and Khullar, Gaurav and Metti, Jessica and Dudley, Joel T. and MacKay, Matthew J. and Nash, Megan and Wang, Jianhui and Liu, Chen and Hui, Pei and Murphy, Steven and Neal, Caleb and Laszlo, Eva and Landry, Marie L. and Muyombwe, Anthony and Downing, Randy and Razeq, Jafar and de Oliveira, Tulio and Faria, Nuno R. and Sabino, Ester C. and Neher, Richard A. and Fauver, Joseph R. and Grubaugh, Nathan D.. (2021) Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biology, 19 (5). e3001236.

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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 COVID-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.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Computational Modeling of Biological Processes (Neher)
UniBasel Contributors:Neher, Richard A
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Public Library of Science
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:24 Feb 2022 09:56
Deposited On:24 Feb 2022 09:56

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