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

Vogels, Chantal B F; Breban, Mallery I; Ott, Isabel M; Alpert, Tara; Petrone, Mary E; Watkins, Anne E; Kalinich, Chaney C; Earnest, Rebecca; Rothman, Jessica E; Goes de Jesus, Jaqueline; Morales Claro, Ingra; Magalhães Ferreira, Giulia; Crispim, Myuki A E; Singh, Lavanya; Tegally, Houriiyah; Anyaneji, Ugochukwu J; Hodcroft, Emma B.; Mason, Christopher E; Khullar, Gaurav; Metti, Jessica; ... (2021). Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS biology, 19(5), e3001236. Public Library of Science 10.1371/journal.pbio.3001236

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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 Coronavirus Disease 2019 (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.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Social and Preventive Medicine (ISPM)

UniBE Contributor:

Hodcroft, Emma Britt


600 Technology > 610 Medicine & health
300 Social sciences, sociology & anthropology > 360 Social problems & social services




Public Library of Science




Andrea Flükiger-Flückiger

Date Deposited:

11 May 2021 19:26

Last Modified:

05 Dec 2022 15:51

Publisher DOI:


PubMed ID:





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