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

• DOI: 10.1371/journal.pbio.3001236
• Publication Date: 2021-05-07T19:27:58Z
• Authors: Chantal B. F. Vogels; Mallery I. Breban; Isabel M. Ott; Tara Alpert; Mary E. Petrone; Anne E. Watkins; Chaney C. Kalinich; Rebecca Earnest; Jessica E. Rothman; Jaqueline Goes de...; Ingra Morales Claro; Giulia Magalhães ...; Myuki A. E. Crispim; ; Lavanya Singh; Houriiyah Tegally; Ugochukwu J. Anya...; ; Emma B. Hodcroft; Christopher E. Mason; Gaurav Khullar; Jessica Metti; Joel T. Dudley; Matthew J. MacKay; Megan Nash; Jianhui Wang; Chen Liu; Pei Hui; Steven Murphy; Caleb Neal; Eva Laszlo; Marie L. Landry; Anthony Muyombwe; Randy Downing; Jafar Razeq; Tulio de Oliveira; Nuno R. Faria; Ester C. Sabino; Richard A. Neher; Joseph R. Fauver; Nathan D. Grubaugh
• Keywords: Transmissibility (structural dynamics); Coronavirus; Multiplex

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 targeted surveillance circulating lineages. It was found B.1.1.7 (also 501Y.V1) variant, first detected in United Kingdom, could be serendipitously by Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion these viruses, spike Δ69-70, would "spike gene target failure" (SGTF) result. However, SGTF result not definitive B.1.1.7, and this cannot detect other concern (VOC) lack such as B.1.351 501Y.V2), South Africa, P.1 501Y.V3), recently Brazil. We identified ORF1a (ORF1a Δ3675-3677) all 3 variants, which has yet been widely SARS-CoV-2 Using Δ3675-3677 primary Δ69-70 to differentiate, we designed validated open-source VOC. Our can rapidly deployed laboratories around world enhance local spread B.1.351, P.1.