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; Dudley, Joel T.; MacKay, Matthew J.; Nash, Megan; Wang, Jianhui; Liu, Chen; Hui, Pei; Murphy, Steven; Neal, Caleb; Laszlo, Eva; Landry, Marie L.; Muyombwe, Anthony; Downing, Randy; Razeq, Jafar; de Oliveira, Tulio; Faria, Nuno R.; Sabino, Ester C.; Neher, Richard A.; Fauver, Joseph R.; Grubaugh, Nathan D.

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.