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.
Bibliographical noteFunding Information:
This work was funded by CTSA Grant Number TL1 TR001864 (TA and MEP), Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z; NRF), a Medical Research Council-S?o Paulo Research Foundation CADDE partnership award (MR/S0195/1 and FAPESP 18/ 14389-0; NRF), Fast Grant from Emergent Ventures at the Mercatus Center at George Mason University (NDG), and CDC Contract # 75D30120C09570 (NDG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
© 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.