Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection

Abstract

To compare the RT-PCR Allplex SARS-CoV-2/FluA/FluB/RSV Assay (Allplex assay) with other methods of detection of VOC B.1.1.7. Suspected and non-suspected cases of VOC B.1.1.7 were defined according to the VirSNiP assay, which detects N501Y and deletion H69-V70. For pre-screening, the Allplex™ and TaqPath assays were used. One hundred and sixteen suspected and 113 non-suspected cases were included. In the suspected cases, the Allplex assay showed N-gene dropout, or delayed Ct values of 6.27 ± 1.21 and 6.66 ± 1.41 compared with those of the RdRP and S-gene target, respectively. Agreement between the Allplex and TaqPath assays was 100% when the RdRP and S-gene targets had Ct values <35. Agreement between the Allplex and VirSNiP assays was 100% with Ct value <30. The Allplex assay showed excellent agreement with the current pre-screening method for VOC B.1.1.7. In addition, its automated processing enhances the feasibility of widespread use in laboratories.

Keywords: 2019-nCoV RT-PCR diagnostic panel; Mutation; SARS-CoV-2; Screening Assays; Variant; Whole-genome sequencing.