Rapid screening for SARS-CoV-2 VOC Alpha (202012/01, B.1.1.7) using the Allplexâ„¢ SARS-CoV-2 / FluA / FluB / RSV Assay

Giovacchini, Nicla; Coppi, Marco; Aiezza, Noemi; Baccani, Ilaria; Malentacchi, Francesca; Pollini, Simona; Antonelli, Alberto; Rossolini, Gian Maria

Background The emergence of SARS-CoV-2 variants of concern (VOCs) for increased transmissibility and potentially capable of immune-escape, mandates for epidemiological surveillance. Genomic alterations present in VOCs can affect the results of RT-qPCR assays for routine diagnostic purposes, leading to peculiar profiles that can be used for rapid screening of variants. In this work, we report on a peculiar profile observed with the Allplex™ SARS-CoV-2/ FluA/ FluB/ RSV Assay and VOC Alpha (202012/01, lineage B.1.1.7, also named VOC-UK), which was the first identified SARS-CoV-2 VOC. Methods Samples were analyzed by two RT-qPCR assays: the Allplex™ SARS-CoV-2/ FluA/ FluB/ RSV Assay (ASFR, Seegene Technologies Inc; Seoul, South Korea), and the TaqPath COVID-19 RT-PCR (Thermo Fisher Scientifics, USA). Definition of SARS-CoV-2 variant was carried out by Sanger sequencing of relevant S-gene regions and, in some cases, by whole genome sequencing (WGS) using the ARTIC-nCoV workflow on a MiniION (Oxford Nanopore Technologies, Oxford, UK) or a MiSeq ILLUMINA platform (San Diego, California, US). Results Of 173 SARS-CoV-2-positive specimens, all those of lineage B.1.1.7 (N=71) showed an average Cq difference between the N and S gene of +11±2 (range, + 8/+15). None of the other specimens, including several different lineages (Wild-type for the analyzed regions, N=22; Gamma, N=63; Delta, N=9; B.1.258, N=3; B.1.160, N=3; B.1.177.7, N=1; B.1.1.420, N=1), exhibited a similar difference of Cq values. Conclusions The peculiar pattern of delayed N gene positivity could constitute a convenient method for screening of VOC Alpha, simultaneous to viral detection, when using the Allplex™ SARS-CoV-2/ FluA/ FluB/ RSV Assay.