Use of the Ct difference between the Nucleocapside (N) and the Spike (S) or RNA-dependent RNA polymerase (RdRP) genes as a preliminary screening for SARS-CoV-2 variants with the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay: Searching the N in Variants

PURPOSE: With the rise of the different Variants of Concern (VOC) and Variants of Interest (VOI) in order to control the SARS-CoV-2 pandemic, strategies for accurately tracking these different variants have been developed. While most of these strategies rely heavily on specific PCRs targeting the characteristic mutations of some lineages, several approaches using the alterations at the cycle threshold (Ct) of different commercial PCR diagnostic tests have been described. The objective of this study is to analyse the use of the Ct difference at the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay (Seegene, Korea) between the Nucleocapside (N) and the Spike (S) or RNA-dependent RNA polymerase (RdRP) genes as a preliminary screening for variant tracking. METHODS: The samples analysed with the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay from 1(st) of March 2021 to 26(th) of December 2021 were selected. The Ct values for N, S, RdRP were collected, and the differences between N and S (ΔS) and N and RdRP (ΔRdRP) were calculated. Using ΔS and ΔRdRP a diagnostic test was designed and these results were compared to the routine Variant assessment. RESULTS: The mean ΔS and ΔRdRP were characteristic for Alpha and Delta. This difference was statistically significant. For Every analysed Variant the diagnostic test achieved a higher than 90% sensitivity with a noteworthy performance with the Omicron variant (97% sensitivity and 90% specificity). CONCLUSIONS: The analysis of the Ct alterations at the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay may be a suitable method for an early approach to SARS-CoV-2 variant assessment.