ABSTRACT
From the very beginning of the SARS-CoV-2 pandemic, one of the very few common opinions was that to control the expansion of the virus as many as the possible test had to be done. Antigen tests, being affordable and easy and fast to use, represented a great opportunity to expand the testing capacities of many healthcare systems. However, in 2021 with the appearance of the new SARS-CoV-2 variants, variant tracking strategies had to be implemented, which often included needing a second test to determine the variant of the patients diagnosed with antigen tests or not taking these samples into consideration at all. Therefore, we proposed recovering the positive antigen test devices to include them in our routine variant tracking strategy. The recovered positive antigen test devices obtained from 1st April 2021 to 15the January 2022 were analysed following the variant tracking protocol in force. The results obtained were compared to the positive samples detected by RT-PCR which were processed for variant tracking during the same period. 21,304 samples were processed, 6297 from the recovered positive antigen devices and 15,007 from the standard nasopharyngeal swabs. Only 773 (3.63%) samples were no conclusive, 104 (1.65%) from the recovered antigen devices and 669 (4.46%) from the RT-PCR positive group. This difference was statistically significant (p < 0.01). Taking this into account the proposed method is suitable and very recommendable, as it is an important measure to have a better and immediate picture of the circulating variants in every community.
Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , Pandemics , SARS-CoV-2/genetics , Sensitivity and SpecificityABSTRACT
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 1st of March 2021 to 26th 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.
Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Testing , Humans , RNA-Dependent RNA Polymerase/geneticsABSTRACT
Detection of mutations by multiplex real-time RT-PCR is a widely used method for the screening of SARS-CoV-2 variants, but this method has several limitations. We describe three cases in which a Mu strain containing the mutation K417N was initially misclassified as the Beta variant. We recommend the detection of P681H to distinguish between these two variants. Our experience highlights the importance of keeping track of new variants and mutations in order to adapt the current workflows.