Early and efficient detection of the Delta and Omicron variantso f SARS-CoV-2 through RT-qPCR screening

Abstract

Introduction. During the COVID-19 pandemic, the rise of so-called variants of concern (VOCs) has been a recurring problem. The gold standard approach for the identification of new and current variantsis genomic sequencing. However, the capacity of the genomic surveillance system is limited and prior screening strategies are required for sample selection. Objectives. To design, validate and apply Reverse-Transcription quantitative Polymerase Chain Reaction (RT-qPCR) strategies for the screening of the Delta and Omicron variants, as well as for the detection of eventual emergence of new variants. Materials and methods. Specific oligonucleotides (primers and probes) were designed to allow the discrimination between the different variants of SARS-Cov2, by hybridizing with regions corresponding to specific deletions. Amplification and melting assays of fluorescent probes were used and validated with samples of different variants. Results. The assays allowed identifying VOCs quickly and efficiently, using standard methodologies in molecular diagnostic laboratories. Variant assignment with this method was in complete agreement with data from sequencing. Conclusions. The protocols validated in this work allowed the early detection of the Delta and Omicron variants in the province of San Luis, as well as in other jurisdictions of Argentina where the methodology was transferred.