Real-Time PCR-Based Test as a Research Tool for the Retrospective Detection and Identification of SARS-CoV-2 Variants of Concern in a Sample

The Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), a causative agent of the COVID-19 disease, has been constantly evolving since its first identification. Mutations that are embedded in the viral genomic RNA affect the properties of the virus and lead to the emergence of new variants. During the COVID-19 pandemic, the World Health Organization has identified more than ten variants of the SARS-CoV-2 virus. Five of these-Alpha, Beta, Gamma, Delta, and Omicron-were classified as variants of concern (VOCs), as they caused significant outbreaks of the disease. Additionally, two progeny variants of Omicron, designated JN.1 and KS.1, are still causing new waves of infections. Due to the emergence of various SARS-CoV-2 variants, in some cases, it has become important to identify a particular variant in a sample. Here, we have developed a multiplexed probe-based real-time PCR system for the identification of SARS-CoV-2 VOCs (Alpha, Beta, Gamma, Delta, Omicron B.1.1.529/BA.1, and Omicron BA.2), as well as modern Omicron variants JN.1 and KS.1. The sensitivity and specificity of the PCR system have been tested using isolated viral genomes and RNA preparations from human nasopharyngeal swabs. The system allows for rapid identification of coronavirus variants in the cryopreserved and fresh samples.