Comparison of a Multiplex Real-Time PCR technique with Oxford Nanopore Technologies Next-Generation-Sequencing for identification of SARS-CoV-2 variants of concern

Abstract Background; The rapid emergence of SARS-CoV-2 variants and their potential to endangering the global health, has increased the demand for a fast-tracking method in comparison to the Next-Generation-Sequencing (NGS) as a gold standard assay, particularly in developing countries. This study was designed to evaluate the performance of a commercial multiplex Real-Time PCR technique (GA SARS-CoV-2 OneStep RT-PCR Kit) for identification of SARS-CoV-2 variants of concern compared to Oxford Nanopore Next-Generation-Sequencing assay. Materials and Methods; A total of 238 SARS-CoV-2 positive respiratory samples from different waves of COVID-19 in Iran were randomly included in this study. To determine the SARS-CoV-2 VOC, the samples were analyzed via the commercial triple target assay, GA SARS-CoV-2 OneStep RT-PCR Kit, and Next-Generation-Sequencing (NGS) as well. Results; The results revealed good concordance between GA SARS-CoV-2 OneStep RT-PCR Kit and NGS for identification of SARS-CoV-2 VOCs. GA SARS-CoV-2 OneStep RT-PCR Kit identified Wuhan, Alpha and Delta variants with 100% relative sensitivity and specificity. Regarding Omicron subvariants of BA.1, BA.2 and BA.4/5 the relative sensitivity of 100%, 100% and 81.5% and the relative specificity of 95.3%, 93.5%, and 100% were observed. Conclusion; Overall, GA SARS-CoV-2 OneStep RT-PCR Kit can be used as a rapid and cost-effective alternative to NGS for identification of SARS-CoV-2 VOCs.