Development of novel RT-PCR assay for detection of COVID-19 in the Post-Omicron Era

ABSTRACT

Background: We are facing a new era of the COVID-19 pandemic by omicron variant. This raises concern about the accuracy of conventional RTqPCR assays. There is a need for a new RTqPCR assay appropriate for the omicron variant with multiple mutations. Material(s) and Method(s) We herein have developed 2 types of new RTqPCR assays which detect G142D/del143-145, 452 and 478 of S, 69/70 of S or N, and internal control (IC) to make a new single tube, quadplex RTqPCR assay of COVID-19 ('GG COVID-19 Omicron and Delta kit'). Analytical performance was analyzed with Twist/BEI controls. Clinical performance analysis was done as a multi-center study in South Korea with specimens from New Jersey, collected between October 2021 and January 2022. Result(s) 400 left over nasopharyngeal swabs including 149 SARS-CoV-2 positive samples were collected and tested on January 2022 out of which 148 were due to omicron variant and 1 delta variant, respectively. S142-145 assay was superior to conventional RT-PCR(sensitivity 100% vs 00.0 to 00.0%, mean Ct value 25.0 vs 30.4 to 31.3). 330 samples including 125 SARS-CoV-2 positive samples from October 2021 and also tested, out of which 78 were due to delta and confirmed by sequencing. Conclusion(s) GG COVID-19 Omicron and Delta kit showed higher sensitivity than conventional RTqPCR (100% vs 95.4%) and 100% specificity in detecting SARSCoV-2 and could differentiate all of omicron variants. These results indicate that our GG COVID-19 Omicron and Delta kit may be more sensitive than conventional PCR assays in detecting Omicron and Delta SARS-CoV-2. Copyright © 2022