Omicron assay

[DOWNLOAD] Omicron assay protocol v1.0 20211210.PDF

COVID-19 variant discrimination assay using one-pot molecular diagnostics [v1.0, 10DEC2021]

– This protocol should be used for research purposes only, not clinical purposes.
– As we continue to update this document with new probe information and protocol, we will upload an updated version at
– We hope this report will serve as a reference for developing and advancing methods of discriminating COVID19 variants without complex and high-end instruments that would be only accessible to a limited number of parties and countries.

The fast-spreading SARS-CoV-2 variant known as Omicron was first reported to the WHO from South Africa on November 24, 2021. Since then, countries worldwide are making every effort to block the inflow of the variant and prevent their spread. In the fight against variants, it is very important to quickly identify the type of variant and thus accurately track how the variant spreads. However, the identification and tracking of Omicron and other variants rely on sequencing technologies, which take many days with high costs. The sequencing of SARS-CoV-2 cannot be easily performed in under-resourced countries around the world. To this end, to accelerate the development of the variant discrimination method, we report here a protocol to discriminate the Omicron variant from SARS-CoV-2 using SENSR (SENsitive Splint-based one-pot isothermal RNA detection) technology. Using the assay, we have distinguished the Omicron variant from SARS-CoV-2. Moreover, we confirmed the compatibility of the SENSR assay with PCR amplicon and proxy RT-qPCR product.
The COVID-19 variant discrimination assay protocol is composed of two steps. It can be completed in 20 minutes, starting from PCR amplicon (or RT-qPCR product). The variant discrimination assay is based on the SENSR technology that relies on an isothermal reaction cascade composed of ligation and transcription reactions generating an RNA aptamer that binds to a fluorogenic dye (See additional information).

Step I. Denaturation (5 min)
Denaturation of PCR amplicon (or RT-qPCR product) at 98°C for 5 min with a set of SENSR probes and intruder DNA.
Step II. Incubation (15 min)
Incubation of the denatured mixture from step I with the SENSR reagent at 37°C for at least 15 min. Fluorescence from the incubated mixture was measured using a plate reader.

See the detail in the shared PDF file.