A CRISPR/Cas12a empowered surface plasmon resonance platform for rapid and specific diagnosis of the Omicron variant of SARS-CoV-2

Abstract The outbreak of the COVID-19 pandemic is partially due to the challenge of identifying asymptomatic and pre-symptomatic carriers of the virus, and thus highlights a strong motivation for diagnostics that can be rapidly deployed with high sensitivity. On the other hand, several concerned SARS-CoV-2 variants, including the Omicron, are required to be identified as soon as the samples are identified as ‘positive’. Unfortunately, a traditional PCR test does not allow their specific identification. Herein, for the first time, we have developed MOPCS (Methodologies of Photonic CRISPR Sensing), which combines an optical sensing technology-surface plasmon resonance (SPR), and the ‘gene scissors’ CRISPR technique to achieve both high sensitivity and specificity of viral variants’ measurement. MOPCS is a low-cost, CRISPR/Cas12a system-empowered SPR gene detecting platform that can analyze viral RNA, without the need for amplification, within 38 min from sample input to results output, and achieve a limit of detection of 15 fM. MOPCS achieves a highly sensitive analysis of SARS-CoV-2 and mutations appear in variants B.1.617.2 (Delta), B.1.1.529 (Omicron), and BA.1 (a subtype of Omicron). This platform was also used to analyze some recently collected patient samples from a local outbreak in China and identified by the Centers for Disease Control and Prevention. This innovative CRISPR-empowered SPR platform will further contribute to various fast, sensitive, and accurate detection of target nucleic acid sequences with single-base mutations.