PCR performance in the SARS-CoV-2 Omicron variant of concern?

The new SARS-CoV-2 Omicron variant (B.1.1.529) has been recently declared a Variant of Concern due to a series of important mutations in the viral spike protein and especially in the receptor-binding domain. While investigations into the spread of this new variant are ongoing, the first cases have been detected in Switzerland. Important questions have been raised: (1) Will the PCR assays commonly used to detect SARS-CoV-2 still work for the Omicron variant? (2) Can specific PCR features, e.g. S-genedropout, be used to identify potential Omicron samples? In this minireview we provide current knowledge on the Omicron variant and guidance on its PCR validation.

Automated summary

The new SARS-CoV-2 Omicron variant has been declared a Variant of Concern due to important mutations in the viral spike protein, especially in the receptor-binding domain. The spread of this variant is being investigated with the first cases detected in Switzerland. Questions have been raised about the effectiveness of PCR assays and specific features for identifying Omicron samples, with guidance provided in this minireview.