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New PCR test developed by the JRC can detect Omicron variant, latest testing by EU scientists confirms

The Omicron variant differs quite significantly from other variants of SARS-CoV-2
Dec 21 2021

The Commission’s Joint Research Centre (JRC) has confirmed the validity of the Omicron-specific detection method it has developed.

All laboratories carrying out PCR tests could use this new method to detect and identify Omicron without the need of an expensive and time-consuming sequencing.

The new PCR method proved to be highly efficient in Omicron-specific tests conducted by the JRC. This means in practice that the method provides the possibility to any laboratory operating standard PCR technology to identify the Omicron variant quickly and without the need for time-consuming sequencing.

The modified reagent developed by the JRC can be ordered by the regular suppliers of the PCR test and can be implemented swiftly. Any laboratory that is carrying out PCR tests today will be able to adapt quickly. This new method will be presented today to Member States at Health Security Committee.

Methodology

The majority of the changes characterising the Omicron variant are found in the gene encoding for the Spike glycoprotein, which is a key component of the virus that facilitates its entry into human cells. It is also the target of mRNA- and viral vector-based vaccines.

By inspecting the Spike protein encoding regions of all Omicron-flagged complete sequences, JRC scientists identified a target region with a unique and Omicron-specific cluster of nucleic acid sequence.

Building upon these findings, they designed an Omicron variant-specific real-time polymerase chain reaction (RT-qPCR).

The sensitivity and specificity of the method was now successfully confirmed: samples from Omicron-infected patients tested positive whereas samples from patients infected with other variants, such as the widespread delta variant, tested negative.

Therefore, this approach allows the quick and cheap identification of Omicron with standard laboratory equipment.

Background

The JRC does not stop its vigilance on Omicron and other Covid-19 variants. It is very important to understand which variant of SARS-CoV-2 is spreading, how and where it is going. Today, the Delta variant is still dominant but it remains critical to identify the Omicron cases and confine them.

The Omicron variant is very different from the original “Wuhan” strain and it may be missed in routine tests. That is the fundamental reason why the JRC is keeping track of all variants and constantly assesses the effectiveness of the diagnostics in use.

JRC scientists keep us safe by constantly monitoring the performance of 17 mostly used PCR testing methods against all the variants of concern. Results are communicated on a dashboard on the COVID-19 In Vitro Diagnostic Devices and Test Methods Database.