GVS S p A : OMICRON Invisible to some PCR Kits

A new version of the Omicron variant (B.1.1.529) was recently put under the spotlight by the Pango-designation group (https://github.com/cov-lineages/pango-designation/issues/361), after which in a few days, dozens of new findings were deposited in the Gisaid database, used by the group to constantly update the map of the mutations identified around the world. The cases that emerged were located in South Africa, Australia, and Canada.

The new form of Omicron shares many mutations with the original variant, but the high number of new mutations detected prompted Pango-designation to put forward the proposal (instance number 359) to separate the original Omicron "strain" into 2 different variants: BA.1 and BA.2.

This proposal will be evaluated in the next few hours by the World Health Organization: given the analytical evidence, however, the opinion will certainly be positive.

The invisibility of this new variant form (BA.2) is given by the absence of a deletion in the S gene (the HV69del) which made the original Omicron form (BA.1) diagnosable even by not specific molecular kits (thanks to the S gene dropout mechanism also mentioned in the recent ECDC document).https://www.ecdc.europa.eu/sites/default/files/documents/Implications-emergence-spread-SARS-CoV-2 B.1.1 .529-variant-concern-Omicron-for-the-EU-EEA-Nov2021.pdf).

Precisely for this reason, the new circulating form was soon renamed "invisible".

The GVS Flame CoViD -19 VARIANTS qPCR Master Kit - CE-IVD kit (item code FLM0002) allows to identify of both circulating forms of Omicron variant (BA.1 and BA.2) thanks to the positive identification of one of the specific mutations in the gene S, the N501Y, shared by the two forms.

As already notified by the FDA, some PCR kits on the market will suffer from the presence of these new mutations so as to invalidate the recognition of the SARS-CoV-2 virus, increasing the risk of false negatives.

The presence of a channel purely dedicated to the N501Y mutation present in our kit, on the other hand, will always allow a positive detection of the virus regardless of the variant under examination.

If at the beginning of the pandemic the detection of variants was closely related to the need for sequencing, today the certainty that a kit can identify a variant is increasingly linked to the risk of false negatives.

Our kit, therefore, is also recommended for those laboratories that have no interest in discriminating circulating variants but who want to ensure the positive detection of the SARS-CoV-2 virus in the context of territorial monitoring.

Additionally, further confirmation in the laboratory is possible by the use of the Flame DELTA VARIANTS REFLEX REAGENT KIT (Item code FLM0003) which allows with a second reflex qPCR run to verify the presence of the mutation of the N501Y gene, common to both the Omicron and Delta Variants.

For further information or to organize a demo, contact us to:

[email protected]