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Omicron-specific PCR test for new Variant of Concern

Our Omicron-specific PCR test assay for the fast identification of the new omicron variant of SARS-CoV-2 is designed for rapid determination of the new variant already in the screening-PCR for SARS-CoV-2. The assay also detects the BA.2 variant. 

VoXcreen and VoXident qPCR assays

Our Omicron-specific PCR test robustly targets distinct deletions in the genome of the three most prevalent Variants of Concern. It thereby efficiently singles out the BA.1 BA.2 and Delta variant for determination.

The assay is available as single- or multiplex assay.

For fastest results, our new multiplex assay “VoXcreen-DO”  differentiates in a single PCR reaction between the Delta- and the Omicron variant  and our VoXcreen-Delta-BA1-2 assay identifies Delta, BA.1 and BA.2.

Since the three variants together represent nearly 100% in all countries, the assay directly detects the VoCs of nearly all positive samples in a single PCR.

In addition, the assay targets  universal sites that are present in all SARS-CoV-2 using a WHO-recommended assay design. Therefore, the variants are identified with the recommended dual-target stratgy. The assay also contains an internal isolation control (RP).

While current tests need at least two separate PCR reactions and often also genome sequencing for the specific identification of Delta, BA.1 or BA.2, our test identifies the variants reliably in a single PCR reaction. This safes time and liberates PCR-capacities that are critically needed. 

Currently, mostly S-gene drop out or S-gene target failure “SGTF” is used to find potential cases of omicron. Since this test does not discriminate between Omicron or Alpha variant, it is not sure if it is really Omicron and additional tests have to be performed. This is cumbersome: the sample has to be searched for in the fridge (usually by hand) and there is a risk of sample-mixing, also the RNA can already be degraded due to additional freeze-thaw cycles.  Also, the “failure” of a test is not a proper diagnostic approach since it may as well be caused by another reason such as partly degraded RNA. Therefore, a positive proof is preferred. Our PCR assays target highly specific mutations onyl described in the Omicron VoC and in the Delta VoC for a clear and precise identification of the different VoCs- during the screening  PCR.

Concerning the BA.2 Variant – falsely denominated “stealth” variant

The subvariant  predecessor of Omicron called BA.2 is often falsely denominated as “stealth” variant. The reason for this is that it does not carry a mutation, (del69/70) which is present in alpha and omicron. This mutation leads to a “drop-out” of a specific PCR product targeting the s-gene, that is used in some widely used PCR tests. This drop-out or “failure” was used to identify the alpha variant and now the omicron variant and is known as “S-gene target failure” (SGTF) (see above). However, the failure can be also caused by other reasons e.g. by degraded RNA, a bad PCR batch or other reasons, also the method cannot distinguish between the Alpha and the Omicron variant. Therefore we do not use the SGTF but a POSITIVE signal caused by a specific PCR product that can only be generated in the omicron variant. In the case of the BA.2 our test will identify the universal target. For a specific determination, our BA.2 specific assay can be used.

New version of our VoXcreen assay: Delta, BA.1 & BA.2 (patent pending)

Our latest VoXcreen kit distinguishes between Delta and the BA.1 and BA.2 variants of omicron that are currently driving the pandemic directly during the screening.  In areas where no Delta Variant is present, BA.1&BA.2 version can be ordered, which discriminates only between BA.1 and BA.2 during the screening assay. For orders please see bottom of page. 

 

 

 

A)	VoC-Identification after screening PCR: positive samples need to be searched for in the freezer for secondary PCR or sequencing. Sample mixing possible. RNA may already be degraded due to more freeze-thaw cycles. Follow-up PCRs need time and sequester urgently needed PCR capacities.  B)	GenXPro VoXcreen PCR identify VoCs during screening PCR to save time, resources and to free PCR capacities.
A) VoC-Identification after screening PCR: positive samples need to be searched for in the freezer for secondary PCR or sequencing. Sample mixing possible. RNA may already be degraded due to more freeze-thaw cycles. Follow-up PCRs need time and sequester urgently needed PCR capacities. B) GenXPro VoXcreen PCR identify VoCs during screening PCR to save time, resources and to free PCR capacities.
Above: Evaluation scheme of our VoXcreen-DO assay for simultaneous dual-target SARS-CoV2 identification and VoC-determination in a single assay.
Above: Evaluation scheme of our VoXcreen-DO assay for simultaneous dual-target SARS-CoV2 identification and VoC-determination in a single assay. In our VoXcreen BA.1-2 version, the “delta” specific assay is replaced with an assay for BA.2.

 

 

Above: PCR results of Omicron VoC (left) and Delta VoC (right) using our VoXcreen-DO assay
Above: PCR results of Omicron VoC (left) and Delta VoC (right) using our VoXcreen-DO assay

Our Omicron-specific assay is also available as single assay with fluorophores of your choice and as primer-probe mix.

For all other SARS-CoV-2 related products including PCR- tests for specific mutations to determine the Lambda, Mu, C.1.2 as well as other VoCs and VoIs please click HERE.

All assays are currently for Research Use Only, certification process is ongoing and our kits are already in use after internal testing of certified laboratories.

About the Omicron-VoC

The Omicron variant (B.1.1.529 is the latest Variant of Concern (VoC)  of SARS-CoV-2, declared the 26th of November by the WHOIt was first identified in South Africa and was considered as VoC because of several local, steeply increasing number of infections.  Moreover, it outnumbered the already highly infectious Delta variant in the concerned areas and therefore was quickly regarded as VoC by the WHO. The variant has  is now the dominant variant in all countries.

The Omicron variant carries numerous mutations some of which are known from the alpha variant and has accumulated a number of additional mutations in the spike gene. Therefore, it may be carrying epitopes that differ from those against which the current vaccines are designed.

Omicron genome SARS-CoV-2 with accumulations of mutations in S-Gene
Above: Omicron genome of SARS-CoV-2 with accumulations of mutations in S-Gene.

 

For orders

Cat. Nr. VXC-NDORP; 96-10.000 reactions (For VoXcreen N1, Delta and Omicron + internal ctrl.)

Cat. Nr. VXC-NEBA1-2RP; 96-10.000 reactions (For VoXcreen N1,  Omicron BA.1 & BA.2 + internal ctrl.)

Cat. Nr. VXI-DORP; 96-10.000 reactions (For VoXcreen Omicron and Delta detection + internal ctrl.)

Cat. Nr. VXI-ADORP; 96-10.000 reactions (For VoXcreen Alpha, Delta and Omicron detection + internal ctrl.)

Cat. Nr. VXI-ORP; 96-10.000 reactions (For VoXcreen Omicron detection + internal ctrl.)

 

Contact

For more information or to purchase our kits or services, please write us an e-mail  (info@genxpro.de), or call us at  +49 69 95739710. 

 

For more SARS-CoV-2  / Covid PCR tests and sequencing solutions please click here.

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