The S Gene Advantage: TaqPath COVID-19 Tests May Help with Early Identification of Omicron Variant

This blog represents the most up-to-date information about the B.1.1.529 SARS-CoV-2 variant as of November 30, 2021.

A new, potentially highly transmissible variant of SARS-CoV-2 discovered in the Southern Africa, B.1.1.529 (or Omicron) has public health organizations and governments on alert. B.1.1.529 is the most divergent variant identified in significant numbers, with over 30 mutations across the S-gene, which raises concerns for disease control and prevention. Due to concerns around a detrimental change in COVID-19 epidemiology, the WHO designated B.1.1.529 as a variant of concern on November 26, 2021. Health officials indicate that more information is needed to understand if Omicron is more transmissible or severe than other variants, including Delta.  The WHO is currently asking countries to:

The S Gene Advantage

The Applied Biosystems TaqPath COVID-19 diagnostic tests use a multi-target design, to compensate for emerging SARS-CoV-2 variants and mutations. Furthermore, the TaqPath tests are unique among the most commonly used molecular tests in that the multi-target design includes an S-gene target. The Omicron variant has been found to include the 69-70del mutation of the S gene, first identified as a mutation in the Alpha variant. This mutation causes a dropout of the S-gene target in results from widely used TaqPath COVID-19 Detection Kits. An S-gene failure does not mean a result is negative, only that the S gene was not detected. Multiple public health organizations have noted that this pattern of detection (i.e. S-gene dropout) can be used as marker for this variant, pending sequencing confirmation.

WHO European CDC Highlight S-Gene dropout for Early Identification of B.1.1.529

As previously indicated with the Alpha Variant, the WHO, European CDC and African CDC all report that the S-Gene dropout from select TaqPath COVID-19 Kits can be used as a screening method for Omicron. Per the European CDC “The presence of the deletion Δ69-70 means that S-gene target failure (SGTF) for the Thermo Fisher TaqPath assay can be used as a screening method for Omicron. In a setting with the Delta variant dominating, this can be used as a proxy for Omicron after confirmation of a subset of samples by sequencing.” The WHO also reports “Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.” Both the WHO and ECDC recommend further characterizing specimens which show S-gene dropout using sequencing.

Reliable Detection

By surveying across multiple genes, the TaqPath COVID-19 Detection kits can report SARS-COV-2 results in the case where one of the targets is impacted by a mutation (as long as the other targets are not impacted and the positive control passed). While the S gene target in the test is impacted, the orf1ab and N gene targets in the TaqPath COVID-19 tests have been determined to not be impacted by any of the mutations in the Omicron variant, based on assessment of sequences in the GISAID public database.

Identify Potential Variants Early to Help Curb the Spread

Being able to distinguish between different, potentially more transmissible SARS-CoV-2 variants is of value for gathering preliminary data on the appearance and spread of SARS-CoV-2 variants and lineages. Because the detection patterns of the TaqPath COVID-19 tests may differ between different variants, test results from these kits may provide initial insight into developments in SARS-CoV-2’s continued evolution. Further genetic surveillance studies using targeted genotyping assays or whole viral genome sequencing techniques should be employed to more thoroughly track this deadly pathogen. As recommended by the WHO, reporting of initial cases/ clusters can help us understand current and future COVID-19 epidemiology and inform public health and social measures.

How to Learn More

Find out more about our TaqPath COVID-19 diagnostic test kits:

Confirmation of the variant strain for surveillance may be accomplished by targeting genotyping or sequencing. There are multiple options available for evaluating of SARS-CoV-2 research isolates:

For Genotyping with existing qPCR equipment:

Specific genotyping assays to detect the Omicron variant are being developed for Thermo Fisher’s TaqMan Mutation Panel*. The panel, which is currently used for research purposes, already has a menu of over 50 assays to assess confirmed COVID-19 cases for the presence of known variants and mutations.

For Sequencing

Learn how we can help your emerging SARS-CoV-2 variant and mutation surveillance efforts with our Sanger sequencing and NGS technologies.

If you have additional questions or would like to discuss your specific situation, please contact our technical support team at


Intended use and regulatory statements of products vary. For specific intended use and regulatory statements please refer to the Instructions for Use (IFU). Product availability by country varies. For product availability in your country, please check the TaqPath COVID-19 Multiplex Diagnostic Solution webpage.

* For research use only. Not for use  in diagnostic procedures