Based on a multi-target design that compensates for emerging SARS-CoV-2 variants and mutations, the Applied Biosystems TaqPathTM COVID-19 diagnostic tests can detect the Omicron Variant of Concern (VOC) and all its currently known lineages. In fact, the TaqPath COVID-19 diagnostic tests can detect all currently known SARS-CoV-2 among patients’ samples.
Independent of the currently known variants, the tests can determine whether a patient’s sample is positive or negative for the virus. The TaqPathTM COVID-19 diagnostic tests listed in Table 1 will show a specific detection pattern for the majority of Omicron variant isolates. Using this detection pattern as a proxy can help identify the Omicron variant.
Table 1: TaqPath COVID-19 Diagnostic Tests
|TaqPath COVID-19 Assay||Cat #||Detects SARS-CoV-2 (Including Omicron B.1.1.529, BA. 1, BA.2 and BA. 3)||Detects S Gene Target Failure (SGTF)
(Detection Pattern Suggestive of Omicron BA. 1 and BA. 3)
|Products with US FDA’s Emergency Use Authorization (EUA)*|
|TaqPath COVID-19 Combo Kit*||EUA||A47814||YES||YES|
|TaqPath COVID-19 Combo Kit Advanced*||EUA||A47813|
|TaqPath COVID‑19 High‑Throughput Combo Kit for use with Amplitude Solution*||EUA||A49869|
|TaqPath COVID-19 Pooling Kit*||EUA||A49918|
|Products Complied with EU’s CE-IVD Requirements**|
|TaqPath COVID-19 CE-IVD RT-PCR Kit**||CE-IVD||A48067||YES||YES|
|TaqPath COVID-19 HT Kit for use with Amplitude Platform**||CE-IVD||A50883|
* For In Vitro Diagnostic Use. For Emergency Use Authorization Only.
**CE-IVD. For In Vitro Diagnostic Use.
The first case of Omicron and its subsequent lineages
The first case of the Omicron VOC was reported in November of 2021 and designated as B.1.1.529 (pangolin lineage, also known as 21M). This new variant has more than 30 mutations in the spike protein alone. Since its first discovery, multiple variations of the Omicron virus have been identified that share the majority of mutations but also harbor their own unique sequence changes. The three sub-lineages identified so far include BA.1 (also known as 21K), BA.2 (also known as 21L), and BA.3 (Table 2).
Table 2: Sub-Lineages of Omicron B.1.1.529 (Pangolin Lineage, Also Known as 21M) and Their Detection Pattern
|Name of Omicron Sub-Lineages||Also Known As||Shows SGTF Detection Pattern by
TaqPath COVID-19 Assay
The 69-70 deletion in the spike protein, a mutation that presents in the majority of the currently circulating Omicron cases worldwide, helps identify the potential presence of the VOC when using any of the TaqPath COVID-19 diagnostic tests listed in Table 1 on patients’ samples. This mutation is present in BA.1 (21K) and BA.3, but not in BA.2 (21L) lineage.1
The worldwide and country-specific prevalence of the Omicron variant and its lineages can be tracked using World Health Organization (WHO)’s Tracking SARS-CoV-2 Variants, WHO’s Technical Brief and Priority Actions for Member States, Outbreak.info hosted by Scripps Research, or the ROSALIND tracker hosted by ROSALIND, Inc. The BA.1 (21K) lineage of Omicron, which has the 69-70 deletion in the spike protein and presents the S Gene Target Failure (SGTF) detection pattern by TaqPath COVID-19 Assay, is currently the most prevalent worldwide. It accounts for >98% of sequences submitted to Global Initiative on Sharing Avian Influenza Data (GISAID) as of 7 January 2022. BA.2 and BA.3 only account for a minority of the submitted sequences worldwide.1
The WHO, the US Food and Drug Administration (FDA), the US Centers for Disease Control and Prevention (CDC), and the European Centre for Disease Prevention and Control (ECDC) have all reported that using SGTF of PCR assays as a proxy for the variant helps in identifying Omicron. 1
TaqPath detects all currently known SARS-CoV-2, including different lineages of the Omicron variant
The Applied Biosystems TaqPath COVID-19 diagnostic tests are capable of detecting samples infected with different Omicron variants. The tests detect SARS-CoV-2 infections by identifying the presence of three gene targets from the orf1a/b, S, and N regions of the virus. The COVID-19 Interpretive Software algorithms utilize the results from all three targets to generate a final call, and a positive result is called if at least two of the three SARS-CoV-2 targets are detected.
Figure 1: Multi-Target Design of the TaqPath COVID-19 Diagnostic Tests Listed in Table 1
For the BA.1 and BA.3 lineages of the Omicron variant B.1.1.529, the TaqPath COVID-19 diagnostic tests detect both the orf1ab and N genes while showing a negative signal for the S gene target. This S Gene Target Failure (SGTF) is also known as S Gene Advantage as it can be used as a marker suggestive of the Omicron variants. The Delta variant, currently the predominant variant worldwide, does not have the S gene 69-70del mutation in the majority of the cases and the S gene is detected by the TaqPath COVID-19 Kits. It is important to note that the 69-70del mutation may also exist in other mutants, and a dropout of the S gene signal could also be caused by other reasons.
For the Omicron variant BA.2 and other SARS-CoV-2 variants without the spike protein mutations, the TaqPath COVID-19 diagnostic tests detect all three gene targets from the orf1a/b, S, and N regions of the virus.
In summary, the TaqPath COVID-19 diagnostic tests can detect all currently known SARS-CoV-2 variants. The S Gene Advantage has already helped detect the Alpha variant, and the WHO, US CDC, European CDC, and African CDC have all reported that using S Gene Target Failure (SGTF) of PCR assays as a proxy for the variant helps in identifying Omicron, and the CDCs have specifically recognized the TaqPath assay for these findings. Both the ECDC and US FDA recommend further characterizing specimens which show S-gene dropout using sequencing.
What to do if SGTF is observed?
Samples that are associated with the S gene dropout reflect either a resurgence of the Alpha variant, a new or emerging mutant that interferes with the S gene detection, or the presence of the new Omicron variant (B.1.1.529, BA.1 and BA. 3). Given that the majority of currently circulating SARS-CoV-2 are the Delta variant which does not produce the SGTF profile, any sample with S gene dropout should be seen as signal to characterize the sample for the presence of Omicron. Due to the novelty and potential risks associated with the new Omicron variant, the WHO, CDC, and ECDC recommend further characterizing specimens with S gene dropout using sequencing.
For surveillance purposes, confirming various variants by genotyping may be performed using the following:
For Genotyping with existing qPCR equipment:
Thermo Fisher’s Applied Biosystems TaqMan Mutation Panel, which is currently used for research purposes, is compatible with real-time PCR instruments already commonly used in laboratories around the world. Laboratories can choose from a menu of over 50 known mutations of SARS-CoV-2 to assess confirmed COVID-19 positive samples for the presence of known variants and mutations. The panel includes a set of assays specifically designed to identify the Omicron variant (Mutations: S.G339D.GGT_GAG, S.Q493R.CAA_CGA, S.T547K.ACA.AAA, orf1ab.A2710T, and orf1ab.T13195C).
Confirming various variants via sequencing
Thermo Fisher Scientific supports variant and lineage conformation by sequencing:
- Ion AmpliSeq SARS-CoV-2 Insight Research Assay***
- Sanger Sequencing Solutions for SARS-CoV-2 Research***
Learn how we can help your emerging SARS-CoV-2 variant and mutation surveillance efforts with our Sanger sequencing and NGS technologies.
*** For research use only. Not for use in diagnostic procedures.
How to Learn More
Find out more about our TaqPath COVID-19 diagnostic test kits:
- COVID-19 testing solutions
- The TaqPath COVID-19 Combo Kitis Emergency Use Authorized (EUA)
- The TaqPath COVID-19 CE-IVD RT-PCR Kitis CE-IVD marked
- Blog: A Reference Guide to Notable SARS-CoV-2 Variants
If you have additional questions or would like to discuss your specific situation, please contact our technical support team at www.thermofisher.com/contactus.
To keep track of SARS-CoV-2 variants and their distributions:
- World Health Organization’s Tracking SARS-CoV-2 Variants
- World Health Organization’s Technical Brief and Priority Actions for Member States
- Omicron Variant Report at Outbreak.info by Scripps Research
- Real-Time Tracker to Support Rapid Genotyping “Project ROSA” Program for SARS-CoV-2 in the United States.