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Choose from a menu of verified real-time PCR research assays to build your own custom Applied Biosystems TaqMan SARS-CoV-2 Mutation Panel, and get the results you need today, while preparing you for what’s to come. This scalable solution lets you run a few or hundreds of samples to identify one or many mutations—all on your current real-time PCR instrumentation.
For Research Use Only. Not for use in diagnostic procedures.
- Customizable—build your own custom panel from a menu of verified real-time PCR research assays that allows you to identify currently relevant SARS-CoV-2 mutations and adapt quickly as additional mutations and variants emerge
- Convenient—use your current real-time PCR instrumentation to conduct research testing of SARS-CoV-2 samples
- Scalable—run a few or hundreds of samples to identify one or many mutations
- Unique, streamlined workflow—combines our gold-standard TaqMan SNP Genotyping Assays with a 1-step RT-PCR reaction; go from RNA to results in just over 1 hour
| Targets | Choose from a menu of verified real-time PCR SNP research assays to build your custom panel |
| Assay design | Sequence-specific forward and reverse primers to amplify the target sequence region. The reverse primer also primes reverse transcription of the SARS-CoV-2 genomic RNA sequences. Each assay includes two TaqMan minor groove binder (MGB) probes with nonfluorescent quenchers (NFQ): |
| Available sizes | 375 reactions 1,250 reactions |
| Sample input | RNA extracted from SARS-CoV-2 samples with a CT value of less or equal to 30 |
| Turnaround time | 1 hour and 10 min from extracted RNA to results |
| Recommended instruments | Any real-time PCR instrument such as the Applied Biosystems 7500, 7500 Fast, QuantStudio 5, and QuantStudio 7 systems |
| Recommended software | QuantStudio Design and Analysis Software v2.5 or later with the Genotyping Analysis Module |
Figure 1. Workflow for TaqMan SARS-CoV-2 Mutation Panel [Click to enlarge]
For Research Use Only. Not for use in diagnostic procedures.
Our menu of verified real-time PCR research assays provide robust detection of SARS-CoV-2 mutations. Below are results (cluster plots) as viewed using QuantStudio Design and Analysis Software v2.5 with the Genotyping Analysis Module. These cluster plots show very clear discrimination between the wild type samples (red dots along the x-axis) and the mutation samples (blue dots along the y-axis).
S gene mutation delH69V70
[Click to enlarge]
Figure 2. S gene mutation delH69V70 cluster plot. delH69V70 (also known as 69-70del) is a known mutation of B.1.1.7 (501Y.V1 or UK variant). delH69V70 is not exclusive to B.1.1.7.
- Wild type detected
- delH68V70 mutation detected
S gene mutation N501Y
[Click to enlarge]
Figure 3. S gene mutation N501Y cluster plot. N501Y is commonly found in B.1.1.7 (UK variant), B.1.351 (South African variant), P.1 (Brazilian variant).
- Wild type detected
- N501Y mutation detected
How it works
Starting with isolated RNA from SARS-CoV-2 positive samples, our unique workflow combines our gold-standard Applied Biosystems TaqMan SNP Genotyping Assays with a one-step RT-PCR reaction to detect whether there are known mutations present in your samples or not.
In this video, we’ll show you how this one-step RT-PCR reaction works and what you can expect your results to look like.
Training support
In this short, two-video tutorial, you will learn how to:
- Set up the instrument software for detecting the SARS CoV-2 mutation panel
- Analyze the data with the Applied Biosystems Design and Analysis Software v2.5 or later with the Genotyping Analysis Module using the run files from all Applied Biosystems real-time PCR instruments
Go to thermofisher.com/educationconnect and log into your account or create a new one!
Analysis software
Tips and tricks for setting up your experiment and analyzing results
In this short video, you will learn:
- How to set up Genotyping Analysis in your instrument software
- How to set up your method with a reverse transcription step
- How to select real-time data in the genotyping analysis settings
- How to view results and read cluster plots
Use QuantStudio Design and Analysis Software v2.5 or later with the Genotyping Analysis Module.
- Fast-track SARS‑CoV‑2 variant and mutation profiling for public health action in the UK using RT‑PCR–based genotyping assays
- Rapid, Cost-effective System for Surveillance of SARS-CoV-2 Variants of Concern using Targeted RT-PCR SARS CoV-2 Mutation Panel
- Comparison of TaqMan and TIB Molbiol SARS-CoV-2 Genotyping Assays for the Identification of B.1.1.7 in S-gene Target Failure
- Quick SARS-CoV-2 surveillance in the central European region using SGTF and a panel of seven mutation of concern RT-PCR SNP assays
- Epidemiological and biological associations of SARS-CoV-2 variants based on real-world observational data
To run the TaqMan SARS-CoV-2 Mutation Panel, you will need to order following:
Naming Convention: Gene.Mutation.Reference Codon.Mutant Codon
Example: S.D215G.GAT.GGT
Note: For multi-nucleotide deletions, the reference codon and mutant codon are not part of the naming convention. (Example: S.delH69V70)
Assays associated with the publication, A method for variant agnostic detection of SARS-CoV-2, rapid monitoring of circulating variants, detection of mutations of biological significance, and early detection of emergent variants such as Omicron by E. Lai, D. Becker, et al. are highlighted below in blue.
Need help selecting assays to detect variants of concern? Learn more here.
For additional assistance on mutation assay selection, please contact us.
NIH-funded project offers efficient approach when tracking SARS-CoV-2 variants
The assays highlighted in grey are the current assays used in the Rosalind Dashboard.
*Recommend running an additional assay in parallel with V213G, such as Q493R, that will produce amplification from BA.1 which is found to a high prevalence in Omicron variants.
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Recommended controls
RNA Wildtype Controls
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For Research Use Only. Not for use in diagnostic procedures.
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