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.

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For Research Use Only. Not for use in diagnostic procedures.

Features of the TaqMan SARS-CoV-2 Mutation Research Panel include:
  • 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
Product details
TargetsChoose 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):

  • One VIC dye labeled probe to detect the reference sequence
  • One FAM dye labeled probe to detect the mutation sequence
  • Available sizes375 reactions 
    1,250 reactions 
    Sample inputRNA extracted from SARS-CoV-2 samples with a CT value of less or equal to 30 
    Turnaround time1 hour and 10 min from extracted RNA to results
    Recommended instrumentsAny real-time PCR instrument such as the Applied Biosystems 7500, 7500 FastQuantStudio 5, and QuantStudio 7 systems 
    Recommended softwareQuantStudio Design and Analysis Software v2.5 or later with the Genotyping Analysis Module

    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).

    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 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:

    1. How to set up Genotyping Analysis in your instrument software
    2. How to set up your method with a reverse transcription step
    3. How to select real-time data in the genotyping analysis settings
    4. 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

    Access posters now

    Ordering information

    To run the TaqMan SARS-CoV-2 Mutation Panel, you will need to order following:


    Custom assays come in two sizes with longer delivery times.

    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.

    Custom assays

    AIF files are included in assay shipment.

    MutationWHO labelTop associated variants
    and sublineages
    Earliest documented samplesAssay IDCatalog #
    375 rxn
    Catalog #
    1250 rxn
    S.F456L.TTT.TTAOmicronEG.5 Various countriesCVRWEK7
    ORF10.S23F.TCT.TTTOmicronEG.5 Various countriesCVU62R2
    ORF1ab.G1819SOmicronFL and all sublineagesVarious countriesCVEPRZU
    ORF1b.G830GOmicronFD and all sublineagesVarious countriesCVH49RJ
    N.L219F.CTT.TTTOmicronEG and all sublineagesVarious countriesCVXGPWV
    Orf1a.Q1198K.CAA.AAAOmicronCH* Various countriesCVAAAAR
    ORF1b.P1953P.CCA.CCG OmicronXBB and all sublineagesVarious countriesCV32Z67
    ORF1b.S959P.TCC.CCCOmicronXBB and all sublineagesVarious countriesCVZTD2D
    ORF1ab:N4060SOmicron BA.2.75Various countries CVCE3VJ
    ORF1b:Y264H OmicronBQ.1 and all sublineagesVarious countriesCV47VR3
    ORF1ab.C7528TOmicronBF.7Various countries CV7DPCZ
    N.E136D.GAG.GATOmicronBA.5.3.1, BE and all sublineages, BQ.1Various countriesCV9HHWW
    M.D3N.GAT.AAT OmicronBA.5, BA.5.1, BE and BF sublineages, BQ.1 and all sublineagesVarious countriesCVAAAAK
    ORF7b.L11F.TTG.TTTOmicronBA.4 and all sublineagesVarious countriesCVCE3VH
    C12880T Omicron BA.5 and all sublineagesVarious countriesCVEPRZD
    S.S704L.TCA.TTAOmicronBA.2.12 and all sublineages, BQ.1Various countries CVMFWVY
    T15009COmicron BA.2.12.1Various countries CVFVKKA
    S.L452Q.CTG.CAGOmicron, LambdaBA.2.12.1, C.37Various countriesCVKA3AV
    ORF1a.A2710T.GCT.ACTOmicronBA.1, BA.1.1Various countriesCVZTDZ7
    ORF1a.T13195COmicronBA.1, BA.1.1Various countriesCVWCWCF
    S.T547K.ACA.AAAOmicronBA.1, BA.1.1Various countriesCVYMJGA
    S.Q954H.CAA.CATOmicronAll Omicron lineagesVarious countriesCVAAAAH
    ORF1ab.Q5412H.CAA.CAC (ORF1b.Q1011H)IotaB.1.526United StatesCVPRJZN
    S.W152C.TGG.TGCEpsilonB.1.427, B.1.429United StatesCVYMJF7
    S.D80A.GAT.GCTBetaB.1.351South AfricaCV32Z6V
    T16176CAlphaB.1.1.7United KingdomCVNKRFR
    S.S486P.TCT.CCT OmicronXBB and all sublineagesVarious countriesCVZTD2E
    S.V486P.GTT.CCTOmicronXBB and all sublineagesVarious countriesCVFVKKN
    S.D614G.GAT.GGT VariousAll Omicron sublineages, B.1.1.207, P.1, B.1.1.33, B.1.1.7, B.1.177, B.1.258, B.1.351, B.1.525, Mink variant Various countriesCVKA3AT
    S.K417N.AAG.AAT Omicron, BetaBA.1 and all sublineages, BA.2 and all sublineages, BA.3, BA.4, BA.5 and all sublineages, B.1.351 Various countriesCVFVKJZ
    ORF10.L37F.CTT.TTT Omicron BA.5.1Various countries CVYMJGD
    S.F157L.TTC.TTAOmicronBA.2.75, BN.1Various countries CVGZE4Y
    ORF1a.S2519P.TCT.CCT OmicronBA.2.11 Various countries CVWCWCH
    S.L452M.CTG.ATG OmicronBA.2.9.1, BA.2.13 Various countries CVXGPWF
    ORF3a.H78Y.CAC.TAC OmicronBA.2.9 and all sublineages Various countries CVZTD2A
    N.P151S.CCT.TCTOmicronBA.4 and all sublineagesVarious countries CV32Z64
    S.G339D.GGT.GATOmicronAll Omicron lineages except BA.2.75 and XBB.1 Various countriesCV47VRX
    S.L452R.CTG.CGGOmicron, Delta, EpsilonBA.5, BA.4, BA.2.11, B.1.617, B.1.617.1, B.1.617.2, B.1.617.3, B.1.429Various countriesCVAAAAD
    S.delH69V70 AlphaBA.2.86, B.1.1.7, B.1.258, B.1.525  United KingdomCVCE3U9
    S.delY144 AlphaB.1.1.7 United KingdomCVTZ76E
    S.N501Y.AAT.TAT Alpha, Beta, GammaP.1, B.1.1.7, B.1.351 United Kingdom , South Africa, Brazil / AmazonCVDJXE6
    S.P681H.CCT.CATAlphaB.1.1.207, B.1.1.7 Nigeria, United KingdomCVPRJZJ

    *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.

    Additional products needed

    Master mix

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    Recommended controls

    RNA Wildtype Controls

    GeneArt strings

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    For Research Use Only. Not for use in diagnostic procedures.

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