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
     
    Workflow
     
    Performance

    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 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:

    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:

    sars-covid2-mutation-panel-order

    Premier assays are high demand assays for popular variants with one standard size.

    Custom assays come in two sizes with longer delivery times.

    We've recently revised our 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 most current assays used in the Rosalind Dashboard as of July 18, 2022.

    New Omicron BA.4, BA.5, B.2 and BA.2.12 variant mutation assays:

    S.S704L.TCA.TTA
    M.D3N.GAT.AAT
    ORF7b.L11F.TTG.TTT
    C12880T

    Premier assays

    The TaqMan SARS-CoV-2 Mutation Panel Premier Assay AIF file can be accessed in the Resources section below.

    MutationWHO labelTop associated variants
    and sublineages
    Earliest documented samplesSizeSKUQty

    S.D614G.GAT.GGT 

    Various

    All 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 countries

    1,250 rxn

    A51818

    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 countries1,250 rxnA51814
    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 countries1,250 rxnA51819
    S.P681R.CCT.CGTDeltaB.1.617.1, B.1.617.2, B.1.617.3India1,250 rxnA51822
    S.E484Q.GAA.CAADelta (absence of this mutation)B.1.617, B.1.617.1, B.1.617.3India1,250 rxnA51820
    S.delH69V70 AlphaB.1.1.7, B.1.258, B.1.525  United Kingdom1,250 rxnA51808
    S.delY144 AlphaB.1.1.7 United Kingdom1,250 rxnA51817
    S.N501Y.AAT.TAT Alpha, Beta, GammaP.1, B.1.1.7, B.1.351 United Kingdom , South Africa, Brazil / Amazon1,250 rxnA51812
    S.P681H.CCT.CATAlphaB.1.1.207, B.1.1.7 Nigeria, United Kingdom1,250 rxnA51816
    S.D215G.GAT.GGTBetaB.1.351South Africa1,250 rxnA51823
    S.E484K.GAA.AAABeta, Gamma, EtaP.1 ,B.1.1.33, B.1.351, B.1.525South Africa, Brazil1,250 rxnA51813
    S.K417T.AAG.ACG GammaP.1 Brazil / Amazon1,250 rxnA51815
    S.L18F.CTT.TTTGammaP.1, B.1.351Brazil / Amazon1,250 rxnA51830
    S.T20N.ACC.AACGammaP.1 Brazil / Amazon1,250 rxnA51821
    S.S13I.AGT.ATTEpsilonB.1.427, B.1.429California1,250 rxnA51828
    S.F888L.TTT.CTTEtaB.1.525 1,250 rxnA51827
    S.S477N.AGC.AAClotaB.1.526New York1,250 rxnA51824
    S.N439K.AAC.AAAB.1.2581,250 rxnA51825
    S.V1176F.GTT.TTTP.2Brazil1,250 rxnA51826

    Custom assays

    AIF files are included in assay shipment.

    Q493R
    Q493R
    MutationWHO labelTop associated variants
    and sublineages
    Earliest documented samplesAssay IDCatalog #
    A49785
    375 rxn
    Catalog #
    A49786
    1250 rxn
    S.S704L.TCA.TTAOmicronBA.2.12 and all sublineagesVarious countries CVMFWVY
    ORF7b.L11F.TTG.TTTOmicronBA.4 and all sublineagesVarious countriesCVCE3VH
    M.D3N.GAT.AAT OmicronBA.5, BA.5.1Various countriesCVAAAAK
    C12880T Omicron BA.2 and all sublineages, BA.4, BA.5, BA.3 Various countriesCVEPRZD
    T15009COmicron BA.2.12.1Various countries CVFVKKA
    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.CATOmicronBA.1, BA.1.1, BA.2, BA.3, BA.4, BA.5 and all sublineagesVarious countriesCVAAAAH
    S.T19R.ACA.AGADeltaB.1.617.2IndiaCVXGPWD
    S.T478K.ACA.AAADeltaB.1.617.2IndiaCVNKRFP
    ORF1a.A13057TMuB.1.621ColombiaCVXGPV9
    ORF1a.F2387V.TTT.GTTLambdaC.37PeruCVH49PY
    S.L452Q.CTG.CAGOmicron, LambdaBA.2.12.1, C.37Various countriesCVKA3AV
    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.R346T.AGA.ACA Omicron BA.4.6Various countries CV47VR2
    ORF10.L37F.CTT.TTT Omicron BA.5.1Various countries CVYMJGD
    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.T376A.ACT.GCTOmicronBA.2 and all sublineages, BA.4, BA.5 and all sublineagesVarious countriesCVNKRFV
    S.V213G.GTG.GGG*OmicronBA.2, BA.4, BA.5 and all sublineagesVarious countriesCV32Z62
    S.G339D.GGT.GATOmicronAll Omicron lineagesVarious countriesCV47VRX
    S.Q493R.CAA.CGAOmicronB.1.1.529, BA.1 and all sublineages, BA.2 and all sublineages, BA.3 and all sublineagesVarious countriesCVH49P2
    S.R346K.AGA.AAAMu, OmicronB.1.621, BA.1.1 and all sublineagesColombiaCVZTDZ3
    S.F157L.TTC.TTAOmicronBA.2.75Various countries CVGZE4Y
    S.N460K.AAT.AAG Omicron BA.2.75Various countries CV9HHWN
    S.Y145H.TAC.CACDelta +AY.4.2IndiaCVFVKJ7
    S.EFR156-158GDeltaB.1.617.2IndiaCVPRJZM
    CoV1.A28272TMuB.1.621ColombiaCV2W7KZ
    T1055A.ACA.GCAMuB.1.621ColombiaCV32Z6X
    S.T95I.ACT.ATTOmicron, Iota, MuB.1.526, B.1.621.1, BA.1 and all sublineages, BA.3 and all sublineagesVarious countries CVRWEKJ
    S.F157S.TTC.TCCIotaB.1.526United StatesCVTZ76G
    S.Q52R.CAG.CGGEtaB.1.525 CV47VRU
    S.Q677H.CAG.CATEtaB.1.525 CVRWEKH
    S.Q677H.CAG.CACEtaB.1.525 CVTZ76F
    S.A701V.GCA.GTAOmicron, BetaBA.1.17.2, B.1.351Various countriesCVZTDZZ
    S.delL242.244LBetaB.1.351South AfricaCV2W7KX
    S.R246I.AGA.ATABetaB.1.351South AfricaCV7DPCP
    S.A570D.GCT.GATAlphaB.1.1.7United KingdomCVU62RC
    S.S982A.TCA.GCAAlphaB.1.1.7United KingdomCVXGPV6
    S.T716I.ACA.ATAAlphaB.1.1.7United KingdomCVWCWA9
    ORF1a.A1708D.GCT.GATAlphaB.1.1.7United KingdomCVYMJF3
    ORF8.Q27ST.CAA.TAAAlphaB.1.1.7United KingdomCVRWEKG
    S.A222V.GCT.GTT B.1.177 CVMFWVP
    S.W152L.TGG.TTG R.1 CVH49PW
    S.Y453F.TAT.TTT B.1.1.298MinkCVNKRFM

    *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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    Resources

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

    Style Sheet for Global Design System