Choose from a menu of verified real-time PCR 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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Features of the TaqMan SARS-CoV-2 Mutation Panel include:
  • Customizable—build your own custom panel from a menu of verified real-time PCR 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 follow-up testing of SARS-CoV-2 samples
  • Scalable—run a few or hundreds of samples to identify for 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 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 Fast Dx, 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 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.


    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)

    Premier assays

    MutationWHO labelAssociated variantsEarliest documented samplesSizeSKUQty

    S.D215G.GAT.GGT

    Beta

    B.1.351

    South Africa

    1,250 rxn

    A51823

    S.D614G.GAT.GGT 

    Various

    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 

    Nigeria, United Kingdom, South Africa, Brazil / Amazon

    1,250 rxn

    A51818

    S.delH69V70 

    Alpha

    B.1.1.7, B.1.258, B.1.525  

    United Kingdom

    1,250 rxn

    A51808

    S.delY144 

    Alpha

    B.1.1.7 

    United Kingdom

    1,250 rxn

    A51817

    S.E484K.GAA.AAA

    Beta,
    Gamma,
    Eta

    P.1 ,B.1.1.33, B.1.351, B.1.525

    South Africa, Brazil

    1,250 rxn

    A51813

    S.E484Q.GAA.CAA

    Delta
    (absence
    of this
    mutation)

    B.1.617, B.1.617.1, B.1.617.3

    India

    1,250 rxn

    A51820

    S.F888L.TTT.CTT

    Eta

    B.1.525

    20A/S:484K United Kingdom

    1,250 rxn

    A51827

    S.K417N.AAG.AAT 

    Beta

    B.1.351 

    South Africa

    1,250 rxn

    A51814

    S.K417T.AAG.ACG 

    Gamma

    P.1 

    Brazil / Amazon

    1,250 rxn

    A51815

    S.L18F.CTT.TTT

    Gamma

    P.1, B.1.351

    South Africa, Brazil/Amazon

    1,250 rxn

    A51830

    S.L452R.CTG.CGG

    Delta,
    Epsilon

    B.1.617, B.1.617.1, B.1.617.2, B.1.617.3, B.1.429

    India, California

    1,250 rxn

    A51819

    S.N439K.AAC.AAA

     

    B.1.258

     

    1,250 rxn

    A51825

    S.N501Y.AAT.TAT 

    Alpha,
    Beta,
    Gamma

    P.1, B.1.1.7, B.1.351 

    United Kingdom , South African, Brazil / Amazon

    1,250 rxn

    A51812

    S.P681H.CCT.CAT

    Alpha

    B.1.1.207, B.1.1.7 

    Nigeria, United Kingdom

    1,250 rxn

    A51816

    S.P681R.CCT.CGT

    Delta

    B.1.617.1, B.1.617.2, B.1.617.3

    India

    1,250 rxn

    A51822

    S.S13I.AGT.ATT

    Epsilon

    B.1.427, B.1.429

    California

    1,250 rxn

    A51828

    S.S477N.AGC.AAC

    lota

    B.1.526

    New York

    1,250 rxn

    A51824

    S.T20N.ACC.AAC

    Gamma

    P.1 

    Brazil / Amazon

    1,250 rxn

    A51821

    S.V1176F.GTT.TTT

     

    P.2

    Brazil

    1,250 rxn

    A51826

    Custom assays

    MutationWHO labelAssociated variantsEarliest documented samplesAssay IDCatalog #
    A49785
    375 rxn
    Catalog #
    A49786
    1250 rxn

    Orf1ab.A13057T

    Mu

    B.1.621

    Colombia

    CVXGPV9

    orf1.A1708D.GCT.GAT

    Alpha

    B.1.1.7

    United Kingdom

    CVYMJF3

    S.A222V.GCT.GTT

    B.1.177

    CVMFWVP

    CoV1.A28272T

    Mu

    B.1.621

    Colombia

    CV2W7KZ

    S.A570D.GCT.GAT

    Alpha

    B.1.1.7

    United Kingdom

    CVU62RC

    S.A701V.GCA.GTA

    Beta

    B.1.351

    South Africa

    CVZTDZZ

    N.D3L.GAT.CTA

    CVDJXE9

    S.D80A.GAT.GCT

    Beta

    B.1.351

    South Africa

    CV32Z6V

    S.delL242.244L

    Beta

    B.1.351

    South Africa

    CV2W7KX

    S.E583D.GAG.GAT*

    B.177

    CVU62RD

    S.E583D.GAG.GAC*

    B.177

    CVWCWCA

    S.EFR156-158G

    Delta

    B.1.617.2

    India

    CVPRJZM

    S.F157L.TTC.TTA

    A.23

    CVGZE4Y

    S.F157S.TTC_TCC

    Iota

    B.1.526

    United States

    CVTZ76G

    S.G446V.GGT.GTT

    CV2W7KY

    S.G769V.GGA.GTA

    CVPRJZK

    S.H66D.CAT.GAT

    CVCE3VC

    ORF1.K1795Q.AAA.CAA

    CVAAAAE

    S.L452Q.CTG.CAG

    Lambda

    C.37

    Mink

    CVKA3AV

    S.N450K.AAT.AAG

    B.1.214

    CVXGPV7

    S.N460K.AAT.AAA*

    CV7DPCR

    S.N460K.AAT.AAG*

    CV9HHWN

    S.N460T.AAT.ACT

    CVZTDZ2

    P5743S.CCA_TCA

    Mu

    B.1.621

    Colombia

    CVYMJF6

    orf8.Q27ST.CAA.TAA

    Alpha

    B.1.1.7

    United Kingdom

    CVRWEKG

    S.Q498R.CAA.CGA

    CVYMJF4

    S.Q52R.CAG.CGG

    Eta

    1.525

    CV47VRU

    S.Q613H.CAG.CAT

    A.23

    CV32Z6W

    S.Q677H.CAG.CAT*

    Eta

    1.525

    CVRWEKH

    S.Q677H.CAG.CAC*

    Eta

    1.525

    CVTZ76F

    S.R246I.AGA.ATA

    Beta

    B.1.351

    South Africa

    CV7DPCP

    S.R346K.AGA_AAA

    Mu

    B.1.621

    Colombia

    CVZTDZ3

    S.S982A.TCA.GCA

    Alpha

    B.1.1.7

    United Kingdom

    CVXGPV6

    T1055A.ACA_GCA

    Mu

    B.1.621

    Colombia

    CV32Z6X

    S.T478K.ACA.AAA

    Delta

    B.1.617.2

    CVNKRFP

    S.T716I.ACA.ATA

    Alpha

    B.1.1.7

    United Kingdom

    CVWCWA9

    S.T95I.ACT_ATT

    Iota, Mu

    B.1.526, B.1.621.1

    United States, Colombia

    CVRWEKJ

    S.V367F.GTC.TTC

    A.23

    CVEPRY6

    S.W152L.TGG.TTG

    R.1

    CVH49PW

    S.Y453F.TAT.TTT

    B.1.1.298

    Mink

    CVNKRFM

    *Recommended to run both assays. Variants may have two different mutant codons that result in the same amino acid change. Please refer to the table above for the naming convention and variants associated with each mutation.


    Additional products needed

    Master mix


    Recommended controls

    Product 
    GeneArt DNA string or plasmid controls thermofisher.com/geneart​

    GeneArt plasmid positive controls are available for selected assays. Contact us ›

     
    Resources
    Style Sheet for Global Design System