PANDAA qDx SARS-CoVar [Variant Genotyping]

SARS-CoV-2 detection and allelic discrimination of variant mutations – including Omicron.

Questions? email us: COVID19@aldatubio.com

  • A focused genotyping approach of the S gene of SARS-CoV-2 that is more time and cost-effective than sequencing for COVID variant genotyping.
  • Using a combination of fluorescent probes in two multiplex PANDAA reactions, each of the eight variants has a distinct fluorescent signature that allows them to be accurately differentiated:
      • Non-variant [i.e. Wuhan strain]
      • Variants of Concern
        • Alpha
        • Beta
        • Gamma
        • Delta
        • Omicron
      • Variants of Interest
        • Epsilon
        • Zeta
        • Eta
        • Theta
        • Iota
        • Kappa
  • Fast – delivers accurate results from RNA in 1 hour
  • Sensitive to < 100 copies
  • Platform-agnostic – compatible with sample prep and qPCR platforms in most labs.

Please enquire below about the availability of this product.

Additional information

Kit Controls

Synthetic RNA and Extraction Controls

Price

$700 [96 reactions / 40 samples + controls]

SKU

PQ.0111.Kit.096.RUO

Kits will be shipped within 48-72 hours.

Overview

PANDAA qDx™ SARS-CoVar is a qualitative real-time PCR (qPCR) multiplex assay designed as a reflex test on SARS-CoV-2 positive RNA for the for the allelic discrimination of five SARS-CoV-2 variants of concern – including Omicron – and three variants of interest, as well as the non-variant Wuhan strain of SARS-CoV-2.

 

Variants of Concern

WHO DesignationPango DesignationGISAID Designation
AlphaB.1.1.7GRY (formerly GR/501Y.V1)
BetaB.1.351GH/501Y.V2
GammaP.1GR/501Y.V3
DeltaB.1.617.2G/452R.V3
OmicronB.1.1.529GR/484A

Variants of Interest

WHO DesignationPango DesignationGISAID Designation
EpsilonB.1.427/B.1.429GH/452R.V1
EtaB.1.525G/484K.V3
KappaB.1.617.1 G/452R.V3

For Research Use Only. This test has not been cleared or approved by the U.S. Food and Drug Administration (FDA). This product is covered by one or more patents, trademarks and / or copyrights owned or controlled by Aldatu Biosciences, Inc.

Overview

PANDAA qDx™ SARS-CoVar is a qualitative real-time PCR (qPCR) multiplex assay designed as a reflex test on SARS-CoV-2 positive RNA for the for the allelic discrimination of five SARS-CoV-2 variants of concern – including Omicron – and three variants of interest, as well as the non-variant Wuhan strain of SARS-CoV-2.

 

Resources​

User guides and protocols

Variants of Concern

WHO DesignationPango DesignationGISAID Designation
AlphaB.1.1.7GRY (formerly GR/501Y.V1)
BetaB.1.351GH/501Y.V2
GammaP.1GR/501Y.V3
DeltaB.1.617.2G/452R.V3
OmicronB.1.1.529GR/484A

Variants of Interest

WHO DesignationPango DesignationGISAID Designation
EpsilonB.1.427/B.1.429GH/452R.V1
EtaB.1.525G/484K.V3
KappaB.1.617.1 G/452R.V3

For Research Use Only. This test has not been cleared or approved by the U.S. Food and Drug Administration (FDA). This product is covered by one or more patents, trademarks and / or copyrights owned or controlled by Aldatu Biosciences, Inc.

Kit Contents

Kit #1 [Amplification + Detection]

 

Contents Volume (µL)
PRxB Buffer 1,020 µL
Variant Sig #1 PANDAA 35 µL
Variant Sig #2 PANDAA 35 µL
RT Enzyme 5 µL
Internal Control RNA 120 µL
Positive Control [Extraction] 75 µL
Negative Control [Extraction] 75 µL

Kit #2 [RNA Controls]

Synthetic RNA covers the assay target regions and is provided at 25 copies / µL to give 250 copies / reaction when using 10 µL RNA / reaction.

 

Variant / Control Volume (µL)
Wild-Type [Non-variant] 50 µL
Alpha [B.1.1.7]
Beta [B.1.351]
Gamma [P.1]
Delta [B.1.617.2]
Omicron [B.1.1.529]
Kappa [B.1.617.1]
Negative

Principles

Variant Signature Assays
Using two multiplex qPCR reactions, each of the eight variants has a distinct fluorescent signature that allows them to be accurately differentiated. Both reaction mixtures contain an optional internal control that is detected by a Cy5-labelled probe.

 

AssayDetection Channel #1Detection Channel #2Detection Channel #3
Variant Signature #1K417N
N501
N501YK417
Variant Signature #2E484KQ
T478K
L452RE484A

 

Compatible Real-Time PCR Instrumentation
Any qPCR instrument that is capable of detecting FAM, VIC and NED fluorophores, with or without the passive reference dye, ROX. For use of the internal control, the instrumentation must be capable of detecting the Cy5 fluorophore.

 

To discuss the availability of alternative fluorophores for your real-time PCR instrument, please email support@aldatubio.com.

 

  • Applied Biosystems: 7500, 7700, 7900, QuantStudio 3, QuantStudio 5, QuantStudio 6, QuantStudio 7 Pro, QuantStudio 12K Flex, StepOne Plus and Viia 7.
Data Interpretation
Based on the combined fluorescence signature patterns from the two qPCR reactions shown below, positive results are indicative of the presence of the respective SARS-CoV-2 variant.

 

WHO DesignationPangoSignature #1
Detection Channels
Signature #2
Detection Channels
Variant Signature
Non-Variant [Wuhan]-#1 [N501]
#3 [K417]
#3 [E484][1, 3] [3]
AlphaB.1.1.7 #2 [N501Y]
#3 [K417]
#3 [E484][2, 3] [3]
BetaB.1.351 #1 [K417N]
#2 [N501Y]
#1 [E484K][1, 2] [1]
GammaP.1 #2 [N501Y]#1 [E484K][2] [1]
DeltaB.1.617.2 #3 [K417]
#1 [N501]
#1 [T478K]
#3 [E484A]
[1, 3] [1, 3]
OmicronB.1.1.529
#1 [K417N]
#2 [N501Y]
#2 [L452R]
#3 [E484]
[1, 3] [2, 3]
EpsilonB.1.427/
B.1.429
#3 [K417]
#1 [N501]
#2 [L452R]
#3 [E484]
[1, 3] [2, 3]
EtaB.1.525 #3 [K417]
#1 [N501]
#1 [E484K]
[1, 3] [1]
KappaB.1.617.1 #3 [K417]
#1 [N501]
#2 [L452R]
#1 [E484Q]
[1, 3] [1, 2]

 

Principles

Variant Signature Assays
Using two multiplex qPCR reactions, each of the eight variants has a distinct fluorescent signature that allows them to be accurately differentiated. Both reaction mixtures contain an optional internal control that is detected by a Cy5-labelled probe.

 

AssayDetection Channel #1Detection Channel #2Detection Channel #3
Variant Signature #1K417N
N501
N501YK417
Variant Signature #2E484KQ
T478K
L452RE484A

 


Compatible Real-Time PCR Instrumentation
Any qPCR instrument that is capable of detecting FAM, VIC and NED fluorophores, with or without the passive reference dye, ROX. For use of the internal control, the instrumentation must be capable of detecting the Cy5 fluorophore.

 

To discuss the availability of alternative fluorophores for your real-time PCR instrument, please email support@aldatubio.com.

 

  • Applied Biosystems: 7500, 7700, QuantStudio 3, QuantStudio 5, QuantStudio 6, QuantStudio 7, QuantStudio 12, StepOne Plus.
  • Roche LightCycler

 


Data Interpretation
Based on the combined fluorescence signature patterns from the two qPCR reactions shown below, positive results are indicative of the presence of the respective SARS-CoV-2 variant.

 

WHO Designation Pango Designation Variant Signature #1Variant Signature #2
Wild-type [Wuhan]-NED [K417]
FAM [N501]
NED [E484]
AlphaB.1.1.7 NED [K417]
VIC [N501Y]
NED [E484]
BetaB.1.351 FAM [K417N]
VIC [N501Y]
FAM [E484K]
GammaP.1 VIC [N501Y]FAM [E484K]
DeltaB.1.617.2 NED [K417]
FAM [N501]
VIC [L452R]
FAM [T478K]
NED [E484]
EpsilonB.1.427/B.1.429 NED [K417]
FAM [N501]
VIC [L452R]
NED [E484]
EtaB.1.525 NED [K417]
FAM [N501]
FAM [E484K]
KappaB.1.617.1 NED [K417]
FAM [N501]
VIC [L452R]
FAM [E484Q]

 

Overview

PANDAA qDx™ SARS-CoVar is a qualitative real-time PCR (qPCR) multiplex assay designed as a reflex test on SARS-CoV-2 positive RNA for the for the allelic discrimination of five SARS-CoV-2 variants of concern – including Omicron – and three variants of interest, as well as the non-variant Wuhan strain of SARS-CoV-2.

 

Kit Contents

Kit #1 [Amplification + Detection]

 

Contents Volume (µL)
PRxB Buffer 1,020 µL
Variant Sig #1 PANDAA 35 µL
Variant Sig #2 PANDAA 35 µL
RT Enzyme 5 µL
Internal Control RNA 120 µL
Positive Control [Extraction] 75 µL
Negative Control [Extraction] 75 µL

Kit #2 [RNA Controls]

Synthetic RNA covers the assay target regions and is provided at 25 copies / µL to give 250 copies / reaction when using 10 µL RNA / reaction.

 

Variant / Control Volume (µL)
Wild-Type [Non-variant] 50 µL
Alpha [B.1.1.7]
Beta [B.1.351]
Gamma [P.1]
Delta [B.1.617.2]
Omicron [B.1.1.529]
Kappa [B.1.617.1]
Negative

Enquiries

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