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SARS-CoV-2 Variant ValuPanel™ assays consist of separately delivered probes and primers that are designed for qualitative detection of specific SARS-CoV-2 mutations by genotyping using reverse transcription-polymerase chain reaction (RT-PCR). Each SARS-CoV-2 Variant ValuPanel consists of 2 BHQplus™ Probes and 2 primers for amplification and simultaneous discrimination between a specific mutation and the wild-type SARS-CoV-2 sequence.

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

Key benefits

  • Reliable results: From the trusted inventor of Black Hole Quencher™ (BHQ™) technology referenced in 7 of 8 WHO COVID-19 protocols.
  • High specificity: Enhanced affinity of the BHQplus Probe technology delivers high-fidelity genotyping results.
  • Flexible assay design: Increased assay design options with separately delivered probes and primers. 
  • Consistent quality: All probes and primers are HPLC purified and are manufactured and shipped from a facility entirely separate from positive control production.

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Several variants of SARS-CoV-2 have emerged bringing challenges to diagnostic tests and pandemic eradication efforts. Of particular significance are variants B.1.1.7 (also known as Alpha, first identified in the United Kingdom), B.1.351 (also known as Beta, first identified in South Africa), B.1.1.28 (also known as P.1 or Gamma, first identified in travelers from Brazil who arrived in Japan) and B.1.617 (including the Kappa and Delta variants, first identified in India). The ability to quickly and reliably identify SARS-CoV-2 mutations will enhance the ability to gather crucial public health information regarding transmissibility kinetics of new variants, and the efficacy of vaccines and therapeutics.

ValuPanel SARS-CoV-2 Mutation Variants containing specified SARS-CoV-2 mutation Availability
    Pango lineage (WHO label)  
SARS-CoV-2 Variant ValuPanel [E484K] E484K B.1.351 (Beta)
P.1 (Gamma)
B1.525 (Eta)
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SARS-CoV-2 Variant ValuPanel [E484Q] E484Q B1.617.1 (Kappa)
B1.617.3
SARS-CoV-2 Variant ValuPanel [del H69-V70] ΔH69-V70 B.1.1.7 (Alpha)
B.1.525 (Eta)
B.1.1.298
B.1.1.529 (Omicron) (BA.1)
SARS-CoV-2 Variant ValuPanel [N501Y] N501Y B.1.1.7 (Alpha)
B.1.351 (Beta)
P.1 (Gamma)
B.1.1.529 (Omicron) (BA.1 and BA.2)
SARS-CoV-2 Variant ValuPanel [P681H]
(Version 2)*
P681H B.1.1.7 (Alpha)
B.1.1.529 (Omicron) (BA.1 and BA.2)
SARS-CoV-2 Variant ValuPanel [P681R] P681R B.1.617.1 (Kappa)
B.1.617.2 (Delta)
B.1.617.3
SARS-CoV-2 Variant ValuPanel [K417N] K417N B.1.351 (Beta)
B.1.1.529 (Omicron) (BA.1 and BA.2)
SARS-CoV-2 Variant ValuPanel [K417T] K417T P.1 (Gamma)
SARS-CoV-2 Variant ValuPanel [L452R] L452R B.1.427/B.1.429 (Epsilon)
B.1.617.1 (Kappa)
B.1.617.2 (Delta)
B.1.617.3
SARS-CoV-2 Variant ValuPanel [H655Y] H655Y P.1 (Gamma)
B.1.1.529 (Omicron) (BA.1 and BA.2)
Coming soon
SARS-CoV-2 Variant ValuPanel [T19R] T19R B.1.617.2 (Delta)
SARS-CoV-2 Variant ValuPanel [T95I] T95I B.1.1.529 (Omicron) (BA.1)
B.1.526 (Iota)
B.1.621 (Mu)
       

*Please note: We replaced the first version of the P681H assay (Cat. No. SCV-P681H-1000) with SARS-CoV-2 Variant ValuPanel [P681H] (Version 2), which was designed to avoid the potential proximal mutation at Q677 and demonstrates improved cluster separation in endpoint genotyping analysis.

Amino acid mutations present in SARS-CoV-2 variants.

Spike protein mutation B1.1.7 (Alpha) B.1.351 (Beta) P.1 (Gamma) B1.617.1 (Kappa) B1.617.2 (Delta) B1.617.3 B.1.427/9 (Epsilon) B1.1.529
(Omicron) (BA.1)
Del H69-V70 Del HV HV HV HV HV HV HV Del HV
L452R L L L R R R R L
P681H
P681R
H P P R R R P H
E484K
E484Q
E484A
E K K Q E Q E A
N501Y Y Y Y N N N N Y
K417T
K417N
K N T K K K K N

 

Important considerations for detecting the Omicron variant

The Omicron sequence contains proximal mutations that have varying effects on the performance of the SARS-CoV-2 Variant ValuPanel assays.

  • The Del H69-V70 assay drops out in Omicron samples. This is likely due to the proximal mutation (A67V) which is present in the binding sequence for the deletion/mutation-specific probe. While this assay can’t be used to specially detect the H69-V70 deletion in Omicron samples, it can be used for S gene dropout assays, also called S-gene target failure (SGTF).
  • The E484K assay drops out in Omicron samples due to several proximal mutations in the assay.
  • The N501Y assay tolerates the proximal mutations in Omicron samples. Assays show reduced fluorescence on Omicron samples (as compared to N501Y detection on the Alpha variant), but it still establishes a distinct scorable cluster along the CAL Fluor™ Orange 560 axis for Omicron samples.
  • The P681H assay tolerates the proximal mutations in the Omicron lineage. The assay shows reduced fluorescence on Omicron samples (as compared to Alpha), but still establishes a distinct scorable cluster. Please note P681H can generate a “heterozygote” cluster due to the P681R mutation present in some variants including Delta and Kappa.
  • The K417N assay performs well on Omicron samples as there are no proximal mutations in this region. For accurate genotyping of tri-allelic mutations we recommend that both assays at each position are used, such as assays for both K417T and K417N. Please see the manual for more information.

Coming soon: We will be adding a ValuPanel assay for the H655Y mutation which will aid in the detection of the Omicron lineage. The H655Y mutation is present in Gamma and Omicron variants (without accompanying proximal mutations). The Gamma variant is no longer circulating or classified as a variant of concern, making this robust assay a good marker for identifying Omicron.

Customers can order the H655Y assay as a custom product prior to product release. Please contact the Assay Design and Development team (ADD@LGCgroup.com) if interested in the H655Y genotyping assay or other custom assay designs.

  Spike protein mutations 
Variants E484K 69-70 Del N501Y K417N K417T P681H P681R L452R H655Y
Alpha                  
Beta                  
Gamma                  
Delta                  
Omicron (BA.1)   * *     *      

*The Omicron sequence contains proximal mutations at these sites, which may affect the performance of the SARS-CoV-2 Variant ValuPanel assays. Please see above for important considerations for detecting the Omicron variant.

Product details

SARS-CoV-2 Variant ValuPanel assays consist of separately delivered probes and primers that are designed for qualitative detection of specific SARS-CoV-2 mutations by RT-PCR-based genotyping. Each SARS-CoV-2 Variant ValuPanel consists of 2 BHQplus™ Probes and 2 primers for amplification and simultaneous discrimination between a single mutation and the wild-type SARS-CoV-2 sequence.

 SARS-CoV-2 Variant ValuPanel assays are for research use only, they are not intended for SARS-CoV-2 diagnosis. The assays are intended for secondary, informational tests only, designed for variant screening in respiratory tract samples that have previously tested positive for SARS-CoV-2 by diagnostic RT-PCR. 

Each panel contains the following:

  • Forward and reverse primers that amplify the SARS-CoV-2 target sequence. One primer also initiates reverse transcription of the target sequence.

  • BHQplus™ Probes that specifically detect the mutation site: 

    • A mutation-specific probe labeled with CAL Fluor™ Orange 560

    • A reference/wild type-specific probe labeled with FAM

       

  Oligo type Target Dye Quencher nmol oligo delivered
Panel components Probe Wild-type allele FAM BHQ-1 Plus 5 nmol
Probe Mutant allele CAL Fluor Orange 560 BHQ-1 Plus 5 nmol
Primer N/A N/A N/A 20 nmol
Primer N/A N/A N/A 20 nmol
           



Probes and primers are supplied in dried format, at 5 nmol of each probe and 20 nmol of each primer. Probes and primers are delivered in separate tubes, they are not premixed.

Each kit can perform at least 1000 reactions, based on 20 uL reactions containing 200 nM/probe and 900 nM/primer. Use our Reaction Estimator Tool to calculate the number of reactions achievable when using other reaction volumes and oligo concentrations. 

SARS-CoV-2 Variant ValuPanel assays are designed to be compatible with all qPCR instruments that are capable of detecting FAM and CAL Fluor Orange 560 (VIC/HEX/JOE channel).

Materials not included in the kit:
PCR master mix, ROX reference dye, and positive controls are not included. We recommend AccuPlex SARS-CoV-2 variant positive controls from LGC SeraCare. See the manual for additional positive control template options.

Analysis of tri-allelic codons:
Mutations occurring at amino acid positions 417, 484 and 681 of the spike protein are attractive targets for genotyping analysis, but additional analysis may be required due to multiple mutations arising within these codons. For accurate genotyping at these positions we recommend that both assays at each position are used. For example, we recommend running both K417T and K417N assays, or both E484K and E484Q, or both P681H and P681R. Concordant results from these companion assays can compensate for the challenges of genotyping tri-allelic codons. Please see the manual for more information.

Resources

Recommended products

PCR reagents* including master mix and enzyme for SARS-CoV-2 assay development are also available

Item name  
AccuPlex SARS-CoV-2 Variant Panel 1 View product
sbeadex viral RNA purification kit View product
RapiDxFire 1-step RT-qPCR System View product

LGC SeraCare Life Sciences offers the AccuPlex SARS-CoV-2 Variant Panel 1 which contains the full SARS-CoV-2 genomic RNA with a focus on S-gene mutations in three prominent variants of concern (VOC): UK variant B.1.1.7, South Africa variant B.1.351, and Brazil variant P.1. The kit has one vial for each variant as well as a fourth wild type control vial. An RNase P negative control vial is also included.

What do you require to develop your SARS-CoV-2 assay?

We offer probes and primers specific to Coronavirus as well as enzymes, master mix, and extraction capabilities.

Let’s discuss your needs

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