ddPCR and RT-PCR Assays for SARS-CoV-2 Variant Surveillance
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SARS-CoV-2 Variant Assays | SARS-CoV-2 Variant Assay Protocols, Kits, and Reagents | Custom Assays for ddPCR and RT-PCR |
With the emergence of SARS-CoV-2 variants that may confer an evolutionary advantage to the virus, the need for fast, sensitive, and reliable tests for researchers to monitor for variants is essential both for tracking purposes and sequencing prioritization.
The SARS-CoV-2 Variant Assays are predesigned mutation detection assays targeting the most prominent variants known to date. These are single-tube duplex assays designed to support detection of a specific mutation in the FAM channel and wild-type sequence in the HEX channel using either Droplet Digital PCR (ddPCR) or RT-PCR.
New assays are expected to be made available for research use as new variants emerge.
The SARS-CoV-2 Variant Assays are for research use only. Not for use in diagnostic procedures.
SARS-CoV-2 Variant Assays for ddPCR and RT-PCR
These assays were designed specifically for Droplet Digital PCR using our Expert Design engine, which is validated to create high-quality assays. The ddPCR assays should be validated using our One-Step RT-ddPCR Kit to detect RNA instead of the standard mix for DNA.
All assays are compatible with RT-PCR when used by researchers as an allelic discrimination assay with our Reliance One-Step Multiplex RT-qPCR Supermix. Those assays indicated with a check mark (✓) have been wet-lab verified for RT-PCR. All assays will require validation prior to use by researchers trained in RT-PCR technology.
gBlocks from IDT are recommended for validation as positive controls for the variant targets. Positive control sequences are included on the assay details page of each duplex assay. The SARS-CoV-2 positive standard can be validated for use as a positive control for the wild-type targets (Wuhan strain). For RT-PCR assays using human samples, the Human RNAse P RPP40 Assay can be used as a sample control to monitor for the presence of amplifiable human RNA in the extracted sample.
Note: Clicking on an Assay ID will redirect you to our Digital PCR Assays ordering portal. The assays may be used for either ddPCR or RT-PCR as indicated. A Bio-Rad.com user login is required to order assays.
SARS-CoV-2 B.1.1.7 Variant (UK Variant) Strain Reported Identifiers
| Nucleotide | Amino Acid | Assay ID | |
|---|---|---|---|
| ORF1ab Gene | |||
| 3267C>T | T1001I | dMDS337202764 | |
| 5388C>A | A1708D | dMDS139995162 | |
| 6954T>C | I2230T | No design available | |
| 11288-11296 deletion | SGF 3675-3677 deletion | dMDS673358073 | |
| Spike Gene | |||
| 21765-21770 deletion | HV 69-70 deletion | dMDS284738817 | |
| 21991-21993 deletion | Y144 deletion | dMDS272537816 | |
| 23063A>T | N501Y | dMDS731762551 | |
| 23271C>A | A570D | dMDS650795708 | |
| 23604C>A | P681H | dMDS231800716 | |
| 23709C>T | T716I | dMDS468536809 | |
| 24506T>G | S982A | dMDS869413688 | |
| 24914G>C | D1118H | dMDS605463947 | |
| Orf8 Gene | |||
| 27972C>T | Q27stop | dMDS684178543 | |
| 28048G>T | R52I | dMDS217054602 | |
| 28111A>G | Y73C | dMDS360594022 | |
| N Gene | |||
| 28280 GAT>CTA | D3L | dMDS357586786 | |
| 28977C>T | S235F | dMDS833788311 | |
SARS-CoV-2 B.1.351 Variant (South Africa Variant) Strain Reported Identifiers
| Nucleotide | Amino Acid | Assay ID | |
|---|---|---|---|
| ORF1ab Gene | |||
| 1059C>T | T265I | dMDS501248615 | |
| 5230G>T | K1655N | dMDS360434193 | |
| 10323A>G | K3353R | dMDS867807078 | |
| Spike Gene | |||
| 21801A>C | D80A | dMDS275239390 | |
| 22813G>T | K417N | dMDS817055273 | |
| 23012G>A | E484K | dMDS661453998 | |
| 23063A>T | N501Y | dMDS731762551 | |
| 23664C>T | A701V | dMDS269740216 | |
| ORF3a Gene | |||
| 25563G>T | Q57H | MDS290356659 | |
| 25904C>T | S171L | dMDS413789282 | |
| E Gene | |||
| 26456C>T | P71L | dMDS660665257 | |
| N Gene | |||
| 28887C>T | T205I | dMDS759245237 | |
SARS-CoV-2 P.1 Variant (Brazil/Japan Variant) Strain Reported Identifiers
| Nucleotide | Amino Acid | Assay ID | |
|---|---|---|---|
| Spike Gene | |||
| 22812A>C | K417T | dMDS673301504 | |
SARS-CoV-2 B.1.429 Variant (California Variant) Strain Reported Identifiers
| Nucleotide | Amino Acid | Assay ID | |
|---|---|---|---|
| Spike Gene | |||
| 22917T>G | L452R | dMDS983315944 | |
✓ Assay has been wet-lab verified for RT-PCR use with Reliance One-Step RT-qPCR Supermix.
Visit the CDC website for more information about emerging variants.
SARS-CoV-2 Variant Assay Protocols, Kits, and Reagents
SARS-CoV-2 Variant Assay Protocols
SARS-CoV-2 Variant Detection ddPCR Assay Protocol
The ddPCR Mutation Detection Assays Protocol is applicable to ddPCR SARS-CoV-2 variant assays for all mutations.
SARS-CoV-2 Variant Detection RT-PCR Assay Protocol
The Variant RT-qPCR Assay Protocol is applicable to RT-qPCR SARS-CoV-2 variant assays for all mutations
SARS-CoV-2 Assay Kits and Reagents
SARS-CoV-2 Droplet Digital PCR (ddPCR) Kit
The Bio-Rad SARS-CoV-2 ddPCR Kit is a powerful diagnostic tool in the battle against COVID-19, with sensitivity and precision beyond that of qPCR assays.
Reliance SARS-CoV-2 RT-PCR Assay Kit
The Reliance SARS-CoV-2 RT-PCR Assay Kit is a molecular in vitro diagnostic test targeting the virus nucleocapsid N1 and N2 genes to detect the coronavirus specifically.
One-Step RT-ddPCR Advanced Kit for Probes
Use this one-step reverse transcription digital PCR supermix to achieve improved efficiency, specificity, and sensitivity with precise RNA target quantification using Droplet Digital PCR (ddPCR).
Reliance One-Step Multiplex RT-qPCR Supermix
Use Reliance One-Step Multiplex Supermix for sensitive amplification of up to 5 targets in a single reaction with challenging templates, difficult targets, or PCR inhibitors.
SARS-CoV-2 Standard
The SARS-CoV-2 Standard contains synthetic RNA transcripts of 5 SARS-CoV-2 gene targets and Human Genomic DNA.
SARS-CoV-2 Negative
The SARS-CoV-2 Negative contains genomic DNA at 75,000 copies/ml formulated in a synthetic matrix.
Custom Assays for ddPCR and RT-PCR
Choose from a large catalog of predesigned, validated ddPCR and qPCR assays or design your own custom assays.
- Expert Design ddPCR assays are designed for optimal performance and manufactured to reduce false positives.
- PrimePCR Assays and panels are carefully designed and validated to yield reliable qPCR data.
ddPCR Expert Design Assays
ddPCR Expert Design Assays are designed specifically for Droplet Digital PCR by the experts that developed the technology.
PrimePCR Assays and Panels
Experimentally validated real-time PCR PCR primer and probe assays for mutation detection, gene expression, copy number variation. Design your own custom assays and panels.
More COVID-19 Surveillance Solutions
COVID-19 surveillance is needed to better inform public health decisions. Obstacles to surveillance work include large sample numbers, supply shortages, and complex sample types. Bio-Rad offers a range of solutions for COVID-19 surveillance.
Learn more about our COVID-19 Surveillance Solutions »
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