JUN 08, 2021 7:00 AM PDT

Primers and Probes to Assay for SARS-CoV-2 Variants in Research Samples

By Netanya Spencer and Erik Wendlandt

Today, many scientists are investigating SARS-CoV-2 variants in their research projects. In order to facilitate screening for variants in these studies, IDT now offers qPCR primers and probes for SARS-CoV-2. I interviewed Dr. Erik Wendlandt, Senior Commercial and Technical Specialist at IDT, who designed these primers and probes.

Hi, Dr. Wendlandt. Thanks for speaking with me today.  We know that many scientists are interested in identifying SARS-CoV-2 variants in samples for research purposes. For this kind of research, when would it be appropriate to select qPCR over next-generation sequencing or NGS? 

NGS has proven instrumental to our understanding of SARS-CoV2 evolution and identification of emerging variants of concern, often abbreviated VoC. While essential for the identification of novel variants, NGS capabilities are not as widespread in the research community as qPCR. This is because qPCR is a more mature technology and offers additional advantages over NGS such as lower costs and rapid results.  The limited availability of NGS, especially in small to midsized facilities, prompted IDT to develop qPCR assays to observe mutations found in the different VoCs.

So, which variants does IDT have assays against?

IDT approached the designing of variants a bit differently than other vendors. Instead of designing an assay to a specific variant, we opted to design to specific point mutations that are found within the VoCs. This approach allows us to adapt quickly to the changing variant landscape and offer assays for emerging variants within days. We have designed assays against over 30 point mutations across the SC2 genome, with many of the assays targeting the spike gene. These assays are available in different dye/quencher combinations as well as separate oligos or premixed at specified concentrations. For a list of internally tested assays, customers can click here.

How did you design these primer and probe sets?  What design tools did you use?

Sequence information for each of the mutation assays was collected using a variety of open-access databases. The primers for each assay were designed using IDT’s PrimerQuest™ design software (RUO). The probes are highly modified qPCR probes and were designed manually using proprietary thermodynamic tools. 

Does IDT have the capacity to design custom primers and probes? 

Due to the complex nature of these designs and the time to complete the design process, we are not offering custom variant design services for new assays or changes to our existing assays. However, we are bringing new designs online regularly, so customers should feel free to contact IDT if their target of interest is not listed. Customers can also use the PrimerQuest tool to design primers for their own assays.

How does IDT ensure quality?

Synthetic template contamination is one of the most significant contamination risks for any oligo manufacturer. At IDT, we control for this risk by isolating certain areas of the facility and certain machines to never touch oligos that can serve as templates. This approach has allowed us to significantly mitigate the risk of synthetic template contamination.

Do these assays utilize the IDT dual-quenched technology? 

As I mentioned previously, the assays contain highly modified probes. To improve their discrimination potential, the probes were designed to be very short. Short probes do not benefit from an internal quencher like conventional hydrolysis probes, so we do not utilize ZEN™ or TAO™ quenchers in the probe design.

RUO - For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.

About the Sponsor
  • Integrated DNA Technologies, Inc. (IDT) is in the business of moving science forward. We are scientists working for scientists. Our innovative tools and solutions for genomics applications are breaking down barriers and inspiring you to dream big and achieve your next breakthroughs.
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