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SARS-CoV-2 coronavirus sequencing

Targeted NGS is a valuable research tool for the detection and characterization of viral genomes. We offer solutions designed for SARS-CoV-2 variant research.


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Next generation sequencing (NGS) can provide valuable information about the spread and genetic evolution of a virus. Targeted NGS is a valuable basic research tool for both detection and characterization of viruses. Since targeted NGS research provides data about viral genetic changes, the data can be used in combination with basic disease research to potentially correlate genetic changes that increase transmissibility or severity of disease.

Hybridization capture and amplicon sequencing are two NGS techniques that are being used to study genetic changes in SARS-CoV-2.

Why sequence the SARS-CoV-2 genome?

The genome sequences we get from sequencing SARS-CoV-2 are crucial to track and trace the ongoing outbreak of COVID-19. Using NGS, we can look at the virus’ genomic sequence from virus-positive samples to help us understand where it may have originated, how it is mutating or evolving, and where it spreads. Knowing the genome sequence information is also critical to research:

  • Origin identification
  • Track mutations and evolution rates
  • Identify transmission routes
  • Population surveillance

Methods for NGS viral sequencing

There are several methods that can be used by researchers to study the SARS-CoV-2 viral genome:

  • Whole genome sequencing (WGS)
  • Target enrichment via multiplex PCR (amplicon sequencing)
  • Target enrichment via hybridization capture

Whole genome sequencing is a rapid way of getting from sample to sequencing and can be a good method to utilize if one is looking for a comprehensive picture of all pathogens in a sample. However, if the interest is solely to study SARS‑CoV‑2, it’s important to keep in mind that samples will also contain host or human genetic material, which could make sequencing inefficient and potentially increase associated costs.

Target enrichment methods are an efficient and cost-conscious way to study the complete SARS-CoV-2 viral sequence, or even select genes from its genome. These methods enrich for those desired regions prior to library prep or sequencing.

IDT provides two target enrichment methods:

Target enrichment via multiplex PCR (amplicon sequencing):

Following RNA isolation, this method requires relatively few steps which makes it faster to get from sample to sequencing without sacrificing genome coverage.

ARTIC V3 Panel with Lotus™ DNA Library Prep Kit:

400 bp long amplicons, compatible with both Oxford Nanopore® and Illumina® sequencers when using Lotus DNA Library Prep Kit.

Figure 1. ARTIC V3 workflow. The steps for amplicon sequencing with the ARTIC V3 Panel and the IDT Lotus DNA Library Prep Kit include cDNA synthesis, amplicon generation, fragmentation, adapter ligation, and a final PCR amplification. The combination results in Illumina and Nanopore-ready libraries.

Midnight Panel with Lotus™ DNA Library Prep Kit:

1200 bp long amplicons, compatible with both Nanopore and Illumina sequencers when using Lotus DNA Library Prep Kit [1].

Figure 2. Midnight panel workflow. The steps for amplicon sequencing with the Midnight Panel and the IDT Lotus DNA Library Prep Kit include cDNA synthesis, amplicon generation, fragmentation, end prep, adapter ligation, and a final PCR amplification. The final library is ready for sequencing with either Illumina or Nanopore technologies.

Swift Normalase™ Amplicon Panel (SNAP):

150 bp long amplicons, currently compatible only with Illumina sequencers.

Figure 3. Swift Normalase Amplicon Panel (SNAP) for SARS-CoV-2 workflow. The steps for amplicon sequencing with the SNAP SARS-CoV-2 panel include cDNA synthesis, amplicon generation, adapter ligation/indexing PCR, and a final normalization step to create equimolar amounts of multiplexed library samples.

Target enrichment via hybridization capture:

Another targeted next generation sequencing method that uses long, biotinylated oligonucleotide baits (probes) to hybridize to regions of interest. It is particularly helpful for enriching viral genomes when sequencing a sample.

COVID-19 Capture Bundle:

Includes xGen™ COVID-19 capture panel (96 rxn), blockers, and capture reagents.


Dr. Adriana Heguy
NYU Grossman School of Medicine
DNA baits are essential to our work, helping us capture human exome sequences and other specific targeted areas of the human genome. From the beginning, as we were designing the library prep and sequencing strategy for the SARS-CoV-2 viral genome sequencing, we sought to use specific baits to fish out this viral genome from our samples. IDT has been an invaluable partner in this research effort to ‘capture’ this viral genome, accelerating our sequencing efforts and making them more cost-effective.

ALIGN Program: SARS‑CoV‑2 sequencing service providers

IDT partners with some of the most comprehensive genomic sequencing providers in the world. These companies are aligned in our commitment to collaboration, and we are aligned in our resolve to break down research barriers. Whether you’re focused on whole genome sequencing or custom panels, our partners have you covered.

More about the ALIGN program

Press releases

News IDT Acquires Swift Biosciences, a Pioneer in the Development of Next-Generation Sequencing (NGS) Library Preparation Genomics Kits for Academic, Translational, and Clinical Research
Combining IDT’s high-quality NGS products with Swift’s broad portfolio of library preparation and enrichment products will be transformative for enabling scientists to conduct research more efficiently
Read more »
News Novogene America Joins IDT Align Preferred Sequencing Partner Program
Latest addition to program is valuable global NGS resource to IDT and its customers
Read more »
News IDT offers powerful new NGS tools for COVID-19 research
Partnerships, products, and solutions facilitate detection, research, and vaccine development to combat the SARS-CoV-2 virus
Read more »


  1. Freed NE, Vlkova M, Faisal MB, et al. Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding. Biol Methods Protoc. 2020;5(1):bpaa014.

*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.